@article {pmid41175312, year = {2026}, author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S}, title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.}, journal = {GeroScience}, volume = {48}, number = {4}, pages = {5575-5596}, pmid = {41175312}, issn = {2509-2723}, support = {22A17//Florida Department of Health/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Aged ; *Cognitive Dysfunction/microbiology/etiology ; Male ; *Cancer Survivors ; *Neoplasms ; Middle Aged ; }, abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.}, }
@article {pmid42733080, year = {2026}, author = {Li, C and Wang, Y and Zhou, ASK and Pan, X and Zhu, Y and Zhang, X and Chen, T and Xiong, A and Ho, YW and Liu, J and Zhou, Z and Wang, J and Adyel, TM and Fang, JK and Bank, MS and Rillig, MC and Jin, LN}, title = {Unraveling the coastal marine plastisphere archaeome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42733080}, issn = {2041-1723}, mesh = {*Archaea/genetics/classification ; *Seawater/microbiology ; Crenarchaeota/genetics/classification ; Phylogeny ; Euryarchaeota/genetics/classification ; Metagenomics ; Ecosystem ; Biodiversity ; Methane/metabolism ; }, abstract = {Plastic pollution has created an expanding anthropogenic microbial niche, the plastisphere, raising questions about microbial ecology and associated impacts. Archaea, the third domain of life with fundamental ecological and evolutionary significance, remain poorly understood in this habitat. Here, using paired plastic debris and bulk-water samples from coastal marine ecosystems, key archaeal habitats increasingly threatened by plastic pollution, we characterize the plastisphere archaeome through archaeal amplicon sequencing and metagenomics. We show that the archaeome is significantly reshaped in the plastisphere, exhibiting higher taxonomic diversity, greater community heterogeneity, and selective enrichment of Euryarchaeota and Crenarchaeota. Archaeal genes involved in methane, nitrogen, and sulfur cycling are enriched in the plastisphere. Taxonomic and functional divergence between the plastisphere and bulk water increases with anthropogenic chemical stress. These findings suggest that plastic pollution could alter marine archaeal diversity, biogeography, and biogeochemical potential, extending understanding of plastisphere impacts to the archaeal domain.}, }
@article {pmid42734183, year = {2026}, author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y}, title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2726620}, doi = {10.1080/19490976.2026.2726620}, pmid = {42734183}, issn = {1949-0984}, mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; }, abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.}, }
@article {pmid42250066, year = {2026}, author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W}, title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {9}, pages = {6906-6925}, pmid = {42250066}, issn = {1559-0291}, support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; }, mesh = {Animals ; Female ; *Metabolome ; *Feces/microbiology ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Disease Models, Animal ; }, abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.}, }
@article {pmid42575184, year = {2026}, author = {Zha, Y and Wang, Z and Sun, W and Meng, J and Liu, Y and Wang, B}, title = {Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.}, journal = {Environmental research}, volume = {307}, number = {}, pages = {125444}, doi = {10.1016/j.envres.2026.125444}, pmid = {42575184}, issn = {1096-0953}, mesh = {*Particulate Matter/analysis ; Metagenomics ; *Bacteria/genetics ; *Microbiota ; *Air Pollutants/analysis ; *Air Microbiology ; *Metagenome ; }, abstract = {Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.}, }
@article {pmid42696749, year = {2026}, author = {Cisneros-Martínez, AM and Flores Varela, MÁ and González-Serrano, F and Rebollar, EA}, title = {Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {9}, pages = {}, doi = {10.1093/femsec/fiag103}, pmid = {42696749}, issn = {1574-6941}, support = {//Secretaría de Ciencia/ ; }, mesh = {Animals ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Skin/microbiology/virology ; Skin Microbiome ; Metagenome ; *Ambystoma/microbiology/virology ; Bacteria/virology/classification/genetics ; Microbiota ; Batrachochytrium ; Metagenomics ; Biodiversity ; }, abstract = {Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.}, }
@article {pmid42729502, year = {2026}, author = {Tagele, SB and Kassa, AS and Tilahun, S and Zegeye, WA}, title = {Editorial: Harnessing genomics to revolutionize plant disease management and preservation of soil biodiversity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1901274}, doi = {10.3389/fmicb.2026.1901274}, pmid = {42729502}, issn = {1664-302X}, }
@article {pmid42729922, year = {2026}, author = {Cong, J and Xu, W and Zhang, Y and Ding, X and Cui, S and Chi, X and Yang, X}, title = {Gut microbiota dynamics and metabolic pathways associated with bleomycin-induced pulmonary fibrosis progression.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21693}, doi = {10.7717/peerj.21693}, pmid = {42729922}, issn = {2167-8359}, mesh = {Animals ; *Bleomycin ; *Pulmonary Fibrosis/chemically induced/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome ; Mice ; Disease Progression ; *Metabolic Networks and Pathways ; Disease Models, Animal ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Lung/pathology ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a progressive respiratory disease characterized by epithelial injury, aberrant repair and excessive extracellular matrix deposition. Although the gut-lung axis is increasingly implicated in respiratory disorders, stage-resolved characterization of gut microbiota taxonomic and functional potential during PF development is limited.<br><br>METHODS: We established a bleomycin-induced murine PF model and performed cross-sectional shotgun metagenomic sequencing of fecal samples from separate cohorts at three defined stages: baseline (control), day 7 (early fibrosis; M7), and day 14 (established fibrosis; M14). Microbial taxonomy, alpha/beta diversity, and predicted functional capacity were inferred using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZy) annotations; associations were assessed using Procrustes and Spearman correlation analyses.<br><br>RESULTS: Histopathology and immunohistochemistry confirmed progressive fibrogenesis with increased TGF-&#x3b2;1 and &#x3b1;-SMA expression. Compared with baseline, bleomycin-treated groups exhibited stage-specific shifts in gut microbial composition, including depletion of mucin-associated taxa (e.g., Prevotella, Akkermansia muciniphila) and expansion of Muribaculaceae- and Clostridiaceae-affiliated taxa. Alpha and beta diversity metrics differed across groups. KEGG/CAZy-based annotations revealed predicted, stage-dependent changes in microbial metabolic potential, including early reductions in pathways related to amino acid and glycan metabolism (M7) and later increases in predicted starch/sucrose catabolism, phosphotransferase system (PTS) representation, and secondary bile acid biosynthesis (M14). Correlation analyses linked compositional shifts to these predicted functional changes.<br><br>CONCLUSION: In a stage-resolved, cross-sectional study, bleomycin-associated pulmonary fibrosis was accompanied by compositional and predicted functional alterations in the gut microbiota. These data identify candidate taxa and predicted pathways for follow-up mechanistic testing, but functional (metabolomic) and causality experiments are required to confirm whether and how microbial changes contribute to PF pathogenesis.}, }
@article {pmid42227352, year = {2026}, author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT}, title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.}, journal = {International endodontic journal}, volume = {59}, number = {10}, pages = {2211-2222}, doi = {10.1111/iej.70190}, pmid = {42227352}, issn = {1365-2591}, support = {//European Society of Endodontology/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Dental Pulp Cavity/microbiology ; *Periapical Periodontitis/microbiology/pathology ; *Metagenomics ; Shotgun Sequencing ; DNA, Bacterial ; }, abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.<br><br>METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (<&#x2009;3&#x2009;mm) or large (>&#x2009;7&#x2009;mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p&#x2009;<&#x2009;0.05 was considered as significant.<br><br>RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p&#x2009;=&#x2009;0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.<br><br>CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.}, }
@article {pmid42723054, year = {2026}, author = {Zhao, J and Chen, X and Wang, X and Cui, Y and Zhuge, J and Zhang, Y and Zhang, L and Yan, Y and Fang, H and Hua, Z and Li, G}, title = {Metagenomic-based quantification of Pseudomonas aeruginosa burden links microbiome collapse to mortality in severe community-acquired pneumonia.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {25}, number = {1}, pages = {}, pmid = {42723054}, issn = {1476-0711}, support = {2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; }, mesh = {Humans ; *Community-Acquired Pneumonia/mortality/microbiology ; *Pseudomonas aeruginosa/genetics/isolation &amp; purification ; Female ; *Microbiota ; Retrospective Studies ; *Pseudomonas Infections/mortality/microbiology ; Metagenomics ; Male ; Aged ; Middle Aged ; Lung/microbiology ; *Community-Acquired Infections/microbiology/mortality ; ROC Curve ; Metagenome ; High-Throughput Nucleotide Sequencing ; Prognosis ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (sCAP) remains a major cause of mortality in critically ill patients, Pseudomonas aeruginosa (P. aeruginosa) is a frequent pathogen associated with poor prognosis in this population. While metagenomic next-generation sequencing (mNGS) is widely used for pathogen detection, its value in quantifying pathogen abundance and linking it to lung microbiome alterations remains unclear.<br><br>OBJECTIVES: This study investigated the association between P. aeruginosa abundance quantified by mNGS and lung microbiome alterations and clinical outcomes in sCAP patients.<br><br>METHODS: This multicenter retrospective study included 130 patients with sCAP caused by P. aeruginosa from five hospitals (September 2021-June 2025). Patients were stratified into low, medium, and high abundance groups according to mNGS-derived reads per ten million (RPTM) values of P. aeruginosa. Lung microbiome diversity and community structure were analyzed, and differences between groups were assessed using appropriate statistical methods. The association between P. aeruginosa abundance and clinical outcomes was evaluated using correlation analysis, sankey diagram, receiver operating characteristic curve, grey zone analysis and logistic regression.<br><br>RESULTS: A total of 130 patients with sCAP due to P. aeruginosa were stratified into low, medium, and high abundance groups based on mNGS-derived RPTM value. Microbial diversity decreased progressively with increasing abundance, and community structures differed significantly among groups (all P&#x2009;<&#x2009;0.05). P. aeruginosa became increasingly dominant, accounting for up to 95.99% of the microbiota in the high abundance group. Higher P. aeruginosa abundance was associated with increased disease severity, including longer mechanical ventilation, prolonged hospital stay, and higher 28-day mortality. Sankey diagram showed a progressive decline in treatment effectiveness and an increase in mortality with increasing P. aeruginosa abundance. P. aeruginosa_RPTM showed moderate predictive value for mortality (AUC&#x2009;=&#x2009;0.761, Sens&#x2009;=&#x2009;69.40%, Spec&#x2009;=&#x2009;75.30%, cutoff: 41122, grey zone: 2287-220339) and remained independently associated with 28-day mortality in multivariable analysis [2.219 (1.509 to 3.262), P&#x2009;<&#x2009;0.001].<br><br>CONCLUSION: In patients with sCAP, higher P. aeruginosa_RPTM measured by mNGS was associated with reduced lung microbiome diversity and unfavorable clinical outcomes. RPTM-based risk stratification may help identify patients at increased risk of poor prognosis.}, }
@article {pmid42723112, year = {2026}, author = {Zhang, S and Zhang, N and Zhang, X and Liu, Y and Feng, Y and Xiang, J and Zhang, J and Ma, H and Lu, Y and Zhang, T}, title = {Integrated landscape of salivary metagenome and multi-biofluid metabolome characterizes a microbial-metabolic axis in upper gastrointestinal cancer progression.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42723112}, issn = {2049-2618}, mesh = {Humans ; *Saliva/microbiology ; *Metabolome ; *Gastrointestinal Neoplasms/microbiology/metabolism/pathology/diagnosis ; *Metagenome ; Disease Progression ; Metagenomics/methods ; Metabolomics/methods ; Female ; Multiomics ; Male ; Middle Aged ; Dysbiosis/microbiology ; Microbiota ; Lysine/metabolism ; }, abstract = {BACKGROUND: Upper gastrointestinal cancer (UGIC) imposes a major global health burden, yet the stage-specific molecular changes along the microbial-metabolic axis remain limited understood. We aimed to delineate this molecular landscape across UGIC progression and evaluate its potential as non-invasive methods for precision screening.<br><br>RESULTS: Derived from a multi-center population-based UGIC screening program, we enrolled 420 individuals, stratified into normal, low-grade intraepithelial neoplasia (LGIN), high-grade intraepithelial neoplasia (HGIN), and UGIC (n&#x2009;=&#x2009;105 per group). Integrated salivary metagenomics and paired salivary/plasma metabolomics were performed to capture local and systemic dysregulation. We uncovered distinct stage-specific divergence during UGIC progression: profound remodeling of the salivary microbiota (104 differential species) and salivary metabolomics (80 differential metabolites) initiated early at the LGIN stage, whereas plasma metabolic dysregulation (40 differential metabolites) peaked significantly later at the HGIN stage. Integrative analysis revealed salivary microbiota related more closely with salivary metabolome than plasma metabolome. Moreover, statistical evidence suggested that dysbiotic salivary microbiota was associated with altered lysine- and tryptophan-related catabolic pathways converging on Acetyl-CoA-related metabolic nodes, supporting a potential metabolic mechanism in precancerous lesions. Finally, the discriminative model integrating metagenomic and metabolomic markers demonstrated promising diagnostic performance in distinguishing these precancerous lesions (LGIN: area under the curve [AUC]&#x2009;=&#x2009;0.83; HGIN: AUC&#x2009;=&#x2009;0.77) and UGIC (AUC&#x2009;=&#x2009;0.76) from normal.<br><br>CONCLUSION: This study characterizes a stage-specific microbial-metabolic axis that facilitates the comprehensive understanding of UGIC pathogenesis. These multi-biofluid signatures offer a promising non-invasive triage strategy for detecting precancerous lesions and optimizing endoscopic resource allocation. Video Abstract.}, }
@article {pmid42723989, year = {2026}, author = {Ma, Z and Bai, X and Tian, J and Yao, C and Yan, Z and Ma, X and Zhang, C and Ma, J and Lin, Y and Zhang, X and Wang, H}, title = {Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1914654}, pmid = {42723989}, issn = {2235-2988}, mesh = {Humans ; Female ; *Histamine/metabolism/blood ; Adult ; Male ; Cytokines/blood ; *Gastrointestinal Microbiome ; *Inflammation ; *Spondylitis/microbiology/pathology/metabolism ; Dysbiosis/microbiology ; Middle Aged ; Histidine Decarboxylase/blood ; Metagenomics ; Lipopolysaccharides/blood ; Fatty Acids, Volatile ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear.<br><br>METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1&#x3b2;, IL-6, IL-10, IL-17A, TNF-&#x3b1;) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed.<br><br>RESULTS: Compared to the healthy control group, the &#x3b1;-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1&#x3b2;, IL-6, IL-17A, and TNF-&#x3b1; were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation.<br><br>CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.}, }
@article {pmid42725663, year = {2026}, author = {Furneaux, B and Roslin, T and Hardwick, B and Kerdraon, D and Autto, H and Banelyte, G and deWaard, JR and deWaard, SL and Farrell, A and Kalttopää, O and Kristensen, E and Rogers, HMK and Sones, JE and Zakharov, EV and Ovaskainen, O}, title = {Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?.}, journal = {Molecular ecology resources}, volume = {26}, number = {7}, pages = {e70195}, doi = {10.1111/1755-0998.70195}, pmid = {42725663}, issn = {1755-0998}, support = {336212//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 101059492//HORIZON-CL6-2021-BIODIV-01/ ; 856506/ERC_/European Research Council/International ; 225-20-002//Naturv&#xe5;rdsverket/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; MSI 42450//Canadian Foundation for Innovation/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; *Metagenomics/methods ; *Insecta/classification/genetics ; }, abstract = {Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3' end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's ⍴ = 0.88-0.99) as do differences in relative dissimilarity between sample pairs (Spearman's ⍴ = 0.55-0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (p > 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (R[2] > 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologically relevant insights into the taxa present in the source community.}, }
@article {pmid42725826, year = {2026}, author = {Chenuil, A and Bouchereau, E and Legrand, T and Calvert, V and Chemin, C and Chenesseau, S and Guillemain, D and Ortega, JMG and Haguenauer, A and Leduc, M and Legendre, F and Marschal, F and Marschal, C and Mirleau, F and Selva, M and Vanbostal, L and Zuberer, F and Mirleau, P and Plaisance, L and Rossi, V and Ruitton, S and Meglécz, E and Dubut, V}, title = {Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys.}, journal = {Molecular ecology resources}, volume = {26}, number = {7}, pages = {e70188}, doi = {10.1111/1755-0998.70188}, pmid = {42725826}, issn = {1755-0998}, support = {OOB_EMBRC FR_AAP2018_n&#xb0;2179//EMBRC France/ ; ANR-17-MART0001-01//Agence Nationale de la Recherche/ ; ANR-17-MART0001-02//Agence Nationale de la Recherche/ ; ANR-17-MART0001-03//Agence Nationale de la Recherche/ ; 145//ERA-Net Mar-TERA/ ; SERA-20181031//Centro para el Desarrollo Tecnol&#xf3;gico e Industrial/ ; 4000141547/23/I-DT//European Space Agency/ ; 1166-39417//European Regional Development Fund/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; Photography/methods ; Electron Transport Complex IV/genetics ; Animals ; Mediterranean Sea ; *Metagenomics/methods ; }, abstract = {Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular outputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across 10 north-western Mediterranean sites to compare and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site-level richness and revealed stronger correlations with geographic distance and environmental gradients-which stemmed from its finer taxonomic resolution-whereas photography provided complementary information on macro-taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β-diversity-distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α-diversity and strengthening β-diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control-driven bioinformatic workflow provides a reproducible, scalable framework for long-term eDNA monitoring and early detection of biodiversity change.}, }
@article {pmid42726321, year = {2026}, author = {Duan, DY and Ran, J and Guo, XL and Liu, L and Liu, GH and Asada, M and Cheng, TY}, title = {Metagenomic analysis of the midgut microbiome in Dermacentor abaensis ticks at different feeding states.}, journal = {Experimental &amp; applied acarology}, volume = {97}, number = {3}, pages = {}, pmid = {42726321}, issn = {1572-9702}, support = {No. 2025JJ50143//Natural&#x2002;Science&#x2002;Foundation&#x2002;of&#x2002;Hunan&#x2002;Province, China/ ; No. kq2502005//Natural&#x2002;Science&#x2002;Foundation&#x2002;of&#x2002;Changsha City, China/ ; No. 31902294//National Science Foundation of China/ ; 2024YFD1800103//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Dermacentor/microbiology/physiology ; Female ; Bacteria/classification/isolation &amp; purification/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Feeding Behavior ; China ; *Metagenome ; }, abstract = {Ticks are blood-sucking ectoparasites of humans and animals, ranking second only to mosquitoes as vectors of diseases. Dermacentor abaensis is distributed in Sichuan, Qinghai, and Gansu, China. Because D. abaensis harbors several pathogens, it poses a threat to public health and livestock production. However, the midgut microbiota of D. abaensis at distinct feeding states remains poorly characterized. Adult D. abaensis ticks at various feeding states were collected from yaks in Gansu Province, China. Genomic DNA was extracted from midguts and midgut contents of unfed, partially fed, and fully engorged female D. abaensis. A metagenomic sequencing approach was employed to profile the midgut microflora among three groups. A total of 83 phyla, 908 genera, and 1857 species were annotated across the three groups. At the phylum level, Pseudomonadota, Mucoromycota, and Ascomycota were the most abundant. At the species level, common bacterial species such as Klebsiella pneumoniae and Anaplasma phagocytophilum, alongside viruses and eukaryotes, were detected in all three groups. Unique microorganisms were also observed in each group: unfed (n = 305), partially fed (n = 59), and fully engorged (n = 20). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the D. abaensis microbiome contains a relatively high abundance of functional genes involved in lipid and amino acid metabolism across the three different feeding states. These findings indicate that while core microbial taxa are shared in the midgut of female D. abaensis, observable trends suggest variations in microbial diversity and composition as blood-feeding progresses. The present study provides a descriptive baseline of the midgut microbial composition of D. abaensis, which may inform future studies on tick biology and the ecology of tick-borne pathogens.}, }
@article {pmid42312840, year = {2026}, author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG}, title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.}, journal = {Clinical microbiology reviews}, volume = {39}, number = {3}, pages = {e0031925}, doi = {10.1128/cmr.00319-25}, pmid = {42312840}, issn = {1098-6618}, support = {T32 AI118689/NH/NIH HHS/United States ; LF-OC-22_001060//LEO Fondet/ ; 310030_189255/SNSF_/Swiss National Science Foundation/Switzerland ; 310030E_219182/SNSF_/Swiss National Science Foundation/Switzerland ; MR/V033417/1//Medical Research Council Centre for Medical Mycology/ ; 200208/WT_/Wellcome Trust/United Kingdom ; 215599/WT_/Wellcome Trust/United Kingdom ; 224323/WT_/Wellcome Trust/United Kingdom ; MR/M026663/2/MRC_/Medical Research Council/United Kingdom ; MR/Y002164/1/MRC_/Medical Research Council/United Kingdom ; APP57173- UKRI1405/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2//Medical Research Council Centre for Medical Mycology/ ; NIHR203320//NIHR Exeter Biomedical Research Centre/ ; }, mesh = {Humans ; *Homeostasis ; Skin Microbiome ; *Fungi/pathogenicity/physiology ; *Host-Pathogen Interactions ; Skin/microbiology/immunology ; *Dermatomycoses/microbiology ; *Inflammation/microbiology ; }, abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.}, }
@article {pmid42323440, year = {2026}, author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD}, title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42323440}, issn = {2045-2322}, support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; }, mesh = {Animals ; *Alouatta/microbiology/parasitology/genetics ; Helminths/genetics/isolation &amp; purification/classification ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Gastrointestinal Tract/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Female ; Host-Parasite Interactions ; Male ; }, abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.}, }
@article {pmid42431299, year = {2026}, author = {Zhang, X and Cai, M and Lin, J and Feng, Z and Wang, W and Jiao, Y and Lu, L}, title = {Multi-year glyphosate exposure impairs soil fertility, microbial communities, nutrient cycling genes, and tea quality in tea plantations.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {407}, number = {}, pages = {128689}, doi = {10.1016/j.envpol.2026.128689}, pmid = {42431299}, issn = {1873-6424}, mesh = {Glyphosate ; *Glycine/analogs &amp; derivatives/toxicity ; *Soil Microbiology ; *Soil/chemistry ; *Camellia sinensis ; *Herbicides/toxicity ; *Soil Pollutants/toxicity ; Nitrogen ; Agriculture ; *Tea/chemistry ; *Microbiota/drug effects ; }, abstract = {Although glyphosate is highly effective for weed control, its potential risks to tea agroecosystems remain a significant concern. Previous studies have shown inhibitory effects on soil microbial communities in tea plantations, yet the multi-year impacts of glyphosate on microbially mediated nutrient cycling remain poorly understood. To address this gap, we conducted a three-year controlled field experiment, applying glyphosate at 0 kg a.i. ha[-1] (CK), 2.3 kg a.i. ha[-1] (G1), and 6.9 kg a.i. ha[-1] (G2), and used metagenomic sequencing to evaluate its effects on soil fertility, microbial communities, nutrient cycling genes, and tea quality. The results showed that glyphosate application significantly increased soil pH but reduced the contents of total organic carbon, total nitrogen, total potassium, available nutrients, and enzyme activities, leading to marked declines in soil fertility. Relative to CK, G2 reduced microbial alpha diversity, with Chao1, Shannon, and Pielou indices decreasing by 33.22%, 14.97%, and 11.50%, respectively. Tea quality was also affected, with free amino acids and caffeine decreasing by 22.67% and 11.30%, respectively, whereas tea polyphenols and the phenol/ammonia ratio increased by 12.16% and 45.08%, respectively. G2 also restructured bacterial communities, including depletion of Actinobacteria and Planctomycetota and more than 70-fold enrichment of Candidatus Rokubacteria. Metagenomic analysis revealed broad suppression of carbon, nitrogen, and phosphorus cycling genes under G2. Overall, these results suggest that repeated glyphosate exposure over three years may alter soil ecological processes and compromise tea quality, highlighting the need for more sustainable weed management strategies and reduced reliance on glyphosate in tea plantations.}, }
@article {pmid42462951, year = {2026}, author = {Jin, Y and Liu, J and Liu, Z and Yuan, Y and Cui, H and Dong, Z and Zhang, F and Lv, M and Hu, L and Zhang, L and Zhou, D and Yang, W}, title = {Linking oral microbiota to clinic air during ultrasonic scaling: Quantitative sequencing and CFD modeling reveal pathogenic aerosol emissions, infection risk, and control strategies.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {407}, number = {}, pages = {128796}, doi = {10.1016/j.envpol.2026.128796}, pmid = {42462951}, issn = {1873-6424}, mesh = {Aerosols/analysis ; *Microbiota ; *Air Microbiology ; *Mouth/microbiology ; Humans ; Hydrodynamics ; Bacteria/isolation &amp; purification/genetics ; *Dental Scaling ; }, abstract = {Microbial aerosols from dental procedures pose a recognized yet unquantified airborne infection risk. During ultrasonic scaling, we performed multi-site sampling (saliva, air, surfaces) and combined metagenomics with quantitative 16S rRNA and ITS amplicon sequencing to profile viral, bacterial, and fungal communities. Using size-resolved aerosol sampling and absolute quantification, we determined the emission strength and size distribution of pathogenic bacterial aerosols (PBA), which were key inputs for computational fluid dynamics (CFD) simulations performed at ventilation velocities of 0.1, 0.2, and 0.4 m/s, corresponding to air exchange per hour (ACH) of 2.4, 4.7, and 9.4 h[-1], respectively. We first linked patient oral microbiota to clinic aerosols, identifying a shared core of 51 viral, 55 bacterial, and 23 fungal families, of which three bacterial families (Streptococcaceae, Pasteurellaceae, Nocardiaceae) were pathogenic. The emission strength of PBA was ∼3.06 × 10[3] copies/min, with 66.7% concentrated in the 2.1∼4.7 μm fraction, a size associated with higher deposition in the lower respiratory tract. CFD simulations, fed with real pathogen concentrations and aerodynamic size spectra, revealed that increasing ACH from 0.1 to 0.4 m/s reduced PBA suspension (-26.4%) and surface deposition (-12.7%) during scaling, lowering the inhalation infection risk (IIR) at the dentist's position by 80.8% and keeping overall IIR below 25%. After scaling, lower velocity favours particle removal, supporting a dynamic ventilation strategy (high during treatment, low afterwards). This integrated framework provides a direct scientific basis for infection control in dental operatories.}, }
@article {pmid42476495, year = {2026}, author = {Chen, M and Cao, J and Fu, S and Han, Y and Zheng, W and Chen, J and Yang, X and Wang, J}, title = {Lambda-cyhalothrin exposure disrupts microbiota-associated bile acid metabolism and enterohepatic feedback in mice.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {407}, number = {}, pages = {128813}, doi = {10.1016/j.envpol.2026.128813}, pmid = {42476495}, issn = {1873-6424}, mesh = {Animals ; *Pyrethrins/toxicity ; *Nitriles/toxicity ; *Bile Acids and Salts/metabolism ; Male ; Mice ; *Insecticides/toxicity ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Enterohepatic Circulation/drug effects ; Microbiota/drug effects ; }, abstract = {Lambda-cyhalothrin (LCT) is a widely used pyrethroid insecticide frequently detected in environmental and food-associated matrices, yet its effects on host bile acid metabolism remain unclear. Male C57BL/6 mice were orally exposed to LCT for 28 days and analyzed using integrated bile acid metabolomics, hepatic and ileal gene-expression profiling, 16S rRNA sequencing, and shotgun metagenomics. LCT reduced hepatic total bile acids but increased plasma and fecal bile acids, indicating compartment-specific bile acid redistribution. This response was accompanied by hepatic Cyp7a1/Cyp27a1 downregulation, selective Cyp8b1 upregulation, altered bile acid transporter expression, and enhanced ileal FXR-FGF15-related feedback responses. LCT also remodeled gut microbial composition and altered bile acid transformation-related functional signatures, particularly those related to 7α-HSDH and 3β-HSDH. Consistently, fecal LCA, 3-ketoLCA, and isoLCA accumulated, consistent with altered microbial LCA oxidation-reduction and epimerization potential. These findings identify microbiota-associated bile acid remodeling as a potential non-neurotoxic metabolic endpoint of pyrethroid-induced gut-liver axis disturbance and provide candidate microbial and host targets for future mechanistic validation.}, }
@article {pmid42545024, year = {2026}, author = {Carlson-Jones, JAP and Goddard, TR and Papudeshi, B and Mallawaarachchi, V and Whiteson, KL and Warner, MS and Morton, JM and Jersmann, HPA and Edwards, RA}, title = {DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.}, journal = {Clinical microbiology reviews}, volume = {39}, number = {3}, pages = {e0035225}, doi = {10.1128/cmr.00352-25}, pmid = {42545024}, issn = {1098-6618}, support = {FL250100019//Department of Education and Training | Australian Research Council (ARC)/ ; //Women's &amp; Children's Hospital Foundation/ ; DP250103825//Department of Education and Training | Australian Research Council (ARC)/ ; 2046960//National Health and Medical Research Council/ ; //CALHN CEO Clinical Rapid Implementation Project Scheme/ ; }, mesh = {*Cystic Fibrosis/microbiology ; Humans ; *Microbiota/genetics ; *Sequence Analysis, DNA/methods ; Metagenomics/methods ; Sputum/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; *Respiratory System/microbiology ; }, abstract = {SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene sequencing have uncovered the complexity of the CF airway microbiome, while shotgun metagenomics, metatranscriptomics, and viromics now provide strain-level, functional, and viral insights beyond bacterial identification. Despite these advances, key technical and logistical challenges remain, including the processing of high-viscosity sputum samples, overwhelming host DNA contamination, managing large data sets, and the integration of complex bioinformatic outputs into clinical workflows. Emerging innovations such as host DNA depletion protocols, targeted enrichment panels, and adaptive sampling on Oxford Nanopore platforms are helping to overcome these barriers, improving microbial recovery and sequencing efficiency. As cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are changing the lives of people with cystic fibrosis (pwCF), sequencing offers an unprecedented opportunity to track potential microbial adaptation in response. This review investigates current advances, limitations, and translational opportunities in DNA sequencing for CF airway microbiome surveillance, highlighting how these technologies can help reshape research and clinical microbiology in the post-modulator era.}, }
@article {pmid42351291, year = {2026}, author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y}, title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42351291}, issn = {2049-2618}, mesh = {Humans ; *Metagenome ; Shotgun Sequencing ; *Microbiota/genetics ; Child ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation ; Female ; }, abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.<br><br>RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.<br><br>CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.}, }
@article {pmid42576026, year = {2026}, author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T}, title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.}, journal = {Nature genetics}, volume = {58}, number = {9}, pages = {2211-2225}, pmid = {42576026}, issn = {1546-1718}, support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology/epidemiology ; Japan/epidemiology ; *Mutation ; *Polyketides/adverse effects ; *Peptides ; Whole Genome Sequencing ; Prevalence ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; Feces/microbiology ; Gene Expression Profiling ; Risk Factors ; East Asian People ; }, abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.}, }
@article {pmid42580037, year = {2026}, author = {Kearney, A and Chau, K and Kotay, S and Martin, J and Kirby, A and Mathers, AJ and Stoesser, N}, title = {Hospital sinks and healthcare-associated infection: ecology, transmission, surveillance and mitigation.}, journal = {EBioMedicine}, volume = {131}, number = {}, pages = {106415}, pmid = {42580037}, issn = {2352-3964}, mesh = {Humans ; *Cross Infection/transmission/epidemiology/prevention &amp; control/microbiology ; *Infection Control/methods ; Hospitals ; Microbiota ; }, abstract = {Hospital sinks are recognised polymicrobial reservoirs for multi-drug resistant organisms and have been implicated in patient transmission and outbreaks. Earlier studies on sink-associated microbes predominantly focused on specific species or resistance mechanisms (e.g. carbapenemases) using targeted microbiological methods. More recently, less selective approaches (e.g. metagenomic sequencing) have enabled broader characterisation of these microbial communities. This review summarises current evidence describing hospital sink-trap microbiomes, examining ecological determinants, surveillance strategies and interventions aiming to mitigate transmission from these reservoirs. We discuss biotic and abiotic factors that shape microbial selection/persistence, assess approaches to managing these reservoirs to reduce patient risk, and highlight priorities for future research to inform evidence-based practice in healthcare settings.}, }
@article {pmid42603474, year = {2026}, author = {Zhang, C and Chen, J and Yang, W and Du, K and Tao, W and Lu, Q and Jiang, M and Hu, J and Zhu, Q and Elrys, AS and Cai, Z and Meng, L and Müller, C and Dan, X and Zhang, J}, title = {Small-sized biodegradable PLA microplastics inhibit plant nitrogen uptake by reshaping soil microbial communities and stimulating microbial metabolism.}, journal = {Journal of hazardous materials}, volume = {516}, number = {}, pages = {143209}, doi = {10.1016/j.jhazmat.2026.143209}, pmid = {42603474}, issn = {1873-3336}, mesh = {*Polyesters/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Microplastics/toxicity ; *Microbiota/drug effects ; Bacteria/metabolism/drug effects ; *Soil Pollutants/toxicity ; *Plants/metabolism ; Particle Size ; Biodegradation, Environmental ; }, abstract = {The effects of microplastics (MPs) varying in polymer type and size on soil microbial community composition, metabolic functions, and nutrient cycling remain insufficiently understood. Here, we conducted a pot experiment using MPs differing in polymer type (non-biodegradable polyethylene [PE], and biodegradable polylactic acid [PLA]) and four particle sizes (1200-1400, 600-700, 120-150, and 25-38 μm), with amplicon sequencing, shotgun metagenomics, and nitrogen-15 ([15]N) tracing model. Our results showed that small-sized PLA-MPs (25-38 μm) reduced bacterial diversity, destabilized microbial networks, and shifted community assembly toward deterministic processes, whereas PE-MPs and larger-sized PLA-MPs exerted minimal effects. This shift was associated with enhanced depolymerization-related enzymatic potential, accompanied by greater dissolved organic carbon (DOC) availability. The resulting increase in C availability stimulated central C metabolism, promoting microbial resource acquisition and biomass synthesis. To maintain microbial C:N homeostasis, microbial N assimilation was stimulated through ammonium (NH4[+]) assimilation mediated by the glutamate dehydrogenase (GDH) and glutamine synthetase-glutamate synthase (GS-GOGAT) pathways and nitrate (NO3[-]) assimilation via assimilatory nitrate reduction to ammonium (ANRA). Consistently, the [15]N tracing model revealed that microbial assimilation rates of NH4[+]-N and NO3[-]-N increased by 10.5-fold and 12.7-fold, respectively, exceeding gross N mineralization rates, thereby depleting soil inorganic N pools and suppressing plant N uptake. Overall, our findings provide mechanistic insights into how PLA-MPs reshape soil functioning by reprogramming microbial communities and metabolism, thereby altering plant-microbe competition for N. These results highlight the potential risks of increasing biodegradable plastic inputs for cropland nutrient cycling and plant N acquisition.}, }
@article {pmid42623872, year = {2026}, author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {A synthetic microbiome drives a multi-omics response to remediate 1,4-dithiane-contaminated soil and simultaneously suppresses antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {516}, number = {}, pages = {143337}, doi = {10.1016/j.jhazmat.2026.143337}, pmid = {42623872}, issn = {1873-3336}, mesh = {*Soil Pollutants/metabolism ; *Microbiota ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Multiomics ; Genes, Bacterial ; }, abstract = {1,4-Dithiane, a degradation product of abandoned Japanese chemical weapons, is a persistent organic pollutant with ecological risks. A synthetic microbiome (SM) was constructed through pollution stress screening and ratio optimization, consisting of Shinella sp., Alcaligenes faecalis, Sphingomonas sp., and Stenotrophomonas sp. at an optimal ratio of 1: 1: 2: 2. The SM achieved a 1,4-dithiane degradation rate of 95.2% and reduced intermediate accumulation. Soil remediation experiments showed complete pollutant removal within 60 days, along with improved soil health: reduced bioavailability of heavy metals (Cu, Zn, Cd), increased pH (6.47-6.95), elevated organic matter and enzyme activities, and decreased salinity and redox potential. Integration of ionomics, 16S sequencing, metagenomics, metabolomics, and HT-qPCR revealed that SM colonization reshaped microbial community structure, suppressed ARG-harboring bacteria (e.g., Pseudomonas), and activated core pathways (oxidative phosphorylation and glutathione metabolism), enhancing metabolic activity and oxidative stress tolerance. Consequently, the diversity, abundance, and diffusion potential of soil ARGs and mobile genetic elements were significantly reduced. These findings provide microbial solutions and a theoretical basis for concurrent organic pollution control and soil ecological risk management.}, }
@article {pmid42623874, year = {2026}, author = {Zhou, R and Ma, Z and Kou, S and Ni, Y and Huang, X and Wei, H and Jin, Q and Xu, H and Ding, Z}, title = {Microplastics as vectors for microbial pollutants: Biofilm-associated transfer of pathogens and antibiotic resistance genes in zebrafish intestine.}, journal = {Journal of hazardous materials}, volume = {516}, number = {}, pages = {143329}, doi = {10.1016/j.jhazmat.2026.143329}, pmid = {42623874}, issn = {1873-3336}, mesh = {Animals ; *Biofilms ; *Zebrafish/microbiology ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects ; *Polyesters/toxicity ; Intestines/microbiology ; Polypropylenes/toxicity ; Genes, Bacterial ; Bacteria/genetics ; Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity ; }, abstract = {As composite carriers of microorganisms and pollutants, biofilm-attached microplastics (MPs) serve as potential vectors for the environmental migration and biotransmission of antibiotic resistance genes (ARGs) and pathogens. In this study, traditional polypropylene (PP) and biodegradable polylactic acid (PLA) MPs were used to investigate the interference effects of biofilms-attached MPs on gut microbiota and ARGs transmission, through a combination of laboratory biofilm cultivation, zebrafish (Danio rerio) exposure simulations, metagenomic sequencing, and metabolomic profiling. Results showed that MP biofilms likely induced gut dysbiosis and were associated with altered diversity and abundance of pathogens and ARGs. At the phylum level, Nitrospira was transferred from PP biofilms to the gut. At the genus level, 23 genera were transferred from MP biofilms, with PLA (23 genera) showing higher transfer capacity than PP (4 genera). Notably, two human pathogens, one opportunistic pathogen, and two ARGs (adeF and oqxB) were specifically transferred from PLA biofilms, highlighting the unique dissemination risk of biodegradable MPs. Mechanistically, MPs may activate mobile genetic elements (e.g., Tn916 transposon) through metabolic remodeling and quorum sensing, thereby promoting horizontal gene transfer and ARGs dissemination within the gut. Our findings highlight the potential role of MPs as carriers of microorganisms and ARGs, underscoring the biotransmission risks of antibiotic resistance caused by composite pollution.}, }
@article {pmid42624114, year = {2026}, author = {Jang, LG and Huh, JW and Kim, S and Lee, JY and Hwang, HS and Yoon, J and Lee, HG and Kim, TI and Lee, YC and Jee, SH and Kim, JF}, title = {Mouth-to-gut microbial transmission signatures enable robust, non-invasive diagnosis of gastrointestinal cancers.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {9}, pages = {1829-1842.e5}, doi = {10.1016/j.chom.2026.07.007}, pmid = {42624114}, issn = {1934-6069}, mesh = {Humans ; *Mouth/microbiology ; Feces/microbiology ; *Gastrointestinal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Middle Aged ; *Microbiota ; }, abstract = {The human microbiome is spatially compartmentalized, yet oral bacteria can ectopically colonize distal sites such as the gut, potentially influencing disease. By analyzing paired oral and fecal microbiomes from 507 participants across healthy controls and patients with metabolic disorders or gastrointestinal cancers, we established a quantitative mouth-to-feces (MF) index to measure MF microbial transmission. The MF index revealed elevated mouth-to-gut transmission in cancer and a strong association with host metabolic and inflammatory indicators. Using transmitted taxa, we developed a random forest classifier that accurately distinguished gastric/colorectal cancer from healthy controls across seven independent cohorts, even when trained solely on oral microbiome data. When benchmarked against the conventional screening test, the MF-based model achieved markedly higher sensitivity than the fecal occult blood test. These findings uncover disease-specific transmission signatures and highlight MF microbial profiling as a generalizable, non-invasive framework for gastrointestinal cancer diagnosis and risk stratification.}, }
@article {pmid42648293, year = {2026}, author = {Oka, A and Bongers, G and Mishima, Y and Baltus, AJ and Gray, SM and Liu, B and Herzog, JW and Benedetto, JR and Fan, TJ and Jang, J and Awoniyi, M and Rousta, E and Hao, LY and Gharaibeh, RZ and Fodor, AA and Ohkusa, T and Atarashi, K and Fukuda, S and Honda, K and San Mateo, LR and Sartor, RB}, title = {Defined human Clostridia consortia reverse colitis via dual effects of tryptophan metabolites on microbiota and immunity.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {9}, pages = {1746-1763.e15}, doi = {10.1016/j.chom.2026.08.003}, pmid = {42648293}, issn = {1934-6069}, support = {K08 DK144596/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Colitis/therapy/microbiology/immunology ; *Tryptophan/metabolism ; Inflammatory Bowel Diseases/therapy/microbiology/immunology ; Mice ; Disease Models, Animal ; Dysbiosis/therapy ; Receptors, Aryl Hydrocarbon/metabolism ; *Clostridium/metabolism ; Interleukin-10/metabolism ; T-Lymphocytes, Regulatory/immunology ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; }, abstract = {Microbial dysbiosis and disrupted mucosal immune homeostasis are integrally involved in the pathogenesis of inflammatory bowel diseases (IBDs). Live biotherapeutic products (LBPs) offer a potential therapeutic strategy to restore beneficial microbes and mitigate disease. We investigated the therapeutic efficacy of 2 LBPs, human Clostridia consortia 17-mix and 11-mix, by treating established colitis in murine models. Both LBPs exhibited therapeutic effects in T cell-mediated chronic colitis models induced by human microbiota and in pathobiont-driven gnotobiotic colitis models established with combinations of IBD-relevant human-derived strains. Metagenomic and metabolomic analyses elucidated mechanisms that go beyond established functions driven by short-chain fatty acids (SCFAs) and interleukin (IL)-10-producing regulatory T cells. Notably, LBPs exerted therapeutic effects by directly inhibiting resident pathobionts and through IL-10-independent activation of host anti-inflammatory aryl hydrocarbon receptor (AhR) pathways by bacterial tryptophan metabolites. These results elucidate SCFA- and IL-10-independent protective mechanisms exerted by defined resident bacterial strains that are depleted in IBD dysbiosis.}, }
@article {pmid42711823, year = {2026}, author = {Saragiotto, GK and de Oliveira, LFV and Geciana Tomaz Dos Santos, B and Nunes Sanches, R and Merizzi de Oliveira, M and Campos Freire, F and Dias de Oliveira Carvalho, R and Sivieri, K and Sartoratto, A and Cabral, L and Azevedo, V and Belli, T and Costa Antunes, AE}, title = {Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {23}, number = {1}, pages = {2725874}, doi = {10.1080/15502783.2026.2725874}, pmid = {42711823}, issn = {1550-2783}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Feces/chemistry/microbiology ; *Adiposity/physiology ; *Obesity/microbiology/physiopathology ; *Marathon Running/physiology ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Body Mass Index ; *Physical Endurance/physiology ; *Running/physiology ; }, abstract = {Understanding variations in gut microbial functional potential among endurance athletes may inform future personalized nutritional strategies. This exploratory case-comparison study aimed to investigate predicted microbial functional potential using shotgun metagenomic sequencing and fecal metabolites, in two post hoc-selected runners who represented extreme and contrasting outcomes from the same single-stage 217 km mountain ultramarathon: a normal-BMI fast-finisher and an obese slow-finisher. The main descriptive findings suggest that the normal-BMI fast finisher exhibited smaller observed differences among the analyzed enzyme-coding functions and pathways in the sample collected after race completion, with a predominance of enzyme-coding functions associated with nucleic acid-related processes and protein biosynthesis. In contrast, the obese slow-finisher showed larger observed differences in predicted functional potential between the pre- and post-race samples. Distinct fecal metabolite patterns were also observed, with selective short-chain fatty acid (SCFA) changes in the normal-BMI fast-finisher and reductions across all analyzed SCFAs in the obese slow finisher. Given the limitations of this study, including the confounding effects of adiposity, unmeasured dietary intake, and post hoc selection bias, these descriptive observations provide hypothesis-generating data rather than establishing causal relationships with performance. Taken together, these findings encourage further investigation in larger cohorts.}, }
@article {pmid42711968, year = {2026}, author = {Liang, G and Wang, C and Liu, R and Ji, Q and Zhang, X and Zhao, L and Liu, X and Zhang, H and Zhuang, G and Zheng, J}, title = {Assembly Dynamics and Functional Divergence of Anaerobic Communities Driven by Iron Oxides.}, journal = {Environmental microbiology}, volume = {28}, number = {9}, pages = {e70412}, doi = {10.1111/1462-2920.70412}, pmid = {42711968}, issn = {1462-2920}, support = {GYY-NYHJ-2023-WT-002//the Weiqiao-UCAS Innovation Research Projects on Carbon Neutrality Technology/ ; }, mesh = {*Ferric Compounds/metabolism/chemistry ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Sewage/microbiology ; Anaerobiosis ; Minerals/metabolism ; Ferrosoferric Oxide/metabolism ; Methane/metabolism ; Iron Compounds ; }, abstract = {Iron oxides play an important role in regulating global biogeochemical cycles, yet how their physicochemical properties influence community structure, function, and assembly remains poorly understood. Here, we investigated the effects of four representative iron oxides-ferrihydrite (Fh), goethite (Gt), haematite (Ht), and magnetite (Mt)-serving as terminal electron acceptors on microbial communities enriched from activated sludge. Metagenomic profiling revealed mineral-dependent divergence in community composition and functional potential. The communities developed on amorphous Fh demonstrated low microbial diversity and were heavily dominated by Pseudomonas_A. In contrast, the communities associated with crystalline oxides (Gt and Ht) maintained intermediate diversity. Notably, the Mt. communities exhibited a more polycentric structure, possessing the highest richness and evenness, alongside a significant enrichment of Geobacter. Methane was detected in crystalline-oxide systems but remained below detection in Fh systems. Mineralogical analyses revealed substantial Fe(III) reduction and secondary mineral formation across treatments. Null-model analysis of pairwise turnover supports mineral-associated community turnover while highlighting that the relative contributions of selection versus undominated processes vary among minerals. Overall, these findings demonstrate that iron oxide identity is associated with differences in anaerobic community structure and biogeochemical outcomes.}, }
@article {pmid42711992, year = {2026}, author = {Farese, M and Moraitou, M and Jin, C and Forsythe, A and Micarelli, I and van der Valk, T and Manzi, G and Parducci, L and Tafuri, MA and Guschanski, K}, title = {Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.}, journal = {American journal of biological anthropology}, volume = {191}, number = {1}, pages = {e70357}, doi = {10.1002/ajpa.70357}, pmid = {42711992}, issn = {2692-7691}, support = {//Bertil Lundman Foundation for Anthropological Studies (Swedish Phytogeographical Society)/ ; DOT1326JZS//Italian Ministry of University and Research (MUR)/ ; }, mesh = {Humans ; *Microbiota/genetics ; Italy ; History, Ancient ; *Life Style/history ; Dental Calculus/microbiology ; DNA, Ancient/analysis ; *Mouth/microbiology ; Roman World/history ; }, abstract = {OBJECTIVES: The fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social élite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall.<br><br>MATERIAL AND METHODS: We analyzed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries (I-III century CE, Lucus Feroniae and Isola Sacra) and one post-Classical cemetery (IV-VIII century CE, Selvicciola), all located in proximity to the city of Rome, Italy.<br><br>RESULTS: We detect significant differences in the taxonomic and functional composition of the oral microbiome between the three sites, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible.<br><br>DISCUSSION: The distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices, in line with previously published isotopic and morphological data. Its rural position may have mitigated the cyclical food crises that affected the contemporary Isola Sacra and the later community of Selvicciola, buffering it against the nutritional stress observed in these two locations. This finding supports the temporal stability of the dental calculus microbiome while highlighting the impact of lifestyle on the oral microbial communities.}, }
@article {pmid42712102, year = {2026}, author = {Pellegrini, C and Ravaioli, F and De Fanti, S and Siliquini, A and Sala, C and Rochat, M and Pollarini, V and Polischi, B and Pasti, A and Grasso, M and Rambaldi, M and Cardoni, F and Grotteschi, N and Caraci, F and Cortelli, P and Provini, F and Lodi, R and Morandi, L and Parchi, P and Pirazzoli, GL and Sambati, L and Tonon, C and Bacalini, MG}, title = {Alterations of gut microbiota in Down syndrome and their association with Alzheimer's disease.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {22}, number = {9}, pages = {e71815}, doi = {10.1002/alz.71815}, pmid = {42712102}, issn = {1552-5279}, support = {PNC0000002//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; B53C22006330001//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; GR-2019-12369983-Theory-enhancing//Italian Ministry of Health/ ; //Italian Ministry of Health - "Ricerca Corrente" funding/ ; }, mesh = {Humans ; *Down Syndrome/microbiology/blood/complications ; *Alzheimer Disease/blood/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Aged ; Adult ; Biomarkers/blood ; Aged, 80 and over ; tau Proteins/blood ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Neurofilament Proteins/blood ; Glial Fibrillary Acidic Protein/blood ; }, abstract = {INTRODUCTION: Adults with Down syndrome (DS) have a higher risk of Alzheimer's disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS.<br><br>METHODS: Fecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing, filtering low prevalent taxa. Major neurocognitive disorder (NcD) was diagnosed with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria. Plasma levels of phosphorylated tau 181 (p-tau181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were measured using Simoa.<br><br>RESULTS: DS showed no changes in overall microbial diversity compared to CTRL, but genera including UBA1819 and Intestinibacter were altered. Specific genera showed changes in DS with NcD, like Alistipes (increased) and Roseburia (decreased), with the latter negatively associated with plasma AD biomarkers.<br><br>DISCUSSION: Adults with DS display AD-associated changes in GM partially resembling those reported previously in euploid AD patients.}, }
@article {pmid42712939, year = {2026}, author = {Tiwari, SK and Telatin, A and Singh, D}, title = {Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {3}, pages = {lqag110}, pmid = {42712939}, issn = {2631-9268}, mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Molecular Sequence Annotation ; }, abstract = {Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.}, }
@article {pmid42713785, year = {2026}, author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A}, title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.}, journal = {MicrobiologyOpen}, volume = {15}, number = {5}, pages = {e70416}, doi = {10.1002/mbo3.70416}, pmid = {42713785}, issn = {2045-8827}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation &amp; purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; }, abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.}, }
@article {pmid42715940, year = {2026}, author = {Jin, CH and Liu, SR and Song, WT and Yuan, SK and Zhang, YZ and Wang, P and Sun, XT and Liu, XQ and Fang, GY}, title = {Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {35}, pages = {27821-27839}, doi = {10.1021/acs.jafc.6c10005}, pmid = {42715940}, issn = {1520-5118}, support = {32401323//National Natural Science Foundation of China/ ; 2024LFR050//Zhejiang A and F University/ ; 2026R412A027//Xinmiao Talent Program/ ; NA//Zhejiang Provincial College Students' Science &amp; Technology Activity Plan/ ; }, mesh = {*Acetic Acid/metabolism/chemistry ; Fermentation ; Acetobacter/genetics/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Flavoring Agents/metabolism/chemistry ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; Saccharomyces cerevisiae/metabolism/genetics ; Metagenomics ; Microbiota ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.}, }
@article {pmid42200417, year = {2026}, author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X}, title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.}, journal = {Insect molecular biology}, volume = {35}, number = {5}, pages = {489-503}, doi = {10.1111/imb.70046}, pmid = {42200417}, issn = {1365-2583}, support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Diptera/microbiology/growth &amp; development ; Metagenomics ; Larva/microbiology/growth &amp; development ; *Vitamin B 6/metabolism ; Symbiosis ; *Gastrointestinal Microbiome ; }, abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.}, }
@article {pmid42442593, year = {2027}, author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W}, title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {592}, number = {}, pages = {121232}, doi = {10.1016/j.cca.2026.121232}, pmid = {42442593}, issn = {1873-3492}, mesh = {Humans ; *Microbiota/immunology ; *Amino Acids/metabolism ; Male ; Multiomics ; Female ; *Respiratory Tract Infections/diagnosis/immunology/metabolism/microbiology ; Aged ; *Lung/microbiology/metabolism/immunology ; Prospective Studies ; Cytokines/metabolism ; Aged, 80 and over ; Metabolomics ; }, abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.<br><br>METHODS: This prospective study enrolled 105 patients aged &#x2265;60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.<br><br>RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1&#x3b2;, IL-6, IL-8, TNF-&#x3b1;, IFN-&#x3b3;), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).<br><br>CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.}, }
@article {pmid42706263, year = {2026}, author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB}, title = {Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42706263}, issn = {2041-1723}, support = {INV-050353//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; K24AI134990//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Yang Biomedical Scholar award//UNC | University of North Carolina at Chapel Hill (UNC-Chapel Hill)/ ; }, mesh = {Animals ; *Aedes/virology ; *Dengue Virus/genetics/isolation &amp; purification ; Humans ; Angola/epidemiology ; *Dengue/transmission/epidemiology/virology ; *Virome/genetics ; *Mosquito Vectors/virology ; Democratic Republic of the Congo/epidemiology ; Female ; Congo ; }, abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collect Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirm high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.}, }
@article {pmid42706609, year = {2026}, author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX}, title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.}, journal = {Virulence}, volume = {17}, number = {1}, pages = {2728506}, doi = {10.1080/21505594.2026.2728506}, pmid = {42706609}, issn = {2150-5608}, mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; }, abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.}, }
@article {pmid42706715, year = {2026}, author = {Sahil, R and Jain, M}, title = {Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.}, journal = {Molecular ecology resources}, volume = {26}, number = {7}, pages = {e70197}, doi = {10.1111/1755-0998.70197}, pmid = {42706715}, issn = {1755-0998}, support = {BT/PR40261/BTIS/137/55/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Microbiota ; *Metagenomics/methods/standards ; *Plants/microbiology ; Benchmarking ; *Computational Biology/methods ; Metagenome ; }, abstract = {Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.}, }
@article {pmid42707963, year = {2026}, author = {Babu, P and Prakash, V and Subhash, S and Vanuopadath, M and Haripriyan, J and Rajan, K and Geetha, AA and P, S and Kumar, GB and Nair, BG and Madhavan, A}, title = {Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1905445}, pmid = {42707963}, issn = {2235-2988}, mesh = {Humans ; *Dysbiosis/immunology/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; *Immunomodulation ; }, abstract = {The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host-microbiota-pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)-Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.}, }
@article {pmid42707980, year = {2026}, author = {Li, ZL and Qu, RN and Liu, SX and Wang, W}, title = {Research progress and clinical translation prospects of the urinary tract microbiome in prostate cancer.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1911969}, pmid = {42707980}, issn = {1664-3224}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/immunology ; *Microbiota ; *Urinary Tract/microbiology ; Translational Research, Biomedical ; Tumor Microenvironment ; Animals ; }, abstract = {Prostate cancer (PCa) is one of the most common malignancies in men worldwide, and its development is influenced by multiple factors, including genetic susceptibility, hormonal dysregulation, chronic inflammation, immune dysregulation, and remodeling of the tumor microenvironment. In recent years, the urinary tract microbiome has emerged as an important component of the tumor ecosystem and has attracted increasing attention in PCa research. Accumulating evidence indicates that patients with PCa exhibit characteristic microbial alterations in urine, expressed prostatic secretions, semen, and prostate tissue, and that certain taxa are associated with tumor grade, stage, and recurrence risk. These microbes may participate in tumor initiation and progression through a variety of mechanisms, such as inducing chronic inflammation, activating signaling pathways including TLR/NF-κB and STAT3, modulating the Treg/Th17 balance, influencing macrophage polarization, and interfering with androgen metabolism. Meanwhile, advances in 16S rRNA sequencing, metagenomics, metatranscriptomics, and multi-omics integration have provided powerful tools for characterizing host-microbe interactions and their functional relevance. In addition, microbiome-based biomarkers derived from non-invasive samples such as urine, together with artificial intelligence and causal inference approaches applied to multi-cohort data, may offer promising opportunities for early screening, risk stratification, treatment monitoring, and personalized intervention in PCa. However, current evidence remains largely associative, and the causal relationship between microbial changes and PCa has not yet been fully established. Major challenges, including contamination in low-biomass samples and inter-cohort heterogeneity, continue to hinder clinical translation. Future research should focus on longitudinal cohort studies, multicenter validation, standardized sampling workflows, and mechanistic experiments to clarify key microbial signatures and their biological functions, thereby accelerating the clinical application of the urinary tract microbiome in precision diagnosis and treatment of PCa.}, }
@article {pmid42708949, year = {2026}, author = {Jiang, Y and Chen, L and Dong, H and Li, Q and Zhao, W and Zhu, F and Jiang, J and Zhang, Y and Huang, S and Xue, S}, title = {Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {35}, pages = {24764-24775}, doi = {10.1021/acs.est.5c18355}, pmid = {42708949}, issn = {1520-5851}, support = {42030711//National Natural Science Foundation of China (NSFC)/ ; 42477437//National Natural Science Foundation of China (NSFC)/ ; 42671661//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil/chemistry ; *Microbiota ; *Dissolved Organic Matter ; Soil Microbiology ; Aluminum Oxide ; Carbon ; }, abstract = {Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.}, }
@article {pmid42708953, year = {2026}, author = {Francescato, L and Ghiotto, G and Valerin, MC and De Bernardini, N and Fraulini, S and Sandon, A and Treu, L and Lavagnolo, MC and Campanaro, S}, title = {Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {35}, pages = {24776-24791}, doi = {10.1021/acs.est.6c05759}, pmid = {42708953}, issn = {1520-5851}, mesh = {*Ammonia ; *Microbiota ; Anaerobiosis ; Methane/metabolism ; }, abstract = {Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.}, }
@article {pmid42236734, year = {2026}, author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L}, title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42236734}, issn = {2052-4463}, support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, mesh = {*Wetlands ; *Microbiota ; *Metadata ; *Metagenome ; Metagenomics ; }, abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.}, }
@article {pmid42315898, year = {2026}, author = {Mishra, S and Mutnuri, S}, title = {Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42315898}, issn = {2045-2322}, mesh = {*Fermentation ; *Metagenomics/methods ; Arctic Regions ; *Hydrogen/metabolism ; Kinetics ; Microbiota ; *Biofuels ; *Ice ; }, abstract = {Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.}, }
@article {pmid42332773, year = {2026}, author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q}, title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.}, journal = {BMC medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42332773}, issn = {1741-7015}, support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Imidazoles/blood ; *Dietary Fiber/administration &amp; dosage ; *Coronary Disease/blood/epidemiology/microbiology ; *Histidine/administration &amp; dosage/metabolism ; Middle Aged ; Prospective Studies ; *Propionates/blood ; Adult ; }, abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.<br><br>METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.<br><br>RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles&#x2009;=&#x2009;1.82; 95%CI&#x2009;=&#x2009;1.17-2.81; p-trend&#x2009;=&#x2009;0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction&#x2009;=&#x2009;0.01). Similar interactions were seen for total fiber (p&#x2009;=&#x2009;0.09), soluble fiber (p&#x2009;=&#x2009;0.09), and insoluble fiber (p&#x2009;=&#x2009;0.11), without statistical significance.<br><br>CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.}, }
@article {pmid42508343, year = {2026}, author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK}, title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.}, journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine}, volume = {237}, number = {}, pages = {112830}, doi = {10.1016/j.apradiso.2026.112830}, pmid = {42508343}, issn = {1872-9800}, mesh = {Animals ; Male ; *Gamma Rays ; *Spodoptera/microbiology/radiation effects ; *Gastrointestinal Microbiome/radiation effects ; Bacteria/radiation effects/genetics ; }, abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.}, }
@article {pmid42518032, year = {2026}, author = {Li, F and Zhao, H and Lei, Y and Luo, J and Chen, B and Li, C and Zhao, X and Jiang, H}, title = {Fufangteng Yixin Formula alleviates myocardial ischemia-reperfusion injury by modulating gut microbiota and resultant metabolites in rats.}, journal = {Journal of natural medicines}, volume = {80}, number = {5}, pages = {1521-1537}, pmid = {42518032}, issn = {1861-0293}, support = {2024GXNSFBA010207//Guangxi Natural Science Foundation Joint Special Project/ ; }, mesh = {Animals ; Rats ; *Myocardial Reperfusion Injury/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats, Wistar ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; }, abstract = {This study aimed to explore whether Fufangteng Yixin Formula (FFTYXF) can ameliorate myocardial ischemia-reperfusion injury (MIRI) by regulating the gut microbiota and resultant metabolites. Wistar rats were given FFTYXF by gavage for 7 days, and MIRI rat model was established. Serum level of inflammatory markers was determined by ELISA, and heart function was evaluated by echocardiography. Myocardial histological changes and infarct size were examined by hematoxylin-eosin and triphenyltetrazolium chloride staining, respectively. 16S rRNA gene and metagenomics analyses were employed to explore gut microbiota, while untargeted metabolomics analysis was used to explore serum metabolites. FFTYXF pretreatment could significantly improve cardiac function, reduce infarct size, decrease level of inflammatory factors (TNF-α and IL-6) and inflammatory cells infiltration. At genus level, g__Oscillibacter and g__Rikenellaceae_RC9_gut_group were identified as key microbial bacteria in MIRI rat response to FFTYXF pretreatment. After FFTYXF pretreatment, the functional categories of gut microbiota were participated in fatty acid (FA) biosynthesis/metabolism, glycolysis _ gluconeogenesis and sphingolipid metabolism. Genes response to FFTYXF pretreatment in MIRI rats included K00023 (phbB), K00281 (GLDC, gcvP), K03879 (ND2), K07827 (KRAS) and K15192 (BTAF1), and they were mainly participated in carbon, butanoate, glyoxylate and dicarboxylate metabolism. Differential metabolites were also mainly participated in FA biosynthesis/metabolism, such as alpha-Linolenic acid, omega-3/omega-6 FA, and flavan-3-ol metabolic pathway. Abundance of g__Rikenellaceae_RC9_gut_group positively correlated with differential metabolites FAHFA 34:0, FAHFA 16:1/18:3, and FA 24:5. FFTYXF could alleviate MIRI by modulating gut microbial bacteria alteration and resultant metabolites, particularly short-chain FAs.}, }
@article {pmid42631636, year = {2026}, author = {Azouz, S and Benabid, M and Zarrouk, S and Elati, J and Aoun, K and Bouratbine, A}, title = {Contribution of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) to the characterization of the gut microbiota in Tunisia, North Africa.}, journal = {FEMS microbiology letters}, volume = {373}, number = {}, pages = {}, doi = {10.1093/femsle/fnag095}, pmid = {42631636}, issn = {1574-6968}, support = {//Ministry of Higher Education and Science/ ; }, mesh = {Humans ; Tunisia ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Pilot Projects ; Adult ; Metagenomics/methods ; Metagenome ; Shotgun Sequencing ; Male ; Female ; }, abstract = {This pilot study aimed to assess the enhanced capabilities of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) for identifying specific microbiota patterns in healthy adults in Tunisia. Shotgun metagenomic sequencing was performed on 21 stool samples. Taxonomic classification was carried out using Kraken2, followed by Bracken analysis. Enterotype (ET) assignment was performed using a publicly available, reference-based classification tool involving Fuzzy-k-means (FKM) clustering. Next, NMF was applied to identify 'enterosignatures' (ESs). The FKM approach revealed a co-dominance of Prevotella-ET (P-ET, 57%) and Firmicutes-ET (F-ET, 38%) with 41% of P-ET samples exhibiting a significant deviation from the reference enterotype center. These latter had a lower proportion of Prevotella-ES and a higher proportion of Bacteroides/Phocaeicola-, Firmicutes- and/or Bifidobacterium-enriched ESs. The F-ET samples were differentially enriched by Blautia (P = 0.007) and Vescimonas (P = 0.007). NMF revealed within this group, a candidate Firmicutes-associated ES driven by Blautia and encompassing Vescimonas, Akkermansia, and Methanobrevibacter. These findings demonstrate the combined power of refined enterotyping and NMF in characterizing gut microbiota, providing a key methodology for future large-scale research. However, our relatively small sample size limits statistical power and biological interpretation, making this study exploratory in nature. Candidate ES requires validation in larger independent datasets.}, }
@article {pmid42641809, year = {2026}, author = {Wang, J and Zhang, D and Hu, S and Guo, H and Zou, L and Wang, N and Xie, J and Wang, Z and Hao, M and Da, Y and Wang, M and Song, L and Li, H and Sun, B}, title = {Limosilactobacillus reuteri and Lactobacillus johnsonii intervention ameliorates gestational diabetes mellitus-associated sex-specific placental nutrient transporter abnormalities: Links with tryptophan metabolism and aryl hydrocarbon receptor signaling.}, journal = {Diabetes research and clinical practice}, volume = {240}, number = {}, pages = {113510}, doi = {10.1016/j.diabres.2026.113510}, pmid = {42641809}, issn = {1872-8227}, mesh = {Female ; Pregnancy ; Animals ; *Limosilactobacillus reuteri/physiology ; *Diabetes, Gestational/metabolism/microbiology/therapy ; Humans ; *Placenta/metabolism ; Mice ; *Tryptophan/metabolism ; *Probiotics/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction ; *Lactobacillus johnsonii ; Male ; Adult ; Gastrointestinal Microbiome ; }, abstract = {AIMS: Gestational diabetes mellitus (GDM) is a common pregnancy complication associated with maternal metabolic abnormalities and adverse offspring outcomes. Although GDM is closely linked to gut microbiota dysbiosis, key probiotic strains and underlying mechanisms remain unclear. This study aimed to identify potential probiotics using microbial signals from clinical GDM cases and a mouse model.<br><br>METHODS: Metagenomic sequencing was performed on fecal samples from normal and GDM pregnant women; a GDM mouse model was then established for candidate probiotic screening. Combined intervention with Limosilactobacillus reuteri and Lactobacillus johnsonii was applied to assess glucose metabolism, inflammation, intestinal barrier, placental structure, nutrient transporter expression and tryptophan metabolism.<br><br>RESULTS: Metagenomic analysis showed reduced Lactobacillaceae in GDM women, and the two strains were identified as candidates. The intervention improved glycemic control, insulin resistance, inflammation and colon barrier function, and alleviated placental lesions. Placental nutrient transporters expression showed sex-specific abnormalities that were normalized by probiotics. Maternal plasma 5-hydroxyindoleacetic acid (5-HIAA) was reduced in GDM mice and restored after intervention, correlating with metabolic indices, placental status, fetal growth and aryl hydrocarbon receptor (AhR) signaling.<br><br>CONCLUSIONS: Combined L. reuteri and L. johnsonii intervention improved GDM-associated maternal metabolic and sex-specific placental abnormalities.}, }
@article {pmid42702602, year = {2026}, author = {Li, Y and Chen, T and Li, P and Zhang, G and Tian, Y and Wang, J and Ni, J}, title = {Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42702602}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Ice Cover/virology ; Tibet ; *Rivers/virology ; Altitude ; Ecosystem ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; }, abstract = {The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.}, }
@article {pmid42702845, year = {2026}, author = {Xue, Z and Xu, H and Zhu, L and Zhao, D}, title = {Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.}, journal = {Chemical biology &amp; drug design}, volume = {108}, number = {3}, pages = {e70397}, doi = {10.1111/cbdd.70397}, pmid = {42702845}, issn = {1747-0285}, mesh = {Animals ; Humans ; Multiomics ; *Prevotella melaninogenica/metabolism/physiology ; *Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy ; *Mycoplasma pneumoniae ; Mice ; *Butyrates/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Disease Models, Animal ; Microbiota ; }, abstract = {Mycoplasma pneumoniae (MP) is one of the main pathogens causing atypical pneumonia in children. The susceptible population is mainly children and adolescents over 5 years old, and the infection rate has increased in recent years. At present, there is limited research on the pulmonary microbiota of patients with Mycoplasma pneumoniae pneumonia, and the characteristics of their microbiota are not yet clear. We included MPP children in stages and established two independent cohorts. Cohort I (n = 175) performed 16S rRNA sequencing on bronchoalveolar lavage fluid (BALF) to explore microbial genus level characteristics, while Cohort II (n = 41) performed metagenomic and transcriptome sequencing to explore microbial species level characteristics and predict inter group differential metabolic pathways. Finally, a murine model infected with MP was established to validate the effects of Prevotella melaninogenica and its metabolite butyrate. Based on Multi-Omic Analysis, we discovered that P. melaninogenica was the most discriminative species enriched in the critically ill group. Functional profiling demonstrated that butanoate metabolism pathways were significantly enriched in the severe group and positively correlated with P. melaninogenica abundance. Transcriptomic analysis revealed that P. melaninogenica-associated host genes were significantly enriched in immune regulation pathways. Animal experiments confirmed that both P. melaninogenica and butyrate pretreatment significantly attenuated MP-induced pulmonary inflammation, pathogen load, and immune cell infiltration. Respiratory microbiota dysbiosis may be associated with MPP severity. Prevotella melaninogenica, a potential protective commensal enriched in severe group MPP patients, may alleviate airway inflammation through its metabolite butyrate.}, }
@article {pmid42703994, year = {2026}, author = {Kar, P and Halder, J and Rout, SR and Dash, P and Das, C and Ghosh, G and Rath, G and Kar, B}, title = {Marine-derived Bioactive Compounds: A Promising Frontier against Multidrug-resistant Microbial Infections.}, journal = {Mini reviews in medicinal chemistry}, volume = {26}, number = {12}, pages = {841-858}, pmid = {42703994}, issn = {1875-5607}, mesh = {Humans ; *Biological Products/chemistry/pharmacology/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation &amp; purification ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria/drug effects ; *Bacterial Infections/drug therapy ; Microbial Sensitivity Tests ; }, abstract = {The global escalation of Multidrug-Resistant (MDR) bacterial infections poses a serious and growing threat to public health, contributing to increased morbidity, mortality, and substantial economic burden worldwide. The widespread and often indiscriminate use of antibiotics in clinical and agricultural settings has accelerated the emergence of resistance, significantly diminishing the efficacy of conventional antimicrobial therapies. This pressing challenge necessitates the exploration of alternative sources for novel antibiotics. Marine ecosystems-renowned for their immense biodiversity and ecological complexity-have gained attention as a rich and largely untapped reservoir of bioactive natural products with potent antimicrobial activity. Marine organisms, such as sponges, tunicates, algae, and bacteria and fungi derived from marine sources, produce structurally diverse and pharmacologically active metabolites, including peptides, polyketides, alkaloids, terpenoids, sterols, lactones, and halogenated compounds. Many of these marine-derived molecules possess unique chemical scaffolds and novel mechanisms of action, offering the potential to circumvent existing resistance pathways. Some compounds have shown promising activity against MDR pathogens, including Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. However, challenges such as low natural abundance, difficulty in cultivation, and structural complexity have limited their clinical translation. Recent advancements in marine biotechnology, genomics, metagenomics, and synthetic biology have opened new avenues for the discovery, biosynthesis, and structural optimization of these compounds. These innovative approaches not only facilitate sustainable production but also enhance the pharmacological properties.}, }
@article {pmid42704537, year = {2026}, author = {de Freitas Germano, J and Leite, G and Pimentel, M}, title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.}, journal = {Current gastroenterology reports}, volume = {28}, number = {1}, pages = {}, pmid = {42704537}, issn = {1534-312X}, mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; }, abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.<br><br>RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.}, }
@article {pmid42704656, year = {2026}, author = {Bates, KA and Rivera, VB and Glicklich, D and Diflo, T and Chaturvedi, V and Nog, R}, title = {Urinary microbiome in renal transplant patients with BK polyomavirus reactivation.}, journal = {Journal of medical microbiology}, volume = {75}, number = {9}, pages = {}, doi = {10.1099/jmm.0.002196}, pmid = {42704656}, issn = {1473-5644}, mesh = {Humans ; *BK Virus/physiology/genetics ; *Kidney Transplantation/adverse effects ; *Polyomavirus Infections/urine/microbiology/virology ; *Microbiota ; Male ; Female ; Middle Aged ; Adult ; *Virus Activation ; Bacteria/classification/genetics/isolation &amp; purification ; *Tumor Virus Infections/urine/microbiology/virology ; Aged ; DNA, Viral/blood ; *Urine/microbiology ; }, abstract = {Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.}, }
@article {pmid42705715, year = {2026}, author = {Li, G and Shen, L and Nie, L and Tang, P and Shan, Q and Qin, L and Fan, S and Guo, X}, title = {Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120307}, doi = {10.1016/j.foodres.2026.120307}, pmid = {42705715}, issn = {1873-7145}, mesh = {*Fermentation ; *Volatile Organic Compounds/analysis ; *Gas Chromatography-Mass Spectrometry/methods ; *Electronic Nose ; *Metagenomics/methods ; *Microbiota ; *Food Microbiology/methods ; Taste ; Odorants/analysis ; *Edible Grain/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/metabolism/genetics ; }, abstract = {The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.}, }
@article {pmid42705723, year = {2026}, author = {Tong, W and Wang, H and Yang, Y and Xu, J and Huang, Z and Huang, D and Luo, H and Zhao, L and Zhang, S}, title = {Enzyme-driven synthesis and metabolic mechanism of ferulic acid in strong-flavor Daqu: pathway elucidation and microbial drivers.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120354}, doi = {10.1016/j.foodres.2026.120354}, pmid = {42705723}, issn = {1873-7145}, mesh = {*Coumaric Acids/metabolism/analysis ; Fermentation ; Carboxylic Ester Hydrolases/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism ; Carboxy-Lyases/metabolism ; Bacteria/metabolism ; Metabolic Networks and Pathways ; Microbiota ; }, abstract = {Ferulic acid (FA) is a bioactive phenolic compound in strong-flavor Baijiu with important health functions. Its microbial synthesis and metabolic mechanisms in strong-flavor Daqu remain unclear, limiting the understanding of its production. This study explored FA synthesis and metabolic dynamics during Daqu fermentation from D0-D90 using physicochemical detection, feruloyl esterases (FAEs) activity assay, and metagenomic sequencing. Results indicated that FA content fluctuated dynamically throughout fermentation, reaching a final level of 4.39 ± 0.17 mg/kg, and FAEs activity was significantly positively correlated with FA content. Genera significantly associated with FA dynamics were identified. High-abundance genera including Lichtheimia, Saccharopolyspora, Aspergillus, Byssochlamys and Rasamsonia exhibited significantly positive correlations with FA accumulation at respective fermentation stages. This phenomenon may be attributed to their capacity to secrete FAEs, thereby promoting the release of FA. The dynamic change of free FA content was also associated with the expression of ferulic acid decarboxylase, a key enzyme potentially involved in free FA degradation. A comprehensive FA metabolic network in Daqu was constructed, including the cell wall release pathway and the shikimate biosynthesis pathway. A metabolic association model was established based on the phasic succession of fungal and bacterial communities and their coupling with FA metabolic enzyme systems, which suggested a potential division of labor. Fungi are likely to participate in free FA release through secretion of FAEs and auxiliary degrading enzymes, while bacteria may mainly participate in the metabolic turnover and consumption of free FA. This study expands the current understanding of phenolic acid metabolism in strong-flavor Daqu, and provides a theoretical basis for interpreting FA metabolic characteristics during Daqu fermentation.}, }
@article {pmid42705725, year = {2026}, author = {Xiao, L and Wan, Y and Jiang, M and Liu, Z and Chen, G and Ke, S and Jiang, J and Guo, S and Yu, P and Wu, H and Wang, A and Ning, M and Zhou, Z}, title = {Effects of extraction methodologies on structural characterization and gut microbiota fermentation properties of Apocynum venetum polysaccharides.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120357}, doi = {10.1016/j.foodres.2026.120357}, pmid = {42705725}, issn = {1873-7145}, mesh = {*Fermentation ; *Polysaccharides/chemistry/isolation &amp; purification/metabolism/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Apocynum/chemistry ; Prebiotics ; Bacillus/metabolism ; *Plant Extracts/chemistry ; Hydrogen-Ion Concentration ; }, abstract = {Apocynum venetum L. polysaccharides are classified into neutral-to-acidic heteropolysaccharides rich in glucuronic acid, exhibiting antioxidant, immunomodulatory, and potential prebiotic activities. Different extraction methods have a significant impact on the structural characterization and biological activity of polysaccharides. This study aims to compare the structural characteristics and in vitro prebiotic activity of the Apocynum venetum L. polysaccharides BAC and CEL-U obtained via Bacillus velezensis fermentation and the combined ultrasonic-cellulase method, respectively. The results showed that BAC and CEL-U were acidic heteropolysaccharides composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, and they all showed linear branching structure. Compared with CEL-U, BAC had lower molecular weight (17.51 kDa), higher uronic acid content (27.27%) and typical triple helix structure. In vitro fermentation showed that BAC can produce more propionic acid and butyric acid, maintain a lower pH, promote the proliferation of beneficial bacteria (Segatella and Prevotella), and inhibit potentially harmful bacteria. Metagenome analysis further revealed that BAC played a prebiotic role by activating specific glycosidase-mediated degradation pathways and enriching functional pathways related to carbohydrate metabolism. These findings clarify the structure-activity relationship of Apocynum venetum polysaccharide and provide a theoretical basis for its targeted application in the field of intestinal health.}, }
@article {pmid42705727, year = {2026}, author = {Xu, S and Li, J and Wang, F and Bian, H and Yan, W and Wang, H and Jiang, C and Sun, J and Wang, Z and Li, X}, title = {Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120362}, doi = {10.1016/j.foodres.2026.120362}, pmid = {42705727}, issn = {1873-7145}, mesh = {*Hydrogen/metabolism ; *Fermentation ; Bacteria/metabolism/classification/genetics ; Archaea/metabolism/genetics/classification ; *Wine/microbiology/analysis ; *Food Microbiology ; *Microbiota ; Metagenomics ; China ; *Alcoholic Beverages/microbiology ; }, abstract = {Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.}, }
@article {pmid42705729, year = {2026}, author = {Li, Y and Li, J and Deng, J and Xia, P and Zhou, G and Zhu, Z and Ding, Y and Yang, J and Zhang, F}, title = {Phocaeicola vulgatus alleviates obesity through cross-species arginine production and hepatic retinoic acid signaling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120365}, doi = {10.1016/j.foodres.2026.120365}, pmid = {42705729}, issn = {1873-7145}, mesh = {*Arginine/biosynthesis/metabolism ; Animals ; *Obesity/therapy/microbiology/metabolism ; *Liver/metabolism ; Signal Transduction ; *Tretinoin/metabolism ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Gastrointestinal Microbiome ; Diet, High-Fat ; }, abstract = {Fecal microbiota transplantation (FMT) shows inconsistent clinical efficacy in treating obesity, and the specific microbial determinants dictating its success remain poorly characterized. Our previous clinical FMT trial identified Phocaeicola vulgatus as a key microbe contributing to the therapeutic efficacy of obesity treatment. Here, to investigate its role in obesity, we established an independent clinical cohort comprising obese and lean individuals, revealing that the P. vulgatus-centered network and ornithine synthesis are impaired in the obese group. We then confirmed causality by utilizing a humanized rat model carrying microbiota from a P. vulgatus-deficient obese patient, demonstrating that P. vulgatus supplementation significantly mitigates HFD-induced obesity, including reductions in body weight and serum total cholesterol levels, as well as the alleviation of hepatic steatosis. To further explore the functional mechanisms of P. vulgatus, integrated metagenomic and metabolomic analyses revealed a potential functional association between P. vulgatus and Phascolarctobacterium faecium that is associated with enhanced intestinal arginine biosynthesis and systemic availability. Furthermore, hepatic transcriptomics linked these elevated circulating arginine levels to the upregulation of retinoic acid (RA) signaling. Taken together, our findings outline a potential microbial-host network wherein P. vulgatus mitigates obesity via the arginine-RA axis, providing a valuable scientific basis for exploring this strain as a probiotic candidate for metabolic health.}, }
@article {pmid42705742, year = {2026}, author = {Han, G and Li, K and Wang, J and Xu, P and Liu, T and Xu, X and Zhao, Y}, title = {Mechanistic insights into flavor deterioration in bitter sturgeon caviar: Evidence from lipidomics and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 2}, pages = {120381}, doi = {10.1016/j.foodres.2026.120381}, pmid = {42705742}, issn = {1873-7145}, mesh = {Animals ; *Metagenomics ; *Fishes ; *Lipidomics ; *Taste ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Microbiota ; Bacteria ; *Seafood/analysis/microbiology ; Humans ; }, abstract = {This study systematically compared the flavor and multi-omics differences between normal caviar and bitter caviar based on quantitative descriptive analysis (QDA), volatile compounds (VOCs) analysis, untargeted lipidomics, and metagenomics. The results showed that bitter caviar was characterized not only by increased bitterness, but also by decreased positive sensory attributes, including buttery, nutty, and marine fresh. VOCs analysis indicated that the volatile profile of bitter caviar was reorganized. Compounds such as 3-hydroxy-2-butanone, 1-octen-3-ol, and (E, Z)-2,6-nonadienal showed higher relative odor activity values (rOAVs); however, these changes did not improve its overall sensory experience. Untargeted lipidomics identified 492 differential lipids. These changes were mainly characterized by decreased PC and increased DG and LPC in bitter caviar. KEGG pathways analysis showed that these differential lipids were mainly associated with glycerophospholipid metabolism, choline metabolism in cancer, and retrograde endocannabinoid signaling. Metagenomic analysis showed that bacteria dominated the microbial community of caviar. Among them, Bacillus and Micromonospora showed relatively high abundance in the caviar microbiota. They were also closely associated with lipid metabolic changes involving PC, DG, and LPC, suggesting their potential as candidate targets for future microbiota-directed regulation of caviar quality. These findings provide new insights into the mechanisms underlying sensory deterioration and flavor formation in bitter caviar, and offer a theoretical basis for improving caviar quality in industrial production.}, }
@article {pmid42566926, year = {2026}, author = {Carvalho, LB and da Silva, GR and de Oliveira Franzote, VH and Larcerda-Júnior, GV and Fernandes-Júnior, PI and Oliveira, VM and Matteoli, FP}, title = {Marked dominance of Actinomycetota and compositional shifts in bacterial communities in Brazilian dryland soils under land-use change.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128660}, doi = {10.1016/j.micres.2026.128660}, pmid = {42566926}, issn = {1618-0623}, mesh = {*Soil Microbiology ; Brazil ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; Forests ; Agriculture ; Soil/chemistry ; *Actinobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; Tropical Climate ; Biodiversity ; *Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Tropical dry forests are among the most threatened and least studied tropical forest ecosystems worldwide. The Caatinga, the largest tropical dry forest in South America, comprises preserved and agriculturally impacted areas, providing a valuable model system to investigate how semiarid soil bacterial communities respond to natural seasonality and land-use change. Here, we evaluated how land-use and seasonality shape microbial community structure and ecological strategies in soils from conserved forest (CEF) and agriculture-influenced areas (BEF) across rainy and dry seasons using a contig-based taxonomy approach combined with ANCOM-BC2 differential abundance analysis and co-occurrence networks inference. A total of 74 phyla and 1015 genera were identified, with marked predominance of Actinomycetota (61.4%). Seasonal responses were mainly detected in BEF, where Trebonia and Mycobacterium were enriched during the dry season, while Solirubrobacter was more abundant in the rainy season. Taxa putatively associated with plant growth promotion and biological soil crust formation were consistently detected in both areas, whereas oligotrophic and methanotrophic groups were more enriched in CEF and taxa related to biocontrol potential were more represented in BEF. The proportion of seasonal generalists was higher in CEF than in BEF, representing 86.0% and 46.6% of the detected taxa, respectively, suggesting greater temporal stability in conserved soils. Co-occurrence networks revealed that CEF exhibited a sparser and more modular structure, whereas BEF displayed a highly interconnected network. Notably, all module hubs belonged to Actinomycetota. Together, these findings demonstrate that land-use intensification reshapes bacterial ecological strategies and network organization, reducing community heterogeneity under agricultural management.}, }
@article {pmid42585836, year = {2026}, author = {Cao, Y and Du, P and Zhai, R and Guo, Y and Lin, M and Wang, Z}, title = {Drought stress adaptation in Ficus carica L.: Modulation of ROS scavenging, nitrogen uptake, and rhizosphere bacterial community assembly and functions.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128678}, doi = {10.1016/j.micres.2026.128678}, pmid = {42585836}, issn = {1618-0623}, mesh = {*Ficus/microbiology/physiology/growth &amp; development/metabolism ; *Nitrogen/metabolism ; *Rhizosphere ; Soil Microbiology ; *Reactive Oxygen Species/metabolism ; Drought Resistance ; *Droughts ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Nitrogen Fixation/genetics ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Photosynthesis ; Adaptation, Physiological ; }, abstract = {Rhizosphere microorganisms are crucial for plant drought resistance; however, their response to drought stress in fig plants remains poorly understood. In this study, potted 'BoJi Red' fig plants were utilized to systematically investigate drought-induced changes in the structure, assembly processes, and functional potential of rhizosphere bacterial communities. The results showed that drought significantly inhibited fig growth, photosynthesis, and nitrogen uptake, while increasing reactive oxygen species (ROS) content and antioxidant enzyme activities, although these enzyme activities declined under severe drought conditions. Bacterial community richness and diversity significantly increased under moderate and severe drought, shifting toward drought-resistant groups, notably Actinomycetota and Bacillota. The number of nodes, links, and key species in the microbial co-occurrence network decreased as drought intensified, with stochastic processes dominating community assembly. Moreover, ecological niche breadth and the proportion of generalist species increased with drought severity. Notably, Nocardioidaceae was significantly enriched under drought, and metagenomic profiling indicated this taxon is strongly associated with carbohydrate metabolism pathways, with predicted genetic potential to participate in soil carbon turnover and nutrient transformation. Additionally, drought significantly reduced the abundance of nitrogen-fixing genes (nifD, nifK) and weakened the relative contribution of Rhizobiaceae to nitrogen fixation; correlative functional profiling suggests Nocardioidaceae may possess alternative nitrogen cycling pathways that could partially offset suppressed rhizosphere nitrogen fixation capacity. Overall, these findings indicate that the fig plant response to drought stress involves both physiological adjustments in the host and functional reconfiguration of the rhizosphere microbial community, with Nocardioidaceae playing a key role in maintaining rhizosphere functions and enhancing drought tolerance.}, }
@article {pmid42636661, year = {2026}, author = {Zeng, Y and Tao, Q and Fan, J and Wang, Y and Tao, R and Rao, J and Zeng, F and Jiang, F and Zhang, C and Xiong, X and Cheng, X}, title = {Desert-derived Ensifer sp. SA403 enhances potato salt tolerance by reshaping rhizosphere microbiome functions and host responses.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128695}, doi = {10.1016/j.micres.2026.128695}, pmid = {42636661}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Solanum tuberosum/microbiology/physiology/growth &amp; development ; *Salt Tolerance ; Soil Microbiology ; *Microbiota ; *Rhizobiaceae/genetics/isolation &amp; purification/physiology/classification ; Plant Roots/microbiology ; Salinity ; Host Microbial Interactions ; Desert Climate ; Metagenomics ; Sodium/metabolism ; Soil/chemistry ; }, abstract = {Soil salinization increasingly threatens global food security, and potato (Solanum tuberosum L.), a moderately salt-sensitive crop, is particularly vulnerable to saline soils. Plant growth-promoting rhizobacteria (PGPR) offer a promising strategy to improve crop performance, yet how PGPR interact with native microorganisms to enhance potato salt tolerance remains poorly understood. In this study, we identified a desert-derived PGPR strain, Ensifer sp. SA403, which substantially enhanced potato performance under high salinity across sterile, non-sterile and field conditions. Physiologically, inoculation with SA403 reduced shoot Na[+] accumulation and increased the K[+]/Na[+] ratio; notably, these effects were markedly stronger in non-sterile substrates than under sterile conditions, indicating that SA403-mediated ion homeostasis relies on cooperation with the resident microbiota rather than on the strain acting alone. Metagenomic profiling indicated that SA403 strain reshaped rhizosphere communities, significantly enriching beneficial taxa such as Priestia and Bradyrhizobium, and upregulated functional pathways involved in glutathione and sulfur metabolism. Furthermore, host transcriptomic analyses showed that SA403 modulated plant responses to salt stress, with differentially expressed genes enriched in jasmonic acid signaling, ethanolamine metabolism and amino-acid biosynthesis pathways. Field trials on saline soils confirmed that SA403 significantly increased seedling emergence and tuber weight. Together, our results demonstrate that SA403 functions as a biological mediator that optimizes rhizosphere microecology and coordinates ion balance and host signaling to enhance potato salt tolerance. These findings support the potential of SA403 as a robust PGPR-based tool for sustainable potato production on saline soils.}, }
@article {pmid42636663, year = {2026}, author = {Wang, D and Huang, Z and Sun, S and Song, W and Li, Y and Sun, K and Li, Z and Feng, J}, title = {Multi-omics reveal microbial functional traits and antifungal metabolites associated with lower Pseudogymnoascus destructans loads in bat cave soils.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128696}, doi = {10.1016/j.micres.2026.128696}, pmid = {42636663}, issn = {1618-0623}, mesh = {Animals ; Multiomics ; *Soil Microbiology ; *Ascomycota/drug effects/isolation &amp; purification ; *Caves/microbiology ; *Chiroptera/microbiology ; Metabolomics ; *Antifungal Agents/pharmacology/metabolism ; China ; Microbiota/genetics ; Metagenomics ; Soil/chemistry ; }, abstract = {White-nose syndrome, caused by Pseudogymnoascus destructans (Pd), is a major fungal disease threatening hibernating bats. Cave soils can serve as environmental reservoirs for Pd, yet the microbial and biochemical mechanisms underlying naturally low Pd burdens in some cave environments remain poorly understood. Here, we integrated soil microbiome profiling, metagenomics, metabolomics, multi-omics network analysis, and in vitro validation to investigate the ecological and functional basis of differential Pd loads in hibernating bat caves in Northeast China. The three caves shared cold, humid, and weakly acidic microenvironments, but differed significantly in electrical conductivity, soil water content, nutrient availability, and extracellular enzyme activities. Soil microbial communities showed significant inter-cave variation in composition, diversity, and niche breadth, with stochastic processes contributing substantially to community assembly. Environmental variables, particularly pH and Pd load, were important predictors of microbial community structure. Functional analyses revealed that the low-Pd Gezi Cave was enriched in genes associated with organic carbon degradation, nitrogen input and retention, and secondary metabolism. Metabolomic profiling further identified cave-specific metabolite signatures, among which Biochanin A, 4-Hydroxybenzaldehyde, Vanillin, and Arachidonic acid were negatively correlated with Pd loads. Integrated pathway and network analyses showed that differential genes and metabolites jointly mapped to secondary metabolite biosynthesis, aminobenzoate degradation, and flavonoid degradation pathways, forming a microbe-metabolite-functional gene coupling network involving key taxa such as Rhodococcus, Pseudorhodoplanes, and Rhodoplanes. In vitro assays confirmed that 4-Hydroxybenzaldehyde, Coumarin, and Vanillin inhibited Pd growth. Structural equation modelling further indicated that environmental heterogeneity was associated with variation in Pd loads through microbial functional attributes and metabolite profiles. These findings suggest that naturally low-Pd cave soils are associated with coordinated environmental filtering, microbial functional specialization, and antifungal metabolite production, providing mechanistic insight into microbial and biochemical constraints on Pd persistence in cave reservoirs.}, }
@article {pmid42420833, year = {2026}, author = {Luo, D and Lu, F and Yang, L and Gan, Z and Zhang, X and Zhao, Z and Dong, R}, title = {Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42420833}, issn = {1471-2164}, support = {GZSTYYCYJSTX-202605//Guizhou Modern Agricultural Industry Technology System of China/ ; 2024 (No. 079//the Guizhou Provincial Key Technology R&amp;D Program/ ; 32460918//the National Natural Science Foundation of China/ ; }, mesh = {*Probiotics/pharmacology ; Multiomics ; *Phenols/toxicity ; Animals ; *Gastrointestinal Microbiome/drug effects ; Bacillus subtilis ; Lipid Metabolism/drug effects ; Metabolomics ; }, abstract = {BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed.<br><br>RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT&#x2012;qPCR and ELISA.<br><br>CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.}, }
@article {pmid42526667, year = {2026}, author = {Cui, P and Zhang, H and Hu, T and Huang, Q and Hu, X and Wang, Q and Diwan, AD and Wang, T and Zhao, X and Lu, S and Chen, X}, title = {The Metabolite indole-3-acetic acid of Bacteroides ovatus ameliorates ovariectomy-induced bone loss by activating AhR and inhibiting oxidative stress.}, journal = {Free radical biology &amp; medicine}, volume = {255}, number = {}, pages = {476-494}, doi = {10.1016/j.freeradbiomed.2026.07.050}, pmid = {42526667}, issn = {1873-4596}, mesh = {Animals ; Ovariectomy/adverse effects ; Female ; *Oxidative Stress/drug effects ; Mice ; *Bacteroides/metabolism ; Humans ; *Indoleacetic Acids/metabolism/pharmacology ; *Osteoporosis, Postmenopausal/metabolism/pathology/etiology/microbiology/prevention &amp; control ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Gastrointestinal Microbiome ; *Bone Resorption/pathology/metabolism/prevention &amp; control ; Osteoclasts/metabolism/drug effects ; *Basic Helix-Loop-Helix Proteins/metabolism/genetics ; Dysbiosis ; }, abstract = {Postmenopausal osteoporosis represents a systemic skeletal condition distinguished by diminished bone mass and heightened skeletal fragility. Emerging evidence has highlighted a significant relationship between bone metabolism and disturbances in gut microbiota (GM) homeostasis. However, the exact mechanisms by which GM dysbiosis contributes to postmenopausal osteoporosis remain insufficiently understood. Herein, integrating weighted gene co-expression network analysis with machine learning, a notable depletion of Bacteroides ovatus (B. ovatus) was identified in the GM of women with postmenopausal osteoporosis. Metagenomic sequencing further validated the reduced abundance of B. ovatus in ovariectomized (OVX) mice. Notably, live B. ovatus (LBO), but not heat-killed B. ovatus (KBO), effectively mitigated bone loss in OVX mice and restored intestinal mucosal barrier integrity. Both untargeted and targeted metabolomic profiling revealed substantial alterations in tryptophan metabolism in OVX mice, particularly a significant reduction in indole-3-acetic acid (IAA). Oral supplementation with IAA notably alleviated bone loss in OVX mice. Mechanistically, IAA stimulated AhR, enhancing NQO1 expression, reducing intracellular ROS buildup, and ultimately suppressing osteoclast differentiation and bone resorption. This investigation demonstrates, for the first time, the protective effects of B. ovatus and its metabolite IAA in counteracting estrogen deficiency-induced bone loss and may present a promising microbial-targeted strategy for osteoporosis prevention.}, }
@article {pmid42571814, year = {2026}, author = {Ge, S and Sun, M and He, J and Pan, Y and Xu, Y and Wang, L and Luo, R and Zhong, Y and Wang, Y and Huang, J and Hu, M and Huang, Z and Wu, G and Wan, Y and Mo, L and Wu, F and Nie, C and Zhou, H and He, Y and Ma, Z and He, X and Gao, J}, title = {Gut microbial DL-endopeptidase protects against alcohol-associated liver disease via hepatocyte NOD2 signaling.}, journal = {Free radical biology &amp; medicine}, volume = {255}, number = {}, pages = {712-729}, doi = {10.1016/j.freeradbiomed.2026.08.020}, pmid = {42571814}, issn = {1873-4596}, mesh = {Animals ; *Nod2 Signaling Adaptor Protein/metabolism/genetics ; Mice ; *Hepatocytes/metabolism/pathology/drug effects ; Signal Transduction ; *Liver Diseases, Alcoholic/pathology/microbiology/genetics/metabolism/prevention &amp; control ; *Gastrointestinal Microbiome ; Humans ; Mice, Knockout ; Ethanol/toxicity ; Male ; Liver/pathology/metabolism/drug effects ; Mice, Inbred C57BL ; Oxidative Stress ; Acetylmuramyl-Alanyl-Isoglutamine/analogs &amp; derivatives/pharmacology ; }, abstract = {Chronic alcohol consumption disrupts gut-liver homeostasis not only by inducing direct hepatotoxic injury, but also by perturbing host-microbial defense mechanisms that normally protect the liver from metabolic and inflammatory stress. We show that hepatocyte-specific deletion of Nod2 exacerbates ethanol-induced steatosis, oxidative stress, and mitochondrial dysfunction, establishing NOD2 as a critical protective factor in alcohol-associated liver disease (ALD). Importantly, beyond its direct hepatotoxic effects, ethanol exposure simultaneously diminishes this protective NOD2 pathway by limiting microbiota-derived ligand availability. Guided by this functional deficit, clinical metagenomic analysis (n = 1516) revealed that alcohol consumption is associated with a selective depletion of gut microbial DL-endopeptidase, a rate-limiting enzyme for NOD2 ligand generation, which inversely correlated with liver injury severity. Mice receiving fecal microbiota from donors with low DL-endopeptidase activity showed increased susceptibility to ALD. Importantly, supplementation with a NOD2 ligand or its clinical analogue, mifamurtide, restored mitochondrial homeostasis and alleviated liver injury. Together, these findings identify the gut microbial DL-endopeptidase-NOD2 axis as a key protective mechanism against ethanol-induced liver injury and a promising therapeutic target in alcohol-associated liver disease.}, }
@article {pmid42586263, year = {2026}, author = {Zhou, Y and Guo, Q and Zhao, X and Zhang, W and Zhang, H and Huang, S and He, Z and Xie, Y and Zhang, W and Gu, J and Pan, S and Li, W}, title = {Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.}, journal = {Virologica Sinica}, volume = {41}, number = {4}, pages = {791-805}, doi = {10.1016/j.virs.2026.08.010}, pmid = {42586263}, issn = {1995-820X}, mesh = {Humans ; *Virome ; *Stomach Neoplasms/virology/blood ; *Anelloviridae/isolation &amp; purification/genetics/classification ; Feces/virology ; Metagenomics ; Female ; Bacteriophages/genetics/isolation &amp; purification/classification ; Male ; Middle Aged ; Aged ; Tumor Microenvironment ; }, abstract = {Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.}, }
@article {pmid42698579, year = {2026}, author = {Murugesan, M and Thankappan, S and Mageshwaran, V and Ramasamy, R and Singaram, A}, title = {Decoding the functional diversity of plant growth-promoting bacterial communities in the soils of Western Ghats, Tamil Nadu, India.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1865342}, doi = {10.3389/fmicb.2026.1865342}, pmid = {42698579}, issn = {1664-302X}, abstract = {Western ghats in India, one of the world's biodiversity hot spots is the reservoirs of microbial resources having agricultural and industrial significance. However, the diversity of plant growth-promoting microbial communities associated with the plants and soil in the Western Ghats is untapped vault. The current emphasis on natural farming is more depending on the indigenous microbial communities and their metabolic functions towards sustainable one -health. With this background, the present study examines the bacterial diversity of soils from the Western Ghats of Nilgiris, Coimbatore and Dindigul regions. Among the 10 soil samples collected (S1 to S10), three soil samples (S2, S4 and S6) representing respective three regions were subjected for metagenomic studies based on their distinct soil chemical and biological properties. The computational analysis of the metagenome revealed the core genus Bradhyrhizobium in all soil samples, while Trebonia, Arthrobacter, Streptomyces, and Pseudomonas are the next most abundant genera, which varied substantially. The results collectively demonstrate that soil sample from Dindigul harbours the richest and most diverse microbial community among the three regions. In culturable studies, a total of 101 bacterial isolates were obtained from 10 soil samples (S1 to S10). Among them four Gram-negative bacterial isolates showed potential plant growth-promoting attributes, such as Ammonia, Indole Acetic Acid, Hydrogen cyanide and siderophore production, phosphorus, potassium, and zinc solubilization. The 16S rDNA analysis revealed that the bacterial isolates were Pseudomonas glycinae S6B1, Pseudomonas tolaasii S2B3, Pseudomonas azotoformans S9H10, and Pseudomonas poae S10B2. The isolate, S10B2, exhibited the maximum inhibition, with 81.25%, 70.1%, and 35% against plant pathogenic fungi, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, respectively, indicating strong biocontrol potential. The effect of bacterial inoculants on chick pea (Cicer arietinum var. JG 62), showed that P. glycinae S6B1 significantly promoted plant growth such as root length, shoot length, and fresh/dry biomass. These findings unlock the core microbiome of soils of Western Ghats, which can be utilized to develop a synthetic microbial consortium to boost agricultural productivity.}, }
@article {pmid41932647, year = {2026}, author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L}, title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {53}, number = {9}, pages = {1688-1702}, doi = {10.1016/j.jgg.2026.03.023}, pmid = {41932647}, issn = {1673-8527}, mesh = {Female ; Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Aging/drug effects/physiology ; *Ovary/drug effects/physiology ; Mice ; Gastrointestinal Microbiome/drug effects ; Fecal Microbiota Transplantation ; Humans ; }, abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.}, }
@article {pmid42097354, year = {2026}, author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S}, title = {Integrative machine learning models to unravel gut microbial dysbiosis and functional disruption in polycystic ovary syndrome.}, journal = {F&amp;S science}, volume = {7}, number = {5}, pages = {394-407}, doi = {10.1016/j.xfss.2026.04.005}, pmid = {42097354}, issn = {2666-335X}, mesh = {*Polycystic Ovary Syndrome/microbiology/metabolism ; Female ; Humans ; *Dysbiosis/microbiology ; *Machine Learning ; *Gastrointestinal Microbiome ; Case-Control Studies ; Metagenomics ; }, abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared with healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.<br><br>DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PCOS MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.<br><br>RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of proinflammatory taxa, such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals, including Roseburia hominis and Prevotella copri. These compositional shifts indicate a proinflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome-based machine learning models achieved a diagnostic accuracy of 84.25% (area under the curve 0.93), underscoring their predictive potential.<br><br>CONCLUSION: The gut microbiome in PCOS is characterized by a proinflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.}, }
@article {pmid42379395, year = {2026}, author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, PP and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM}, title = {Oat-Rich Low-Gluten Diet Modulates Plasma Short-Chain Fatty Acids without Significant Changes in Fecal Microbiome or Inflammatory Markers-A Randomized Clinical Trial in People with Cardiometabolic Risk.}, journal = {The Journal of nutrition}, volume = {156}, number = {9}, pages = {101690}, doi = {10.1016/j.tjnut.2026.101690}, pmid = {42379395}, issn = {1541-6100}, mesh = {Humans ; *Avena ; *Feces/microbiology ; Male ; *Fatty Acids, Volatile/blood ; Female ; Biomarkers/blood ; Middle Aged ; Cardiometabolic Risk Factors ; *Diet ; *Inflammation/blood ; Oryza ; *Cardiovascular Diseases ; Adult ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.<br><br>OBJECTIVES: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers (IM) during a 6-wk oat- or rice-rich LGD in individuals with increased cardiometabolic risk.<br><br>METHODS: The participants (n = 69) were allocated into 2 parallel groups following a 6-wk LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (NovaSeq X Plus) and characterized using metagenomic phylogenetic analysis, version 4 (MetaPhlAn4). Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by ultra-HPLC-mass spectrometry, and IM were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with a linear mixed-effects model.<br><br>RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. In particular, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (PtimeXgroup = 0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (PTimeXgroup = 0.025) and more changes in the microbiome. This is possibly due to more substantial dietary changes from low rice consumption compared with the habitual diet at baseline. No significant differences between or changes within the groups in IM were observed.<br><br>CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and IM in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome toward a potentially unfavorable direction. This trial was registered at clinicaltrials.gov as NCT05526092.}, }
@article {pmid42392574, year = {2026}, author = {Vita, AA and Brown, J and Norby-Adams, L and Ghanem, N and Weir, TL and Goldenberg, JZ}, title = {Microbial-Derived Polyphenol Metabolites and the Gut Microbiota: A Scoping Review of Clinical Studies.}, journal = {The Journal of nutrition}, volume = {156}, number = {9}, pages = {101700}, doi = {10.1016/j.tjnut.2026.101700}, pmid = {42392574}, issn = {1541-6100}, mesh = {Humans ; *Polyphenols/metabolism ; *Gastrointestinal Microbiome/physiology ; Bacteria/metabolism ; }, abstract = {BACKGROUND: Dietary (poly)phenols are widely recognized for their health-promoting properties, yet their bioactivity is largely contingent upon gut microbial metabolism. Individual differences in microbiome composition lead to variable production of microbial-derived (poly)phenol metabolites (MPMs) and thus contribute to divergent health outcomes.<br><br>OBJECTIVES: This scoping review aimed to systematically map the scope of clinical evidence reporting relationships between MPMs and gut microbiota composition and function, highlighting research gaps to guide future investigations.<br><br>METHODS: Using predefined search criteria, 2 reviewers identified human clinical studies reporting relationships between metabolite concentrations and microbiome outcomes.<br><br>RESULTS: Fifty-six studies were included. Evidence was frequently focused on phenolic acids (n = 20), phytoestrogens (n = 18), and urolithins (n = 17), with relationships between microbiota and other MPMs being reported in only 1 to 2 studies. The majority of studies across MPM categories used 16S rRNA gene sequencing for the identification of gut microbiota (n = 42), among other methods, with only 6 studies using metagenomic shotgun sequencing, thus limiting taxonomic resolution and functional inference. Findings revealed recurrent associations between specific microbes and MPMs. Although some reflected known producer taxa (e.g., Gordonibacter and urolithins), others may represent broader community-level interactions (e.g., Alistipes and equol). However, these results varied across (poly)phenol class, intervention type, and host-specific context.<br><br>CONCLUSIONS: This scoping review identified recurrent microbiota-MPM associations alongside major evidence gaps, including limited functional microbiome characterization and sparse investigation of several MPM classes/subclasses (e.g., resveratrol-, flavanone-, and flavan-3-ol-related MPMs). Future research using standardized, high-resolution multi-omics approaches is needed to improve the identification of reproducible microbial signatures and mechanisms underlying (poly)phenol metabolism and to link these features with functional health outcomes.}, }
@article {pmid42693766, year = {2026}, author = {Baños, E and Segura, CR and De Boer, EJ and Cundy, AB and Barrera, XT and Nogué, S and Holman, LE and Rius, M}, title = {Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.}, journal = {Molecular ecology resources}, volume = {26}, number = {7}, pages = {e70200}, doi = {10.1111/1755-0998.70200}, pmid = {42693766}, issn = {1755-0998}, support = {TED2021-132228B-C21//TEMPOINVASIONS/ ; TED2021-132228B-C22//TEMPOINVASIONS/ ; PID2023-146307OB//TEMPOINVASIONS/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Biota ; }, abstract = {Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.}, }
@article {pmid42694408, year = {2026}, author = {Young, D and Stüer-Patowsky, K and Huang, L and Elshahed, MS and Youssef, NH and Hanafy, R and Cheng, Y and Moon, CD and Soni, P and Joshi, A and Stabel, M and Ochsenreither, K and Dagar, SS and Hillman, E and Solomon, KV and Fliegerová, KO and Griffith, GW and Callaghan, TM and Podmirseg, SM and Sczyrba, A and Flad, V and Lebuhn, M and Wurzbacher, C}, title = {Full ribosomal operon sequencing of anaerobic gut fungi (phylum Neocallimastigomycota): insights on its markers and phylogenetic resolution.}, journal = {IMA fungus}, volume = {17}, number = {}, pages = {e195921}, pmid = {42694408}, issn = {2210-6340}, abstract = {The phylogenetic affiliations of anaerobic gut fungi (Neocallimastigomycota) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.}, }
@article {pmid42694564, year = {2026}, author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Sun, Y}, title = {Synergistic Regulation of Alzheimer's Disease and Intestinal Microbiota Metabolism Mediated by the Gut-Brain Axis: A Comprehensive Analysis from a Multidisciplinary Perspective.}, journal = {International journal of medical sciences}, volume = {23}, number = {9}, pages = {2939-2962}, pmid = {42694564}, issn = {1449-1907}, mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/immunology/therapy ; *Gastrointestinal Microbiome/immunology/physiology ; *Brain/metabolism/immunology ; Animals ; Multiomics ; *Brain-Gut Axis/immunology/physiology ; *Dysbiosis/microbiology/immunology ; }, abstract = {Alzheimer's disease (AD), as a neurodegenerative disease with the interaction of multiple factors, has a close association between its pathological process and the metabolic imbalance of the gut microbiota mediated by the gut-brain axis. This review systematically summarizes the molecular mechanisms by which the gut microbiota regulates the functions of the central nervous system bidirectionally through molecular pathways such as metabolites (e.g., short-chain fatty acids, tryptophan-kynurenine metabolites), immunomodulatory mediators (e.g., cytokines, chemokines), and bioactive substances (e.g., γ-aminobutyric acid, 5-hydroxytryptophan) via the gut-brain axis. It synthesizes current evidence suggesting the imbalance of microbiota homeostasis may be closely associated with the core pathologies of AD (including β-amyloid deposition and tau protein hyperphosphorylation) through mechanisms such as the activation of the C/EBPβ-AEP signaling pathway, induction of chronic neuroinflammation, oxidative stress cascade reactions, and metabolic network remodeling. These findings, primarily derived from preclinical models and correlational human studies, indicate potential mechanisms but require further causal validation and rigorous clinical translation, including the downregulation of butyrate synthesis pathways and their associated epigenetic and immunomodulatory consequences (as mechanistically dissected in Section 5.2). Multi-omics integration (metagenomics, metabolomics, spatial transcriptomics) has delineated characteristic microbial and metabolic alterations in AD, while computational approaches are beginning to elucidate the complex networks underlying these associations (see Sections 6 and 7 for details).Intervention strategies based on microbiota regulation (such as microbiota-targeted dietary interventions and postbiotics) are emerging as promising approaches, although their clinical applications remain in early stages. Preliminary evidence suggests that fecal microbiota transplantation may improve cognitive outcomes in AD patients with comorbid conditions; however, rigorous randomized controlled trials are essential to validate its efficacy and safety. Critically, translating these mechanistic insights into clinical practice requires overcoming three translational bottlenecks: inferring causality from correlational multi-omics data, resolving species/strain-level functional heterogeneity masked by genus-level taxonomy, and establishing standardized safety protocols for live biotherapeutic products. Addressing these challenges defines the near-term roadmap for precision medicine in AD. However, current research still faces challenges such as the heterogeneity of cross-omics data, the lack of technical standardization, and insufficient interdisciplinary cooperation mechanisms. In the future, it is necessary to promote the early molecular diagnosis and personalized targeted treatment of AD through longitudinal multi-omics dynamic monitoring, modeling of the microbiota-host interaction network, and optimization of the ethical-translational medicine framework.}, }
@article {pmid42694612, year = {2026}, author = {Davis, EE and Younger, J and Burridge, C and Armbrecht, L}, title = {How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag113}, pmid = {42694612}, issn = {2635-0041}, abstract = {MOTIVATION: Sedimentary ancient DNA (sedaDNA) is genetic material extracted from paleoarchives. It provides insights into the composition and dynamics of ecosystems over time. Such information can be crucial in anticipating how ecological communities may respond to environmental shifts within the context of the current climate crisis. However, challenges exist in accurately verifying ancient DNA from ecologically significant vertebrate species (e.g. fishes, aquatic birds, and mammals). These species occur only in trace amounts in sedimentary records. Here, we benchmark a stringent bioinformatic pipeline using synthetic and empirical metagenomic sedaDNA data from IODP Expedition 382 (Scotia Sea). Our objectives are threefold: (i) test taxonomic assignment precision for rare marine eukaryotes, (ii) evaluate taxonomic assignment sensitivity across different sediment ages, and (iii) establish the minimum sequence quantity necessary for robust identification.<br><br>RESULTS: We demonstrate that taxonomic assignment precision varied significantly with sequence quantity and metagenomic context. Assignment sensitivity decreased with taxonomic rank and database representation. Reliable detection of low-abundance taxa in sedaDNA is achievable with 250 and 500 DNA fragments at the family and genus level, respectively. The reanalysis of IODP Exp. 382 sedaDNA data, using a custom built marine vertebrate-focused reference database, resulted in the first genetic reconstruction of the vertebrate community in the Scotia Sea. This lays the groundwork for future investigations into the presence and biodiversity of Southern Ocean vertebrates using sedaDNA.<br><br>All project related scripts and generated simulated datasets are available in ae_fishing_benchmark repository (https://github.com/33davis/ae_fishing_benchmark). The demultiplexed raw data in relation to the IODP Exp. 382 U1538 reanalysed during this study is available in the NCBI Sequence Read Archive database (https://www.ncbi.nlm.nih.gov/sra) under Accession code/BioProject PRJNA861836 (BioSamples SAMN29928044 - SAMN29928123) and includes metadata for each sediment and control sample.}, }
@article {pmid42695179, year = {2026}, author = {Nett, N and Dumack, K}, title = {A Pan-European Whole-Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {5}, pages = {e70112}, doi = {10.1111/jeu.70112}, pmid = {42695179}, issn = {1550-7408}, support = {556896378//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; }, mesh = {*Wastewater/microbiology/parasitology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Europe ; *Microbiota ; *Eukaryota/classification/genetics/isolation &amp; purification ; Seasons ; Animals ; }, abstract = {Microbial communities entering wastewater treatment plants (WWTPs) through untreated sewage represent an important interface between human, environmental, and treatment-associated microbiomes, yet our understanding of their biogeography remains poorly resolved, particularly for microbial eukaryotes. Using shotgun metagenomic time-series data from influent samples of seven WWTPs across a European latitudinal gradient, we analyzed the taxonomic composition and dynamics of bacteria, protists, fungi, and microscopic metazoa. Influent community composition varied with geographic location and season, with a pronounced north-south divergence driven by dominant taxa and stronger seasonal shifts observed at higher latitudes. Cross-domain associations were pervasive, suggesting that co-varying bacterial and eukaryotic components structure the incoming microbial pool. Our findings provide a pan-European baseline for whole-microbiome wastewater surveillance and highlight that influent communities differ regionally and seasonally. These patterns may be relevant for downstream treatment-stage microbiomes, but direct effects on reactor community assembly and treatment performance require targeted sampling across treatment stages.}, }
@article {pmid42697668, year = {2026}, author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T}, title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.}, journal = {Pesticide biochemistry and physiology}, volume = {223}, number = {}, pages = {107299}, doi = {10.1016/j.pestbp.2026.107299}, pmid = {42697668}, issn = {1095-9939}, mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; }, abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.}, }
@article {pmid42687165, year = {2026}, author = {Wang, Y and Wang, L and Cai, Z and Yu, L and Guo, Y and Zhang, L and Zhu, M and Liu, Z and Zhao, Y and Liu, L and Cao, A}, title = {Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {}, pmid = {42687165}, issn = {1471-244X}, mesh = {Humans ; *Diet, Ketogenic ; *Fecal Microbiota Transplantation ; Female ; Male ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/therapy/microbiology/diet therapy ; Child ; Child, Preschool ; Treatment Outcome ; }, abstract = {OBJECTIVE: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, along with restricted, repetitive patterns of behavior. It is often accompanied by gastrointestinal dysfunction and gut microbiota dysbiosis. Fecal Microbiota Transplantation (FMT) and the Ketogenic Diet (KD) are interventions targeting the gut microbiota for ASD.<br><br>METHODS: 30 participants were diagnosed with ASD according to DSM-5 and ADOS-2. ASD core symptoms were evaluated with CARS and ABC. Gut microbiota composition was analyzed by shotgun metagenomic sequencing.<br><br>RESULTS: Both groups demonstrated significant improvements in core symptoms. In the FMT group, the mean CARS score significantly decreased from 34.87 to 33.53 (p&#x2009;<&#x2009;0.01); in the KD group, it declined from 35.13 to 33 (p&#x2009;<&#x2009;0.01). The mean ABC score reduced from 79.93 to 69.33 (p&#x2009;=&#x2009;0.064) in the FMT group and from 63.07 to 42.73 (p&#x2009;<&#x2009;0.01) in the KD group. Following the intervention, no statistically significant changes were observed in &#x3b1;-diversity or &#x3b2;-diversity within either group. LEfSe analysis revealed distinct post-intervention microbial signatures: FMT significantly enriched butyrate-producing taxa (Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus), while KD elevated Blautia massiliensis and decreased propionate metabolism -associated taxa (Veillonella sp. S12025-13 and Veillonella nakazawae). KEGG enrichment analysis revealed that KD enriched propionate metabolism (Fold enrichment&#x2009;=&#x2009;3.747, q&#x2009;=&#x2009;0.010) and aromatic compound degradation (Fold enrichment&#x2009;=&#x2009;3.591, q&#x2009;=&#x2009;0.010).<br><br>CONCLUSIONS: Both interventions significantly improved clinical symptoms among children with ASD, potentially through distinct patterns of gut microbiota modulation.<br><br>CLINICAL TRIALS NUMBER: NCT06348433 (03/21/2024).}, }
@article {pmid42687643, year = {2026}, author = {Jeon, D and Unno, T}, title = {Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {8}, pages = {e2605007}, doi = {10.71150/jm.2605007}, pmid = {42687643}, issn = {1976-3794}, support = {RS-2025-02633155//Rural Development Administration/ ; }, mesh = {Animals ; *Metagenomics/methods ; Cattle ; *Plasmids/genetics ; Swine ; Humans ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Drug Resistance, Multiple, Bacterial/genetics ; Metagenome ; }, abstract = {While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.}, }
@article {pmid42687714, year = {2026}, author = {Velsko, IM and Hübner, A and Fagernäs, Z and Yates, JAF and Mann, AE and Hofman, CA and Ozga, AT and Lewis, CM and Speller, C and Fiddyment, S and Francken, M and Wahl, J and Krause, J and Radini, A and King, T and Warinner, C}, title = {The Oral Microbiome of King Richard III of England.}, journal = {American journal of biological anthropology}, volume = {191}, number = {1}, pages = {e70350}, doi = {10.1002/ajpa.70350}, pmid = {42687714}, issn = {2692-7691}, support = {//Werner Siemens Stiftung/ ; //Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy/ ; //Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM)/ ; //Max Planck Society/ ; }, mesh = {Humans ; *Microbiota/genetics ; England ; *Dental Calculus/microbiology/history ; DNA, Ancient/analysis ; History, 15th Century ; *Mouth/microbiology ; History, Medieval ; History, Ancient ; Phylogeny ; Metagenome/genetics ; }, abstract = {OBJECTIVES: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452-1485).<br><br>MATERIALS AND METHODS: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome-assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity.<br><br>RESULTS: The dental calculus of King Richard III was well-preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated.<br><br>DISCUSSION: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000&#x2009;years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well-preserved.}, }
@article {pmid42688151, year = {2026}, author = {Cai, S and Xu, X and Sun, X and Luo, Q and Chen, W and Wang, X and Zhu, J and Liu, Y and Xiao, L and Zhang, H and Zou, Y and Zhong, Y}, title = {Alleviation of allergic rhinitis symptoms in an animal model by Lactiplantibacillus plantarum BGI-N6.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1923543}, pmid = {42688151}, issn = {1664-3224}, mesh = {Animals ; *Probiotics/therapeutic use ; Disease Models, Animal ; *Rhinitis, Allergic/immunology/therapy/microbiology ; Rats ; *Lactiplantibacillus plantarum/immunology ; Cytokines/blood ; *Gastrointestinal Microbiome/immunology ; Nasal Mucosa/immunology/pathology ; Male ; }, abstract = {Allergic rhinitis (AR) is a chronic inflammatory disease with rising global prevalence and a substantial public health burden. Current treatments have limited efficacy and tolerability, highlighting the need for new strategies. Probiotics represent a promising approach due to their ability to modulate gut microbiota and host immunity. Here, we investigated the preventive potential of Lactiplantibacillus plantarum BGI-N6 in an OVA/ALUM-induced AR rat model. BGI-N6 administration alleviated AR symptoms and nasal mucosal pathology, reduced key allergic mediators, shifted serum immunoglobulin and cytokine levels toward normal, and restored the Th1/Th2/Th17/Treg balance. Metagenomic sequencing of cecal contents showed that these effects were accompanied by expansion of Bacteroidota-affiliated SCFA-producing taxa, restoration of microbial functional capacity, and identification of 41 core functional genes (KEGG Orthologues) consistently shifted across all three dose groups, with Bacteroides showing the strongest enrichment. Correlation analyses further connected these microbial shifts with immune parameters. These findings support BGI-N6 as a probiotic intervention for AR and implicate gut microbiota remodeling as a central correlate of probiotic-induced immunomodulation.}, }
@article {pmid42688840, year = {2026}, author = {Li, J and Liu, Y and Gao, T and Ding, H and Hu, R and Wang, Y and Wu, B}, title = {Progress in interventions for vaginal microecology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1888581}, pmid = {42688840}, issn = {2235-2988}, mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota ; *Probiotics/administration &amp; dosage/therapeutic use ; *Dysbiosis/therapy/microbiology ; Prebiotics/administration &amp; dosage ; Synbiotics/administration &amp; dosage ; }, abstract = {A balanced vaginal microbiome is fundamental to reproductive and gynecologic health, yet dysbiosis is common and clinically consequential. This narrative review synthesizes recent advances in microecological interventions, including probiotic, prebiotic, and synbiotic regimens; combination therapies; and vaginal microbiota transplantation. We place a particular focus on emerging delivery platforms like hydrogel-based carriers, which improve probiotic viability, mucosal adhesion, and controlled release. The review also explores how metagenomic analysis is refining community state typing, identifying pathogenic consortia, and enabling data-driven patient stratification and response monitoring. Despite these advances, key challenges remain, such as strain selection, functional validation, colonization durability, heterogeneous clinical endpoints, and clear regulatory pathways for live biotherapeutics. Future priorities must include developing functionally defined strain consortia, standardizing clinical outcomes, integrating multi-omics with biomaterials engineering, and conducting rigorous multicenter trials to deliver durable, safe, and truly individualized therapies.}, }
@article {pmid42690486, year = {2026}, author = {Wen, Y and Luo, Z and Li, Z and Li, K and Li, J and Yin, S and Zou, Y and Zhang, H and Zhang, Y and Chen, K and Zhang, Y and Liu, S and Chen, Z and Yu, L and Ding, Y}, title = {Oral and gut microbiota profiles in patients with locally advanced rectal cancer with varying responses to neoadjuvant chemoradiotherapy.}, journal = {Functional &amp; integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42690486}, issn = {1438-7948}, support = {2023A0060//Science and Technology Plan Project of Jiangxi Provincial Administration of Traditional Chinese Medicine/ ; 2024A1515013292//Guangdong Basic and Applied Basic Research Fundation/ ; 2025A1515010567//Guangdong Basic and Applied Basic Research Fundation/ ; 2026A1515012094//Guangdong Basic and Applied Basic Research Fundation/ ; 32300085//National Natural Science Foundation of China/ ; 82504340//National Natural Science Foundation of China/ ; 82473567//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy/pathology ; *Neoadjuvant Therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Chemoradiotherapy ; Aged ; Feces/microbiology ; Saliva/microbiology ; }, abstract = {Recent research has focused on gut bacteria in colorectal cancer, but the influence of other microbiota, including oral and nonbacterial gut microbiota, on treatment efficacy remains insufficiently explored. This study aimed to investigate their relationship with the efficacy of neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC). Saliva and fecal samples were collected from patients with LARC before treatment. Shotgun metagenomic sequencing was used to profile bacterial, archaeal, eukaryotic, and viral taxonomic groups and to examine oral and gut microbial functions. An artificial intelligence-based prediction model was developed by integrating oral and gut microbiome data with clinical information. Statistical analyses compared diversity and response-associated microbial features between responders and non-responders to nCRT. Response-associated differences were observed in bacterial and nonbacterial taxonomic profiles and in oral and gut microbial functional profiles. In the internal test subset, the integrated analysis yielded an observed AUC of 0.917. Given the small cohort and the exploratory comparison of candidate classifiers, this estimate requires confirmation in larger, independent cohorts. Baseline oral and gut microbiome profiles were associated with response to nCRT. Integrating microbiome and clinical features showed potential for response prediction, but the model remains exploratory and requires validation in larger, independent cohorts before clinical application. Retrospectively registered on 01/08/2026, NCT07346729.}, }
@article {pmid42692606, year = {2026}, author = {Ma, C and Geng, R and Hou, Q and Zhao, Y and Yue, Y and Xue, T and Wen, L and Li, T and Yang, J and Hu, J}, title = {Structure and protection of Cichorium glandulosum polysaccharides against sarcopenic obesity through activating mitophagy via butyrate-GPR43-AMPK pathway.}, journal = {Carbohydrate polymers}, volume = {390}, number = {}, pages = {125722}, doi = {10.1016/j.carbpol.2026.125722}, pmid = {42692606}, issn = {1879-1344}, mesh = {Animals ; *Mitophagy/drug effects ; *Butyrates/metabolism ; AMP-Activated Protein Kinases/metabolism ; *Obesity/drug therapy/metabolism ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/drug effects ; *Asteraceae/chemistry ; *Polysaccharides/chemistry/pharmacology ; Male ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; }, abstract = {Sarcopenic obesity (SO) is a major complication of type 2 diabetes with limited therapeutic options. This study characterized CGP-A, a novel branched fructan (6.722 kDa) from Cichorium glandulosum. Its backbone consists of →1)-β-D-Fruf-(2→ and →6)-α-D-Glcp-(1→ residues, interspersed with →1,6)-β-D-Fruf-(2→ branching points. The side chains consist of terminal β-D-Fruf-(2→ units attached to the C-6 position of the fructofuranosyl residues in the backbone. In db/db mice, CGP-A dose-dependently ameliorated insulin resistance, hepatic steatosis, muscle loss and intestinal barrier dysfunction. Importantly, CGP-A significantly improved grip strength, reflecting an enhancement in muscle quality. Integrated multi-omics analysis combining metagenomics, multi-organ proteomics, and metabolomics revealed that CGP-A altered the gut microbiota, specifically enriching Ligilactobacillus, Bacteroides and Alistipes, while elevating serum butyrate. These findings suggest that butyrate may activate the GPR43-AMPK signaling pathway in both liver and skeletal muscle. Hepatic AMPK activation upregulated PPARα to enhance fatty acid oxidation; concurrently, muscular AMPK stimulated PINK1/Parkin-mediated mitophagy, restoring mitochondrial function and attenuating protein degradation. Antibiotic depletion abolished these effects, establishing the microbiota as a crucial mediator. These findings elucidate the gut microbiota-butyrate-GPR43-AMPK pathway through which CGP-A contributes to multi-organ metabolic improvements, offering a promising prebiotic strategy for managing SO.}, }
@article {pmid42692700, year = {2026}, author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z}, title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.}, journal = {Food research international (Ottawa, Ont.)}, volume = {243}, number = {Pt 1}, pages = {120303}, doi = {10.1016/j.foodres.2026.120303}, pmid = {42692700}, issn = {1873-7145}, mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; }, abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.}, }
@article {pmid42692847, year = {2026}, author = {Budinská, E}, title = {Microbiome in early cancer detection - biomarker potential and limitations.}, journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti}, volume = {39}, number = {Supplementum 1}, pages = {63-66}, doi = {10.48095/ccko2026S63}, pmid = {42692847}, issn = {1802-5307}, mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; }, abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.<br><br>AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.}, }
@article {pmid42693026, year = {2026}, author = {Han, R and Gu, YW and Dong, J and Zhang, XZ and Cao, L and Wang, ZZ and Xiao, W and Jiang, S}, title = {[Mechanism of Tianshu Capsules in treating migraine rats based on gut microbiota].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {51}, number = {16}, pages = {4734-4743}, doi = {10.19540/j.cnki.cjcmm.20260509.701}, pmid = {42693026}, issn = {1001-5302}, mesh = {Animals ; *Migraine Disorders/drug therapy/metabolism/genetics/microbiology ; Rats, Sprague-Dawley ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration &amp; dosage ; Calcitonin Gene-Related Peptide/genetics/metabolism ; Male ; Humans ; Disease Models, Animal ; Endothelin-1/metabolism/genetics/blood ; Capsules/administration &amp; dosage ; Serotonin/blood/metabolism ; Proto-Oncogene Proteins c-fos/metabolism/genetics ; }, abstract = {This study aims to investigate the therapeutic effect of Tianshu Capsules(TS) on migraine rat model and explore its potential mechanism of action from the perspectives of the structure of the gut microbiota and functional pathway regulation. A migraine rat model was established via subcutaneous injection of nitroglycerin. The Sprague-Dawley rats were randomly divided into a control group, a model group, a low-dose TS group, a medium-dose TS group, a high-dose TS group, and an ibuprofen group. The efficacy of TS in improving migraine was evaluated by general condition observation and measurement of the craniofacial pain threshold. The expression of the gene c-fos in the trigeminal ganglion was determined by quantitative real-time polymerase chain reaction(PCR). The contents of endothelin-1(ET-1), calcitonin gene-related peptide(CGRP), and 5-hydroxytryptamine(5-HT) in serum were measured by enzyme-linked immunosorbent assay(ELISA). Fecal samples were subjected to metagenomic sequencing for systematic analysis of gut microbial diversity, taxonomic composition difference, and functional pathway changes of Kyoto Encyclopedia of Genes and Genomes(KEGG), and their correlations with behavioral and biochemical indices were further evaluated. The results show that TS significantly improves the increased body temperature and decreased craniofacial pain threshold in migraine rats. It also markedly suppresses the elevated expression levels of the gene c-fos in the trigeminal ganglion and reduces the levels of ET-1, CGRP, and 5-HT in serum. Metagenomic beta diversity analysis and differential taxonomic abundance analysis reveal that the migraine model induces significant gut microbiota dysbiosis, characterized by enrichment of harmful genera, including Streptococcus and Enterococcus, as well as a decline in the abundance of beneficial bacteria such as Allobaculum, Eubacterium, and Muribaculum. Functional pathway analysis results of KEGG further reveal that the relative abundances of pathways associated with biosynthesis of phenylalanine, tyrosine, and tryptophan, bacterial secretion system, citrate cycle, and biosynthesis of secondary metabolites are significantly decreased in the model group. TS intervention increased the abundance of the genus, such as Parabacteroides, Eubacterium, Allobaculum, and Muribaculum, while decreasing levels of microbiota, including Staphylococcus. TS also significantly upregulated pathways associated with barrier function(tight junction), amino acid biosynthesis pathways, and biosynthesis pathways of neurotransmitter precursors such as cysteine and methionine metabolism. In addition, it downregulated inflammatory pathways(Toll and IMD signaling) and pathways related to Staphylococcus aureus infection, thereby restoring the structure and function of the microbiota to a state close to those of the normal group. Spearman correlation analysis reveals that partial gut microbiota are significantly associated with migraine-related behavioral and biochemical indices(c-fos, ET-1, CGRP, and 5-HT). In conclusion, TS can regulate the disrupted gut microbiota structure and microbial functions related to neurotransmitter metabolism, intestinal barrier function, and inflammatory regulation in migraine model rats, which may be one of the potential key ways through which TS exert its anti-migraine effect.}, }
@article {pmid42483952, year = {2026}, author = {Oyama, LB}, title = {From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.}, journal = {Essays in biochemistry}, volume = {70}, number = {3}, pages = {387-398}, doi = {10.1042/EBC20250036}, pmid = {42483952}, issn = {1744-1358}, support = {BB/X012794/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; BB/Z515346/1//UK Research and Innovation (UKRI)/ ; }, mesh = {*Microbiota ; *Antimicrobial Peptides/chemistry/pharmacology/metabolism/genetics/therapeutic use ; Humans ; Animals ; }, abstract = {Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.}, }
@article {pmid42484341, year = {2026}, author = {Sato, Y and Uda, Y and Nagao, Y}, title = {Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0167726}, pmid = {42484341}, issn = {2165-0497}, support = {25K18347//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Rumen/microbiology/virology ; Cattle ; *Virome ; Female ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Microbiota ; Age Factors ; Ruminococcus/genetics ; }, abstract = {Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.}, }
@article {pmid42488935, year = {2026}, author = {Whelan, FJ}, title = {How the social lives of bacteria affect their pangenome.}, journal = {Essays in biochemistry}, volume = {70}, number = {3}, pages = {473-482}, doi = {10.1042/EBC20250039}, pmid = {42488935}, issn = {1744-1358}, support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; }, mesh = {*Bacteria/genetics ; *Genome, Bacterial ; *Microbiota/genetics ; Genetic Variation ; Phylogeny ; Metagenomics ; Computational Biology ; }, abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.}, }
@article {pmid42489451, year = {2026}, author = {Roques, S and Tournayre, J and Dou, PS and Yanibada, B and Boudra, H and Popova, M and Morgavi, DP}, title = {Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0026926}, pmid = {42489451}, issn = {2165-0497}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Female ; Propanols/pharmacology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/drug effects ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; *Microbiota/drug effects ; Metagenomics ; Metabolome ; }, abstract = {Enteric methane emission from dairy cattle is an environmental challenge. The most efficient mitigation strategies nowadays include the use of methanogenesis inhibitors that specifically target the rumen methanogens. Specific inhibitors, such as 3-nitrooxypropanol (3-NOP), reduce methane emissions without negative effects on the products of fermentation that serve as energy metabolites for the host. However, the concomitant effects of methanogenesis inhibition on rumen microbiota and host metabolism are poorly characterized. Thus, the objective of this study was to explore the association between rumen microbiota and host metabolism when methanogenesis is inhibited. Thirteen dairy cows were used as controls, and 12 were supplemented with 3-NOP for 6 weeks. Rumen microbiota composition and activity were characterized using metagenomics and metatranscriptomics. The host metabolism was assessed in a previous publication by a metabolomic analysis of the plasma. Microbiota data were used as explanatory variables of the metabolome data in a multiblock sparse partial least squares analysis. Overall, the association between rumen microbiota and host metabolism was moderate. Notwithstanding this, a few downregulated transcripts related to glycolysis, hydrogen transfer, and protein synthesis, together with a decrease in the proportion of taxa of the Oscillospirales order, showed a correlation with host one-carbon metabolites (|r| > 0.6). These associations raised novel hypotheses that remain to be elucidated, especially with regard to the effects of dihydrogen on the accumulation of microbial glycolysis and methanogenesis metabolite intermediates.IMPORTANCEDairy cattle produce a substantial amount of methane, a potent greenhouse gas. Several strategies have been designed to reduce methane production by targeting the rumen microbiota. One such strategy specifically inhibits methanogens with a molecule called 3-nitrooxypropanol. This study uses an integrative data analysis approach, combining rumen microbiota and host metabolome information, to explore the consequences of inhibiting methanogenesis on the holobiont. This provides additional holistic insight into the effect of methane mitigation strategies on dairy cattle.}, }
@article {pmid42496113, year = {2026}, author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC}, title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0076326}, pmid = {42496113}, issn = {2165-0497}, support = {//Cornell University Start-up Funds/ ; CUP E53C25000400001//Ministry of University and Research/ ; 101045015//European Union/ ; NextGenerationEU//European Union/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Starch/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Feces/microbiology ; Metagenomics ; Dietary Supplements/analysis ; *Resistant Starch/metabolism ; }, abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.}, }
@article {pmid42515960, year = {2026}, author = {Kopp, AR and Uhlemann, AC}, title = {Gut dysbiosis and multidrug-resistant colonization in solid organ transplantation.}, journal = {Current opinion in organ transplantation}, volume = {31}, number = {5}, pages = {247-254}, doi = {10.1097/MOT.0000000000001303}, pmid = {42515960}, issn = {1531-7013}, mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Organ Transplantation/adverse effects/mortality ; Risk Factors ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Multiple, Bacterial ; Treatment Outcome ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Host-Pathogen Interactions ; *Bacteria/drug effects/pathogenicity ; Animals ; *Bacterial Infections/microbiology/drug therapy/immunology ; }, abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize recent advances in the understanding of the interplay between gut dysbiosis and MDRO colonization and infection in SOT patients.<br><br>RECENT FINDINGS: Recent studies have added complementary metagenomics, internal transcribed spacer sequencing, metabolomics, and pathway analysis to descriptive microbiome profiling. Enhanced ecologic frameworks have identified microbial, functional, and clinical signatures associated with MDRO colonization and infection. Microbiome-targeting interventions are emerging as strategies to reduce morbidity associated with MDRO infection.<br><br>SUMMARY: MDRO infection is a significant cause of post-transplant mortality. Persistent gut dysbiosis peri-transplant reduces colonization resistance and predisposes patients to adverse clinical outcomes. Understanding the dynamics of this process will aid in the care of these high-risk patients.}, }
@article {pmid42517626, year = {2026}, author = {Price, DC and Bezhani, FL and Meng, Z and Porfirio-LaStrapes, M and Wagner, NE and Javanmard, M and Han, T and Barnes, MM}, title = {Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0093826}, pmid = {42517626}, issn = {2165-0497}, support = {1R21AI159459 - 01/NH/NIH HHS/United States ; AMCARF 2018-01//American Mosquito Control Association/ ; Multistate NE1943//United States Department of Agriculture/ ; }, mesh = {Animals ; *Virome/genetics ; *Feces/virology ; *Culex/virology ; *RNA Viruses/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; *Mosquito Vectors/virology ; North America ; Humans ; RNA, Viral/genetics ; Female ; *Culicidae/virology ; }, abstract = {Nearly 30% of emerging infectious disease events worldwide are transmitted by arthropod vectors, and this proportion continues to rise. Rapid and accurate detection is critical for directing vector control interventions, thereby reducing the likelihood of widespread transmission. Surveillance of infected mosquitoes can provide an early warning of impending human infection; however, conventional virus testing relies on processing large pools of mosquitoes and requires labor-intensive pre-processing. During rapidly developing epidemic or panzootic events, these delays may limit the effectiveness of public health responses. Mosquito excreta has recently emerged as a promising alternative substrate for pathogen detection. Sugar-fed mosquitoes regularly excrete gut contents, offering a rich source of nucleic acids. In this study, we developed and applied custom superhydrophobic excreta-collection funnels that efficiently aggregate excreta produced by field-collected Culex mosquitoes into attached microcentrifuge tubes. Shotgun metagenomic sequencing of this material revealed a diverse RNA virome, including both globally distributed viruses and those reported here for the first time from the Americas. Beyond virus detection, additional analyses enabled confirmation of host mosquito species and identification of trypanosomatid parasites, demonstrating the broader utility of mosquito excreta for integrated surveillance. We anticipate that methods and devices of this type will become valuable components of vector surveillance programs, particularly in remote or resource-limited settings where repeated collections are challenging. Overall, our findings highlight the potential of excreta-based monitoring to improve early detection of emerging or unknown pathogens of One Health importance, refine our understanding of mosquito virome biogeography, and facilitate the discovery of previously undescribed viruses.IMPORTANCEMany infectious diseases that affect people and animals are spread by mosquitoes and other biting insects, and the number of these outbreaks is increasing. Detecting pathogens in mosquito populations early can provide a critical warning before human cases begin, allowing health officials to act quickly. However, traditional surveillance requires collecting and processing large numbers of mosquitoes, which can be slow and labor-intensive during fast-moving outbreaks. Here we demonstrate a simpler approach: testing mosquito waste. When mosquitoes feed on sugar, they excrete material that contains genetic traces of viruses and other organisms. Using specially designed collection devices and modern genetic sequencing, we show that mosquito excreta can reveal a wide range of viruses and parasites while also identifying the mosquito species present. This method could make disease surveillance faster and more practical in remote or resource-limited settings, improving our ability to detect emerging pathogens that threaten human, animal, and environmental health.}, }
@article {pmid42545016, year = {2026}, author = {Seo, Y and Kim, J and Yeom, M and Park, S-Y and Lee, S and Ahn, S and Hahm, D-H and Kim, K and Kwon, S-K and Park, H-J}, title = {Gut microbiota contributes to the therapeutic effect of acupuncture in atopic dermatitis.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0391225}, pmid = {42545016}, issn = {2165-0497}, support = {RS-2023-00211512//National Research Foundation of Korea/ ; RS-2024-00409969//National Research Foundation of Korea/ ; }, mesh = {*Dermatitis, Atopic/therapy/microbiology ; Humans ; Animals ; *Acupuncture Therapy/methods ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Mice ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Disease Models, Animal ; Treatment Outcome ; Adult ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; }, abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a central regulator of immune homeostasis, metabolic balance, and therapeutic outcomes. Atopic dermatitis (AD), a chronic inflammatory skin disease, is closely linked to gut microbial dysbiosis. Traditionally regarded as a neurostimulatory therapy, acupuncture (Acu) has demonstrated increasing efficacy in alleviating AD symptoms and improving gastrointestinal function. These observations suggest that the therapeutic effects of Acu in AD may be mediated, in part, by modulation of the gut microbiome. In this study, AD patients were stratified into responder (R) and non-responder (NR) groups based on clinical improvement. Gut microbiome profiling revealed that R patients exhibited greater microbial diversity and compositional stability, indicative of a more balanced gut ecosystem. Specific taxa, including Alistipes ihumii and Odoribacter splanchnicus, were enriched in R individuals and may serve as microbial predictors of treatment responsiveness. Importantly, fecal microbiota transplantation (FMT) from R donors restored Acu efficacy in a mouse model of AD, whereas FMT from NR donors did not. These findings support the gut-skin axis and highlight the integral role of the gut microbiome in mediating the therapeutic effects of Acu for AD, suggesting potential for microbiome-based personalized treatment.<br><br>IMPORTANCE: Increasing evidence supports the gut microbiome's role in modulating treatment responses in atopic dermatitis (AD), but direct evidence linking acupuncture efficacy with microbiome composition has been lacking. Previous studies did not assess causal relationships via fecal microbiota transplantation (FMT) or functional metagenomics. This study identifies specific gut microbes associated with acupuncture response in AD and confirms their causal role using FMT. It also links functional metabolic pathways to therapeutic efficacy, offering a mechanism-based insight. Our findings support microbiome-informed personalized acupuncture approaches for AD and suggest gut microbiota as a therapeutic modulator in neuroimmune regulation.<br><br>CLINICAL TRIALS: This study was registered in the Korean Clinical Trial Registry (CRIS, registration number: KCT0005422).}, }
@article {pmid42578670, year = {2026}, author = {Li, Z and Sun, J and Yang, J and Han, P and Min, L and Cheng, Y and Zou, Y and Liu, Z}, title = {Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0315324}, pmid = {42578670}, issn = {2165-0497}, mesh = {Humans ; *Bacteroides/genetics/isolation &amp; purification/classification/physiology ; Metagenomics ; Feces/microbiology ; *Depression/microbiology ; Metagenome ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Nitric Oxide/metabolism/biosynthesis ; }, abstract = {Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.}, }
@article {pmid42578673, year = {2026}, author = {Mirăuță, B and Riza, A-L and Streata, I and Pirvu, A and Dorobantu, S and Dragos, A and Surleac, M and Netea, MG}, title = {Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0052826}, pmid = {42578673}, issn = {2165-0497}, support = {PN-IV-P6-6.1-CoEx-2024-0196 (17CoEx/2026)//Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI)/ ; PNRR/2022/C9/MCID/I8, Contract No. 760057/23.05.2023//Ministry of Research, Innovation and Digitalization, Romania - National Recovery and Resilience Plan (PNRR), Pillar III, Component 9, Investment I8/ ; P_37_745, MySMIS 103454, Contract No. 31/01.09.2016//Ministry of European Funds, Romania - Competitiveness Operational Programme/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Romania ; Metagenomics ; Feces/microbiology ; }, abstract = {The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favorable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. This first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort, a population underrepresented in microbiome studies and characterized by high antibiotic consumption, addresses a gap in current microbiome research. We report an enrichment of Enterobacteriaceae although overall composition is more comparable to other European than non-European cohorts. Community configurations align with established enterotype patterns, and our analysis provides insight into their relationship with within-phylum diversity. The analysis of antimicrobial resistance provides insight into the prevalence of resistance genes within this reservoir. We specifically report the presence of cfr(E), a Clostridioides difficile gene, and tet(X5), a variant from the ubiquitous tet family, genes not previously reported in healthy European populations. Integration with data from the European Centre for Disease Prevention and Control links the overall prevalence of resistance genes in this reservoir to antibiotic classes with higher community consumption in this population, notably beta-lactams and quinolones, highlighting potential targets for antibiotic stewardship programs. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify potential immune-priming roles for Collinsella, Flavonifractor, and Bifidobacterium species.IMPORTANCEThis first comprehensive study of the healthy gut microbiome in a Romanian cohort addresses a gap in current microbiome research, dominated by data sets from a limited number of regions. It sets a baseline for the microbiome and resistome composition of this population, and, while definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such study helps contextualize future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes and the concordance with commonly used antibiotics in the community reinforce the need to address antibiotic use in public health strategies. Although gut microbiome-immunity relationships remain incompletely understood, our findings support a role for microbiome composition in immune-related traits and provide a valuable resource for future studies.}, }
@article {pmid42584065, year = {2026}, author = {Roush, C and Whiteley, M}, title = {Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.}, journal = {Microbiology spectrum}, volume = {14}, number = {9}, pages = {e0182026}, pmid = {42584065}, issn = {2165-0497}, support = {R01 DE023193/DE/NIDCR NIH HHS/United States ; R01DE020100/DE/NIDCR NIH HHS/United States ; R01DE023193/DE/NIDCR NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics/classification/isolation &amp; purification ; *Wastewater/virology/microbiology ; Humans ; Genome, Viral ; *Mouth/virology/microbiology ; Metagenomics ; Microbiota ; *Bacteria/virology/classification/genetics ; Metagenome ; Phylogeny ; Tannerella forsythia/virology ; Porphyromonas gingivalis/virology ; }, abstract = {Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.}, }
@article {pmid42680742, year = {2026}, author = {Low, A and Yang, Z and Anantaya, KT and Zhao, S and Tan, WC and Perez, RL and Chung The, H and Lim, SZY and Liu, L and Gounot, JS and Kwah, JS and Ong, RT and Nagarajan, N and Lee, JWJ and Mo, Y}, title = {Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42680742}, issn = {2041-1723}, mesh = {Humans ; *Escherichia coli/genetics/isolation &amp; purification/classification ; *Escherichia coli Infections/microbiology/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metagenomics ; *Carrier State/microbiology ; Asia, Southeastern/epidemiology ; Intestines/microbiology ; }, abstract = {Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.}, }
@article {pmid42683728, year = {2026}, author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G}, title = {Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2725403}, doi = {10.1080/19490976.2026.2725403}, pmid = {42683728}, issn = {1949-0984}, mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Metagenome ; Mice ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Feces/microbiology ; Irritable Bowel Syndrome/therapy/microbiology ; Computer Simulation ; }, abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remain limited, in part because the role of donor‒recipient metabolic interactions in shaping the post-FMT community remains poorly understood. Here, we leverage metagenome-scale metabolic modeling to quantify metabolic niche complementarity between donor and recipient microbiomes and predict post-FMT community composition. Using MICOM-derived metabolic models, we show that donor genomes whose metabolic flux profiles are more dissimilar from the recipient community colonize at significantly higher rates in a murine FMT model. In a human IBS trial, the same metric predicted post-FMT community composition via leave-one-out cross-validation and captured known disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to evaluate personalized donor screening, identifying super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition. Together, these results support metabolic niche complementarity as a potential determinant of post-FMT community composition and provide a mechanistic basis for evaluating donor-recipient metabolic compatibility. This framework offers a scalable approach for generating testable hypotheses for personalized donor selection.}, }
@article {pmid42685266, year = {2026}, author = {Colajanni, A and Uricaru, R and Darko, S and Subramanian, R and Douek, DC and Thiébaut, R and Thebault, P}, title = {Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {5}, pages = {}, doi = {10.1093/bib/bbag454}, pmid = {42685266}, issn = {1477-4054}, mesh = {Humans ; *Microbiota/genetics ; Benchmarking ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; }, abstract = {Human RNA sequencing (RNA-seq) data originally generated for human transcriptome profiling are overwhelmingly dominated by host sequences, yet they often contain a small fraction of non-human reads that can be exploited for microbial detection. When such datasets are repurposed for secondary microbiome-oriented analyses, extracting and accurately classifying this weak microbial signal becomes technically challenging, and no ready-to-use pipeline currently exists. In this study, we evaluate computational strategies for filtering host reads and classifying microbial transcripts in host-dominated RNA sequencing data. We compare assembly-based approaches similar to those used in a previous study focusing on microbial translocation with state-of-the-art assembly-free methods, and assess their respective strengths and limitations using simulated datasets reflecting low microbial abundance. Our results show that assembly-based methods yield accurate taxonomic predictions but struggle at low read depth, whereas assembly-free methods are more robust in sparse settings at the cost of reduced precision. To leverage the complementarity of both approaches, we propose a hybrid pipeline that integrates assembly-based and assembly-free classification. On simulated data, this hybrid strategy improves microbial classification performance compared with either approach alone. Application to a real human metatranscriptomic dataset analyzed in a microbial translocation context illustrates the broader microbial signal captured by the hybrid approach, despite intrinsic challenges related to the absence of reliable ground truth and the risk of host read misclassification. Our work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.}, }
@article {pmid42252320, year = {2026}, author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W}, title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42252320}, issn = {2045-2322}, support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; }, mesh = {Humans ; *Gout/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Dysbiosis/microbiology ; Bacteria/genetics/classification ; Biodiversity ; }, abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.}, }
@article {pmid42296622, year = {2026}, author = {Pravara, R and Praveen, R and Seema, B}, title = {Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {60}, number = {}, pages = {101902}, doi = {10.1016/j.cbd.2026.101902}, pmid = {42296622}, issn = {1878-0407}, mesh = {Animals ; Symbiosis ; *Microbiota ; *Gossypium/parasitology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Hemiptera/microbiology/growth &amp; development ; }, abstract = {BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus.<br><br>RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism.<br><br>CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.}, }
@article {pmid42497006, year = {2026}, author = {Arjunan, S and Pemberton, I and Li, XS and Sangwan, N and Akino, L and Opoku, E and Verbovetskiy, D and Nemet, I and Kim, HS and Masumiya, H and Wang, Z and Lupica, JA and Tian, MY and Mao, K and Mallela, DP and Mohan, ML and Schumacher, SM and Rennison, JH and Prasad, SVN and Laurita, KR and Chodisetty, V and Chung, MK and Van Wagoner, DR and Barnard, J and Smith, JD and Wazni, O and Hazen, SL and Koeth, RA}, title = {Gut microbial trimethylamine N-oxide generation promotes risk of atrial fibrillation via muscarinic receptor-mediated autonomic dysfunction.}, journal = {The Journal of clinical investigation}, volume = {136}, number = {17}, pages = {}, pmid = {42497006}, issn = {1558-8238}, mesh = {Animals ; *Methylamines/metabolism ; *Atrial Fibrillation/metabolism/microbiology/physiopathology/genetics/pathology ; Humans ; Mice ; *Gastrointestinal Microbiome ; *Receptors, Muscarinic/metabolism/genetics ; Male ; Female ; Mice, Inbred C57BL ; Choline/pharmacology/analogs &amp; derivatives ; Mice, Transgenic ; Middle Aged ; Aged ; Cyclic AMP Response Element Modulator/genetics/metabolism ; }, abstract = {Gut microbiota-derived trimethylamine N-oxide (TMAO) plays a role in the pathogenesis of cardiovascular disease, but its role in the pathogenesis of atrial fibrillation (AF) remains uncertain. TMAO levels were quantified in plasma from serial subjects undergoing elective cardiac catheterizations and shown to independently associate with prevalent AF following adjustment for risk factors. Human cAMP response element modulator isoform IbΔC-X transgenic mice (CREM-IbΔC-X) supplemented with a TMAO diet developed AF sooner. C57BL/6J mice on and off a TMAO diet had more inducible AF via a transesophageal pacing study compared with chow-fed controls. Dietary choline supplementation increased circulating TMAO levels and significantly accelerated AF onset in CREM-IbΔC-X mice. Iodomethylcholine (IMC) reduced circulating TMAO levels and choline-induced AF onset. Cecal metagenomic analyses showed that choline supplementation induced changes in microbial communities associated with AF, while many of these changes were attenuated by IMC. Choline supplementation promoted overall adverse atrial remodeling with left atrial dilation. Optical mapping studies showed that mice supplemented with choline exhibited reduced conduction velocity, shortened action potential duration at 80% repolarization, and decreased wavelength. TMAO inhibited muscarinic receptor 2, resulting in autonomic dysfunction that promotes AF. In summary, TMAO, independently associated with AF risk in subjects, enhanced AF in multiple mouse models via autonomic dysfunction and is a therapeutic target for preventing AF.}, }
@article {pmid42675564, year = {2026}, author = {Akyol, CK and Bilaç, &#xd6; and Çam, FS}, title = {Does the Gut Microbiota Play a Role in Attention-Deficit/Hyperactivity Disorder in Childhood? A Pilot Study From Turkey.}, journal = {Developmental neurobiology}, volume = {86}, number = {4}, pages = {e70057}, doi = {10.1002/dneu.70057}, pmid = {42675564}, issn = {1932-846X}, support = {2022-146//Manisa Celal Bayar University Scientific Research Projects Coordination Unit/ ; }, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology ; Male ; Pilot Projects ; *Gastrointestinal Microbiome/physiology ; Turkey ; Female ; Child ; Feeding Behavior/physiology ; Sleep/physiology ; }, abstract = {The pathophysiology of attention-deficit/hyperactivity disorder (ADHD) is not fully understood, but increasing evidence suggests that gut microbiota may play a role. This study compared the gut microbiota of children with ADHD with that of a control group of healthy children, and examined their dietary and sleep habits. Ten medication-naïve children aged 612 years who had recently been diagnosed with ADHD and ten healthy controls were included. ADHD diagnoses were confirmed using the Schedule for Affective Disorders and Schizophrenia for School-Age ChildrenPresent and Lifetime Version (K-SADS-PL). Sleep and eating habits were assessed using the 2nd Level Sleep Disorder Short Form, the Children's Eating Behaviour Inventory, and a form to collect sociodemographic and clinical information. The gut microbiota were analysed using 16S NGS metagenome analysis. A significant decrease in the Shannon and Simpson diversity index values was observed in the ADHD group compared to the control group. Despite the presence of a percentage difference, no statistically significant differences were observed between the groups with respect to species, genus, family, order, class or phylum. Following evaluation of the sleep and eating habit scale scores, no statistically significant difference between the groups was determined.These findings suggests that children with ADHD may alter gut microbiota diversity.However, the absence of significant taxonomic differences and the small sample size mean that these results should be interpreted with caution. Further, larger, adequately powered studies are needed to validate these findings and clarify the potential role of gut microbiota in the pathophysiology of ADHD.}, }
@article {pmid42675742, year = {2026}, author = {Shaikh, SS and Malek, F}, title = {Healthy subjects gut microbiome modulation by Bacillus coagulans BCP92: A randomized, double-blind, placebo-controlled clinical trial.}, journal = {Medicine}, volume = {105}, number = {35}, pages = {e50435}, doi = {10.1097/MD.0000000000050435}, pmid = {42675742}, issn = {1536-5964}, mesh = {Humans ; *Probiotics/administration &amp; dosage ; *Bacillus coagulans/physiology ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Male ; Adult ; Fatty Acids, Volatile/analysis/metabolism ; Female ; Healthy Volunteers ; Young Adult ; Metagenome ; }, abstract = {BACKGROUND: Probiotics are recognized for their ability to restore balance in the gut microbiome during dysbiosis. However, their effects on the gut microbiota of healthy individuals have rarely been investigated. This study aimed to evaluate the safety and efficacy of Bacillus coagulans (Heyndrickxia coagulans) BCP92 and its influence on microbiota composition in healthy subjects.<br><br>METHODS: In the present investigation, healthy participants (n&#x2005;=&#x2005;48) were allocated into 2 groups and administered either Bacillus coagulans BCP92 capsules (1 billion CFU/capsule) or a placebo containing maltodextrin for 42 days. Microbiome composition and short-chain fatty acid analyses were subsequently conducted.<br><br>RESULTS: Analysis of metagenomes showed no major alterations in gut microbiome composition among participants who received B. coagulans BCP92 supplementation. However, subtle beneficial changes were observed in the treatment group, suggesting that probiotic administration may increase advantageous phyla, classes, orders, families, and some genera, while decreasing potentially harmful groups. A slight increase in short-chain fatty acids (SCFA) was also observed in the fecal samples.<br><br>CONCLUSIONS: This study implies that extended supplementation with the probiotic B. coagulans BCP92 may lead to substantial improvements in gut microbiome composition and SCFA levels.}, }
@article {pmid42677031, year = {2026}, author = {Ceja-Navarro, JA and Patel, D and Genco, G and Byer, A and Ning, D and Wan, KH and Celniker, SE and Zhou, J and Dijkstra, P and Hungate, BA and Pett-Ridge, J and Brodie, EL}, title = {Ecosystem retrogression enhances cross-domain microbial stability and increases the genetic potential for nutrient cycling.}, journal = {mLife}, volume = {5}, number = {4}, pages = {486-506}, pmid = {42677031}, issn = {2770-100X}, abstract = {Ecosystem retrogression drives nutrient depletion, reduced productivity, and profound reorganization of soil microbial communities. Using amplicon sequencing and genome-resolved metagenomics, we examined how cross-domain microbial networks and functional gene potential respond to long-term phosphorus and nitrogen limitation along the well-characterized Ecological Staircase chronosequence in Mendocino, California, USA. Microbial diversity and abundance declined sharply with terrace age for prokaryotes, predatory protists, and bacteriophages, whereas fungi and phototrophic protists increased in nutrient-depleted, acidic soils. These compositional shifts were accompanied by major changes in reconstructed microbial networks: relative modularity increased alongside robustness, indicating adaptive reorganization that may sustain ecosystem function under resource scarcity. Fungi emerged as central stabilizers in these restructured networks, carrying enriched genetic potential to degrade plant polymers and mobilize phosphorus and nitrogen. Despite a decline in overall phage diversity, the relative abundance of phages encoding phosphorus-mobilizing auxiliary metabolic genes increased, suggesting that viral contributions to host phosphorus metabolism may be enhanced under nutrient limitation. Together, these results demonstrate that ecosystem retrogression drives cross-domain microbial reorganization toward fewer but more interconnected lineages, characterized by greater integration of functional genetic potential. This reorganization enhances the potential for functional resilience under extreme nutrient limitation, revealing how microbial networks adapt to maintain the capacity for nutrient cycling and stability as soils age and fertility declines.}, }
@article {pmid42677827, year = {2026}, author = {Chen, K and Yang, Z and Peng, J and Liu, C and Yu, Y and Cai, X and Liu, B and Li, S and Chen, T and Jung, S and Tian, Y and Xu, Q and Rao, X and Wu, Z and Wang, H and Di, Y and Wang, L and Wang, J and Lee, MS and Zou, Y and He, N and Li, S}, title = {Bacteroides cellulosilyticus-derived 2-hydroxyphenylacetic acid rectifies hepatic lipid homeostasis in MASLD by targeting the PPARγ-CD36 axis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2725392}, doi = {10.1080/19490976.2026.2725392}, pmid = {42677827}, issn = {1949-0984}, mesh = {*PPAR gamma/metabolism/genetics ; *CD36 Antigens/metabolism/genetics ; Humans ; *Phenylacetates/metabolism ; *Lipid Metabolism/drug effects ; Homeostasis ; *Fatty Liver/metabolism/microbiology ; *Bacteroides/metabolism ; *Liver/metabolism ; Hepatocytes/metabolism ; Signal Transduction/drug effects ; Gastrointestinal Microbiome ; }, abstract = {The gut microbiota plays an important role in the occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD), but the specific molecular mechanisms involved have not been fully elucidated. In this study, human cohort studies were performed to identify that the relative abundance of Bacteroides cellulosilyticus (B. cellulosilyticus) was significantly decreased in patients with MASLD. Through the integration of metagenomic and metabolomic analyses, it was confirmed that B. cellulosilyticus and its metabolite 2-hydroxyphenylacetic acid (2HPAA) are key factors regulating the occurrence and development of MASLD. Single-cell sequencing and lipidomic analyses revealed that 2HPAA can enter the liver through the enterohepatic circulation to exert regulatory effects. Specifically, 2HPAA inhibits the peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway, thereby suppressing the expression of the fatty acid transporter CD36. Meanwhile, 2HPAA regulates lipid metabolism in hepatocytes by significantly enhancing palmitate conversion efficiency and inhibiting CD36 palmitoylation. This dual regulatory effect on CD36 expression and palmitoylation can reduce lipid accumulation in hepatocytes and ultimately alleviate MASLD progression. These findings reveal the mechanism by which B. cellulosilyticus and 2HPAA alleviate MASLD by targeting the PPARγ-CD36 pathway. This work provides a new perspective for the study of gut microbiota-host interactions in regulating liver diseases.}, }
@article {pmid42680271, year = {2026}, author = {Zhu, D and Xie, J and Li, P and Mei, J}, title = {Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 3}, pages = {119937}, doi = {10.1016/j.foodres.2026.119937}, pmid = {42680271}, issn = {1873-7145}, mesh = {*Multiomics ; *Food Microbiology/methods ; *Artificial Intelligence ; *Food Preservation/methods ; *Microbiota ; Metabolomics ; Metagenomics ; }, abstract = {In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.}, }
@article {pmid42680349, year = {2026}, author = {Li, S and Zhang, H and Yang, Y and Xia, Y and Ni, B and Ai, L}, title = {Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 3}, pages = {120059}, doi = {10.1016/j.foodres.2026.120059}, pmid = {42680349}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; *Food Microbiology ; Bacteria/metabolism/genetics/classification ; Metabolomics ; *Fermented Foods/microbiology/analysis ; Metagenomics ; Ethanol/analysis ; }, abstract = {Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.}, }
@article {pmid42230654, year = {2026}, author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F}, title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42230654}, issn = {2055-5008}, mesh = {Animals ; *Rumen/microbiology ; *Methane/metabolism ; Cattle ; *Metabolome ; *Pichia/physiology/metabolism ; Female ; *Microbiota ; Lactation ; Animal Feed/analysis ; Bacteria/classification/genetics/metabolism ; Multiomics ; }, abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.}, }
@article {pmid42289444, year = {2026}, author = {Masuoka, H and Miyatake, T and Park, J and Negishi, H and Kurokawa, R and Tsuchihashi, H and Makino, S and Suda, W}, title = {Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42289444}, issn = {2045-2322}, support = {J24K18210//Japan Society for the Promotion of Science, Japan/ ; J24K01676//Japan Society for the Promotion of Science, Japan/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Adult ; Feces/microbiology ; *Fatigue/microbiology/metabolism ; Japan ; Male ; Female ; *Bacteria/genetics/classification ; Oxidative Stress ; Middle Aged ; East Asian People ; }, abstract = {Emerging evidence suggests that fatigue caused by accumulated stress may serve as a prodromal symptom of psychiatric disorders, and gut microbiome dysbiosis has been reported in many such conditions. However, little is known about microbial and metabolic signatures associated with fatigue in otherwise healthy individuals. This study aimed to investigate associations between fatigue, the gut microbiome, and fecal metabolites in healthy Japanese adults. We identified characteristic microbial and metabolic differences specific to fatigued healthy individuals. Taxonomic analysis revealed a reduction in potentially beneficial bacteria and an enrichment of Escherichia coli in their gut microbiome. Functional profiling demonstrated enrichment of KEGG orthologs related to oxidative stress and depletion of energy-producing pathways. Correspondingly, key energy metabolites such as citrate were decreased. Notably, some fatigue-associated bacterial alterations overlapped with findings from external datasets on psychiatric disorders and myalgic encephalomyelitis/chronic fatigue syndrome, suggesting associative overlap in gut microbial alterations. These findings suggest associations between host fatigue and gut microbiome alterations involving oxidative stress and impaired energy metabolism. The consistent overlap of fatigue-associated microbial changes with those observed in psychiatric disorders highlights the potential relevance of gut microbial signatures in fatigue-related biological states. This study provides a foundation for future studies on gut microbial and metabolic pathways.}, }
@article {pmid42316284, year = {2026}, author = {Wang, X and Cheng, L and Yin, K and Wang, B and Yan, X and Chen, S}, title = {Chronic proton pump inhibitor exposure aggravates intestinal injury by impairing intestinal stem cell self-renewal through the microbiota-7-ketolithocholic acid Axis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42316284}, issn = {1479-5876}, mesh = {Animals ; *Proton Pump Inhibitors/adverse effects ; *Stem Cells/pathology/drug effects ; *Intestines/pathology/injuries ; *Lithocholic Acid/analogs &amp; derivatives/metabolism ; *Cell Self Renewal/drug effects ; Intestinal Mucosa/pathology ; Mice, Inbred C57BL ; Wnt Signaling Pathway/drug effects ; Male ; Rabeprazole ; *Gastrointestinal Microbiome/drug effects ; Organoids/drug effects/pathology ; }, abstract = {BACKGROUND: Long-term proton pump inhibitor (PPI) use is associated with increased intestinal disease risk, but its damaging mechanisms remain unclear.<br><br>METHODS: Mice were administered rabeprazole (Rab) for 4&#x2009;weeks before dextran sulfate sodium (DSS) or ionizing radiation (IR) injury. We employed RNA sequencing, metabolomics, and metagenomics, evaluated intestinal stem cell (ISC) function, and used organoids for validation.<br><br>RESULTS: Long-term Rab induced small intestinal mucosal injury and exacerbated DSS/IR-induced damage, manifesting as crypt/villus atrophy and reduced ISC numbers. Mechanistically, Rab downregulated the Wnt pathway and impaired mucosal defense and regeneration. Microbiota involvement was indicated by fecal transplantation. Integrated metagenomic and metabolomic analyses revealed that Rab induced intestinal dysbiosis and reduced ileal bile acids, particularly 7-ketolithocholic acid (7KLCA) and chenodeoxycholic acid (CDCA). Faecalibaculum rodentium supplementation restored ISC self-renewal by converting CDCA to 7KLCA. In vitro, 7KLCA activated Wnt signaling to rescue Rab-induced stem cell impairment. In vivo, both 7KLCA and Gly-&#x3b2;-MCA (intestinal FXR antagonists) suppressed the FXR-FGF15 axis, restored the expression of hepatic bile acid synthesis enzymes, and promoted epithelial repair, thereby mitigating DSS-induced injury.<br><br>CONCLUSIONS: Chronic PPI use impairs ISC self-renewal by disrupting the microbiota-7KLCA-Wnt axis. F. rodentium or 7KLCA supplementation ameliorates PPI-induced effects, highlighting a microbe-metabolite axis as a pivotal mechanism and potential therapies for PPI-associated intestinal damage.}, }
@article {pmid42629980, year = {2026}, author = {Hexter, JC and Tang, W and Fortin, SG and Jayakumar, A and Ward, BB}, title = {Denitrification Modularity and Its Environmental Controls in Transiently Versus Permanently Anoxic Marine Systems.}, journal = {Environmental microbiology}, volume = {28}, number = {8}, pages = {e70407}, pmid = {42629980}, issn = {1462-2920}, support = {OCE-2342493//National Science Foundation/ ; Myhrvold-Havranek Graduate Fellowship//Department of Geosciences, Princeton University/ ; }, mesh = {*Denitrification/genetics ; *Metagenome ; Aquatic Organisms/genetics ; Anaerobiosis ; *Microbiota ; *Bays/chemistry/microbiology ; *Bacteria/genetics/metabolism ; Seawater/chemistry/microbiology ; }, abstract = {Denitrification is a modular process that is mediated by an assemblage of microbes with varying denitrification gene combinations. The controls on these gene combinations, known as modularity, are poorly understood and marine observations are mostly limited to permanently anoxic systems. In this global metagenomic analysis representing 69 water column metagenome samples we report different modularity patterns associated with environmental parameters based on the permanence of anoxia. Thermodynamic favourability alone is not enough to explain the distribution of modularity patterns. Instead, variables such as the permanence (or transience) of anoxia, oxygen availability, biogeography and ratios of organic matter to nitrogen supply all help shape the denitrifier community gene assemblage. Environmental correlates in transiently anoxic compared to permanently anoxic systems suggest that the pressures of a more complex environment may favour shorter pathways due to resource allocation trade-off regardless of organic matter availability. Nitrate reduction is the dominant step compared to the rest of the denitrification pathway irrespective of anoxia type. As increases in global temperature result in more seasonally anoxic and hypoxic waters, these results highlight the importance of understanding the controls on denitrification modularity under varying states of anoxia.}, }
@article {pmid42669658, year = {2026}, author = {Huey, SL and Cole, NL and Pagani, I and González, A and Finkelstein, JL and Haas, JD and Udipi, SA and Ghugre, P and Potdar, RD and Knight, R and Mehta, S}, title = {Effect of a complementary feeding intervention based on iron- and zinc-biofortified pearl millet on the gut microbiota in 12-18-month-old children: a randomized trial.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42669658}, issn = {2041-1723}, support = {2021-67017-34008//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 5T32HD087137//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; }, mesh = {Humans ; *Zinc/administration &amp; dosage ; *Pennisetum/chemistry ; Infant ; *Iron ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; *Food, Fortified ; *Infant Nutritional Physiological Phenomena ; Dietary Supplements ; Feces/microbiology ; }, abstract = {Iron supplementation studies in children under five suggest potentially adverse gut microbiota shifts. Given iron's importance during early childhood, food-based approaches may offer a more viable supplementation strategy. Using shotgun metagenomics, we examined the effects of 9 months' daily consumption of iron/zinc-biofortified pearl millet (FeZnPM; 8.70 mg/100 g iron) versus control pearl millet (CPM; 3 mg/100 g iron) on the gut microbiome in 12-18-month-old children without severe anemia (hemoglobin ≥9.0 g/dL) from Mumbai urban slums through a randomized controlled trial, the primary outcomes of which were iron status biomarkers and infant growth (ClinicalTrials.gov ID: NCT02233764). In paired (n = 81) and endpoint (n = 108) analyses, FeZnPM consumption was not associated with detectable adverse effects on developing microbiomes and exploratory analyses suggest that it may support beneficial metabolic adaptations via direct modulation of antibiotic, antioxidant, and pollutant degradation pathways. This suggests biofortified crops could provide a sustainable approach to addressing iron deficiency while maintaining healthy microbiome development in early life.}, }
@article {pmid42669679, year = {2026}, author = {Zheng, R and Wang, C and Sun, C}, title = {Multi-omics and cultivation reveal laminarin-degrading PVC bacteria in the deep sea.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42669679}, issn = {2041-1723}, mesh = {*Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Glucans/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Multiomics ; Microbiota/genetics ; Phylogeny ; Glycoside Hydrolases/metabolism/genetics ; }, abstract = {The deep sea is home to a vast and largely unexplored microbial biosphere, along with large amounts of complex organic matter (COM). However, the functional capacity of the deep-sea microbiome to metabolize organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years (2018 and 2022) and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside a widespread genetic potential for organic matter metabolism. Notably, the PVC (Planctomycetota-Verrucomicrobiota-Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, exemplified by the isolation of Planctomycetota strain WC338 and Lentisphaerota strain WC36 via laminarin enrichment. Growth experiments and transcriptomics confirm their strict laminarin dependence and characterize the underlying catabolic machinery-specifically, the deployment of different glycoside hydrolase (GH) families, which are broadly distributed and prevalent across the PVC superphylum. Furthermore, we demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings reveal that PVC bacteria-an overlooked group in laminarin degradation-possess specialized adaptations for polysaccharide breakdown and actively participate in laminarin turnover in deep-sea environments.}, }
@article {pmid42671637, year = {2026}, author = {Sample, JW and Johnson, S and Hoskin, TL and Redaelli, M and Walther-Antonio, MR and Chen, J and Degnim, AC and Hieken, TJ}, title = {Body mass index-associated gut microbial taxa and functional pathways in women with benign and malignant breast disease.}, journal = {Breast cancer research and treatment}, volume = {219}, number = {2}, pages = {}, pmid = {42671637}, issn = {1573-7217}, support = {UL1TR002377/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Female ; *Breast Neoplasms/pathology/microbiology/etiology ; *Body Mass Index ; Middle Aged ; *Gastrointestinal Microbiome ; *Obesity/complications/microbiology ; Aged ; Adult ; Metagenomics/methods ; Metagenome ; }, abstract = {PURPOSE: Obesity is an established risk factor for breast cancer and is associated with alterations in gut microbial composition. We evaluated associations among body mass index (BMI), breast density, gut microbial diversity and composition and microbial functional pathways in women undergoing surgery for benign, high-risk/non-invasive, and invasive breast disease.<br><br>METHODS: Preoperative stool samples were collected from 131 women (median age 59) with benign (n&#x2009;=&#x2009;23), high-risk/non-invasive (n&#x2009;=&#x2009;47), or malignant (n&#x2009;=&#x2009;61) disease. Shallow shotgun metagenomic sequencing was performed. Taxonomic profiling used Sourmash 4.2.4 (GTDBv207 reference database); functional profiling employed HUMAnN 3.6 with gene families mapped to MetaCyc pathways.<br><br>RESULTS: &#x3b1;-diversity differed across diagnosis groups and inversely correlated with increasing BMI (Inverse Simpson p&#x2009;=&#x2009;0.025). &#x3b2;-diversity differed by diagnosis group and BMI. No significant differences in diversity were observed based on age, menopausal status or mammographic breast density. BMI was also associated with enrichment of Dorea, Blautia, and Streptococcus species. Functional pathway profiling showed greater relative abundance of genes involved in NAD biosynthesis, folate metabolism, and aromatic amino acid metabolism pathways with higher BMI. Cross-referencing the most significant taxonomic and functional pathway findings suggested enrichment of Blautia species, via tryptophan metabolism, might link to NAD biosynthesis.<br><br>CONCLUSION: In this study of women with benign, high-risk/non-invasive, and invasive breast disease, BMI was associated with distinct differences in gut microbial taxonomy and functional pathway profiles. These hypothesis-generating findings provide a rationale for future study to determine how the obesity-associated microbiome contributes to breast cancer development.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42671657, year = {2026}, author = {Nazrin, MRR and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Subramanian, S}, title = {Species-specific structuring of gut bacterial and fungal communities in honey bees Apis cerana and Apis mellifera.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {9}, pages = {}, pmid = {42671657}, issn = {1572-9699}, mesh = {Animals ; Bees/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Species Specificity ; Metagenomics ; Phylogeny ; Biodiversity ; *Mycobiome ; }, abstract = {Honey bee gut microbiome studies have primarily emphasized bacteria, leaving fungal communities comparatively overlooked despite their ecological and functional importance. Whole-genome shotgun metagenomics of Apis cerana and Apis mellifera revealed fungal assemblages dominated by Ascomycota, with Basidiomycota and Microsporidia in minor proportions, alongside gut bacterial communities composed mainly of Pseudomonadota, Bacillota, and Actinomycetota. The bacterial diversity was markedly higher in A. mellifera (Shannon = 5.90; Simpson = 0.98) than in A. cerana (Shannon = 4.01; Simpson = 0.94; p > 0.05), while fungal diversity remained comparable between species (p > 0.05). Beta-diversity analyses revealed strong host-specific clustering for both bacterial (PERMANOVA R[2] = 0.7989, p > 0.05) and fungal communities (R[2] = 0.7218, p > 0.05), indicating distinct microbial organization driven by host species. Bacterial-fungal co-occurrence patterns exhibited host-specific structuring, suggesting differential inter-kingdom community organization between A. cerana and A. mellifera. Linear Discriminant Analysis Effect Size (LEfSe) identified 93 discriminatory fungal taxa (45 enriched in A. cerana, 48 in A. mellifera), highlighting yeast-dominated signatures in A. mellifera and Basidiomycota-affiliated enrichments in A. cerana. KEGG and CAZy profiling revealed host- and kingdom-specific functional differences, with bacterial communities of A. mellifera showing distinct representation of carbohydrate metabolism and nutrient-cycling functions, while fungal communities exhibited a comparatively narrower functional repertoire. Together, these findings provide a high-resolution view of honey bee bacterial and fungal microbiomes, highlighting strong host-driven divergence in taxonomy, function, and cross-kingdom interactions.}, }
@article {pmid42673455, year = {2026}, author = {Farrell, SP and D'Angelo, T and Yiu, DS and Kelminal Pakkir Shah, A and Stincone, P and Countway, PD and Petras, D and Brady, DC and Rasher, DB}, title = {Kelp forest collapse alters the reef microbiome and associated metabolome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {36}, pages = {e2525548123}, doi = {10.1073/pnas.2525548123}, pmid = {42673455}, issn = {1091-6490}, support = {OIA-1489227//NSF (NSF)/ ; NA//Louise H. &amp; David S. Ingalls Foundation/ ; 2124-390838134//Deutsche Forschungsgemeinschaft (DFG)/ ; NA//Essex Avenue Foundation/ ; NA//PADI Foundation (The PADI Foundation)/ ; }, mesh = {*Microbiota/physiology ; *Kelp/microbiology ; *Metabolome ; *Coral Reefs ; Ecosystem ; Climate Change ; }, abstract = {In many temperate regions experiencing rapid ocean warming, kelp forests are being replaced by low-lying turf algae. Yet, whether this change in biogenic habitat alters reef-level microbial structure and function, including carbon and nutrient cycling, remains largely unknown. Here, we integrated shotgun metagenomics and nontargeted metabolomics to reveal that kelp forest loss alters the composition of the reef microbial community and its associated biochemical machinery, resulting in distinct metabolomes and microbially driven elemental use/transformations on kelp- vs. turf-dominated reefs. Our results therefore suggest that microbes play a key role in shaping kelp forest ecosystem functioning. Further, they demonstrate that human-induced ocean warming has cascading effects on microbially mediated chemistry, with implications for coastal carbon storage and nutrient regeneration.}, }
@article {pmid42575975, year = {2026}, author = {Pust, MM and Mohamed, AMT and Stražar, M and Arias-Rojas, A and Cunningham-Oakes, E and Brown, EM and Bumber, A and Pishchany, G and Li, C and Ananthakrishnan, AN and Darby, AC and Vlamakis, H and Plichta, DR and Xavier, RJ}, title = {Antisense transcription reveals disease-associated adaptations in the human gut microbiome.}, journal = {Nature microbiology}, volume = {11}, number = {9}, pages = {2464-2477}, pmid = {42575975}, issn = {2058-5276}, support = {R01 DK127171//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; R01 AI172147//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 DK043351//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 AI172147/AI/NIAID NIH HHS/United States ; 530694780//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Humans ; Animals ; Inflammatory Bowel Diseases/microbiology ; Mice ; *Gastrointestinal Microbiome/genetics ; *RNA, Antisense/genetics ; Feces/microbiology/chemistry ; Disease Models, Animal ; Colitis/microbiology ; Metagenomics ; *Transcription, Genetic ; Gastroenteritis/microbiology ; Bacteria/genetics/classification ; RNA, Bacterial/genetics ; Leukocyte L1 Antigen Complex/analysis ; Adaptation, Physiological ; }, abstract = {The gut microbiome is a dynamic ecosystem in which microorganisms constantly adjust their transcriptional programmes. Here we developed metastrand, a framework that integrates strand-aware metatranscriptomics and metagenomics to quantify mRNAs and antisense RNAs (asRNAs) in complex microbial communities at gene-level resolution. In inflammatory bowel disease (IBD), microbial asRNA programmes converged across patients during active disease, correlated with faecal metabolites and calprotectin levels and remained stable during persistent inflammation, highlighting their potential as biomarkers of inflammatory activity in the gut. These programmes involved antisense-to-sense transcriptional shifts at insertion sequence elements with functionally diverse passenger genes and preceded their detection at new genomic locations, linking asRNA dynamics to structural genome rearrangements and redistribution of adaptive functions under selective pressure. Similar dynamics were observed in a mouse model of colitis, oxidative stress in vitro and in patients with pathogen-confirmed gastroenteritis, establishing asRNAs as an important dimension of microbial adaptation in health and disease.}, }
@article {pmid42665998, year = {2026}, author = {Lu, J and Sun, Y and Zeng, Y and Lau, EYT and Lan, Z and Ye, S and Zhang, R and Hu, R and Cui, C and Liang, JQ}, title = {Agathobacter rectalis suppresses colorectal tumorigenesis via an epigallocatechin-SREBF2 axis controlling cholesterol metabolism.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2724227}, doi = {10.1080/19490976.2026.2724227}, pmid = {42665998}, issn = {1949-0984}, mesh = {Animals ; *Cholesterol/metabolism ; *Sterol Regulatory Element Binding Protein 2/metabolism/genetics ; *Colorectal Neoplasms/metabolism/microbiology/prevention &amp; control/pathology ; Mice ; *Catechin/metabolism/analogs &amp; derivatives ; Humans ; *Eubacteriales/metabolism/physiology ; *Carcinogenesis/metabolism ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Feces/microbiology/chemistry ; }, abstract = {Beneficial effects of the gut commensal Agathobacter rectalis (Ar) are reported in diseases, yet its role in colorectal cancer (CRC) remains unclear. Here, metagenomic analysis revealed consistent fecal Ar depletion across CRC cohorts. In Apc [min/+] mice, Ar inhibited colon tumorigenesis, reducing tumor number and volume versus E. coli and PBS controls. LC-MS/MS metabolomics showed decreased fecal cholesterol and altered lipid/cholesterol pathways after Ar treatment. In vitro, Ar-conditioned medium suppressed CRC cell growth, clonogenicity, migration, and cell cycle progression. LC-MS/MS identified (-)-epigallocatechin (EGC) as an Ar-derived metabolite absent in control bacteria. EGC recapitulated Ar-mediated anti-CRC effects in vitro and in vivo, with metabolic changes linked to lipid/cholesterol pathways. Transcriptomics showed that EGC suppressed SREBP signaling, cholesterol metabolism, and MAPK pathways. Mechanistically, EGC reduced nuclear SREBF2 and its transcriptional activity, downregulated cholesterol synthesis/metabolism genes, including FDPS and PCSK9, and suppressed MAPK signaling. Molecular docking suggested that EGC may bind pSREBF2 or SCAP. Cellular thermal shift assay revealed that EGC interacts with and stabilizes pSREBF2, but not SCAP. Co-immunoprecipitation demonstrated that EGC reduces pSREBF2-SCAP interaction, thereby inhibiting SCAP-mediated SREBF2 cleavage activation. Together, these findings define an Ar-EGC microbe-metabolite axis and support Ar/EGC-based interventions targeting cholesterol metabolism in CRC.}, }
@article {pmid42666020, year = {2026}, author = {Fan, Y and Tao, Y and Hua, B and Kardol, P and Kuzyakov, Y and Pang, S and Wu, Y and Li, T and Yang, W and Wu, H and Goncharov, AA and Korotkevich, AY and Mao, R and Zhang, Y and Zhang, X}, title = {Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition.}, journal = {Global change biology}, volume = {32}, number = {9}, pages = {e71083}, doi = {10.1111/gcb.71083}, pmid = {42666020}, issn = {1365-2486}, support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; //Top-Notch Young Talents Program (to Ximei Zhang) of China/ ; //RUDN University Strategic Academic Leadership Program/ ; }, mesh = {*Soil Microbiology ; *Nitrogen/analysis/metabolism ; China ; *Microbiota ; *Biodiversity ; Forests ; Grassland ; Metagenomics ; Nitrogen Cycle ; Soil/chemistry ; Bacteria ; }, abstract = {Simulated manipulation experiments, such as nitrogen addition to mimic atmospheric nitrogen deposition, are widely used in global change research. However, experimental manipulations may differ from real-world environmental change in their intensity, duration, and co-occurrence, leaving long-term changes in soil microbial communities and soil health insufficiently understood. To address this gap, we resampled soils from 38 forest and grassland ecosystems across eastern China in 2009 and 2019 and assessed microbial taxonomic and functional diversity using shotgun metagenomics. Microbial diversity increased by 17% over the decade, accompanied by clear shifts in community composition. Among the environmental variables considered, nitrogen deposition (~19 kg nitrogen ha[-1] year[-1] across ecosystems) was the strongest predictor of changes in seven of 12 microbial community metrics. Larger nitrogen deposition was also associated with increased relative abundances of nitrogen-cycling genes and reduced spatial turnover in microbial community composition. These effects were consistent with a potential alleviation of nitrogen limitation and weakening of deterministic community assembly, although these mechanisms could not be directly established. In addition, increases in genes associated with carbon degradation and phosphorus cycling, together with declines in the relative abundances of pathogens, antibiotic resistance genes, and DNA viruses, coincided with the raise of the composite soil health index. Our findings demonstrate widespread decadal increases in soil microbial diversity and soil health across eastern China, with nitrogen deposition emerging as their strongest environmental factor. These results highlight that microbial responses to long-term ambient environmental change can differ markedly from responses inferred from short-term or high-intensity manipulation experiments.}, }
@article {pmid42667435, year = {2026}, author = {De, P and Chakraborti, S and Bhabai, B and Nath, S and Ghosh, PK and Khatun, N and Asif, SM}, title = {From traditional retting to precision bioprocessing: microbial ecology, enzymatic selectivity, and systems biology of jute retting.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {9}, pages = {}, pmid = {42667435}, issn = {1572-9699}, mesh = {*Systems Biology/methods ; *Lignin/metabolism/chemistry ; Microbial Consortia ; Bacteria/metabolism ; }, abstract = {Jute is one of the world's most important lignocellulosic fibre crops, yet its commercial value remains highly dependent on retting, a biologically mediated fibre extraction process still largely governed by empirical practices and variable environmental conditions. Recent advances in microbial ecology, enzymology, molecular biology, and bioprocess engineering have transformed retting from a traditional post-harvest operation into a controllable lignocellulosic bioconversion process. This review synthesizes current understanding of the structural organization of jute bast fibres, selective degradation of plant cell-wall polymers, microbial succession, extracellular enzyme networks, and physicochemical factors regulating fibre liberation. It highlights the coordinated interactions among cell-wall architecture, microbial communities, enzyme specificity, and environmental conditions that collectively determine retting efficiency and fibre quality. Emerging precision retting strategies, including defined microbial consortia, enzyme-assisted retting, ribbon retting, controlled processing systems, and water-efficient technologies, are critically evaluated for their potential to improve process reproducibility, fibre quality, and environmental sustainability. The review also examines metagenomics, metatranscriptomics, metaproteomics, metabolomics, systems biology, and artificial intelligence as enabling technologies for microbiome-guided process monitoring, predictive modelling, and digital decision support. Furthermore, this review discusses the integration of precision retting within circular bioeconomy frameworks through resource recovery, pollution mitigation, climate-resilient processing, and lignocellulosic biorefineries. Key knowledge gaps, including limited understanding of microbial interactions, lack of standardized microbial consortia, insufficient process-monitoring tools, fragmented multi-omics datasets, and challenges in industrial scale-up, are identified. Overall, this review presents a systems-level framework for advancing jute retting toward standardized, predictive, and environmentally sustainable precision bioprocessing.}, }
@article {pmid42668212, year = {2027}, author = {Huang, X and Luo, R and Wang, Y and Zheng, W and Lu, X and Liu, G and Abdulla, P and Niu, R and Tu, Y and Xing, J and Hong, J and Zheng, W and Liu, J}, title = {Correlation between microbial communities, metabolites, and bioactivities in fermented mare's milk revealed by metagenomics and metabolomics.}, journal = {Food microbiology}, volume = {141}, number = {}, pages = {105278}, doi = {10.1016/j.fm.2026.105278}, pmid = {42668212}, issn = {1095-9998}, mesh = {Animals ; Metagenomics ; Fermentation ; Metabolomics ; *Microbiota ; Horses ; *Milk/microbiology/chemistry/metabolism ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Cultured Milk Products/microbiology/analysis ; Lactobacillales/metabolism/genetics/isolation &amp; purification/classification ; Female ; Antioxidants/metabolism/analysis ; }, abstract = {Koumiss exhibits various functional properties, including antioxidant, hypoglycemic, and antihypertensive effects; however, natural fermentation is characterized by an uncontrollable microbial community structure, significant fluctuations in product quality, and a lack of specialized fermentation agents. The mechanisms underlying the links between microbial communities, functional metabolites, and bioactivity in natural and inoculated fermentation systems remain unclear. Therefore, this study employed bioactivity assays, metagenomics, and non-targeted metabolomics to systematically analyze differences in microbial communities, metabolite composition, and functional activities of mare's milk under different fermentation regimes. The results indicated that, compared with natural fermentation, inoculated fermentation with a mixed lactic acid bacteria (LAB) culture significantly enhanced the antioxidant, α-glucosidase, α-amylase inhibitory activities, and ACE inhibitory activity of mare's milk; microbial diversity in fermented samples was significantly reduced, with a more pronounced decrease in the inoculated group. Metabolomic analysis revealed that inoculated fermentation significantly enriched functional metabolites, including lipids and organic acids. Correlation analysis indicated that the abundance of Lactiplantibacillus and Limosilactobacillus was significantly positively correlated with beneficial metabolites (e.g., linoleic acid, α-linolenic acid) and functional activities. The lipid and amino acid metabolic pathways are closely associated with the differences in in vitro biological activity of inoculated fermented mare's milk. This study provides a fermentation starter that can improve the in vitro functional activity of mare's milk and reveals the potential metabolic links between LAB fermentation and the altered functional traits of mare's milk, thereby providing a theoretical basis and technical support for the development of high-value-added fermented mare's milk products.}, }
@article {pmid41803498, year = {2026}, author = {Zhou, H and Sun, R and Nie, X and Xia, L and Dong, H and Liu, Y and Hou, S and Dong, W and Zhu, X and Yao, Y and Zhao, GP and Lu, S and Wang, Y and Yang, C}, title = {A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.}, journal = {Nature microbiology}, volume = {11}, number = {4}, pages = {993-1007}, pmid = {41803498}, issn = {2058-5276}, support = {82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31925001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073152//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241227//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030045//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Mice ; Humans ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; *Immunotherapy/methods ; Fecal Microbiota Transplantation ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology ; *Gastrointestinal Microbiome ; *Lung Neoplasms/therapy/immunology ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cell Line, Tumor ; Female ; *Immune Checkpoint Inhibitors/therapeutic use ; Mice, Inbred C57BL ; CD8-Positive T-Lymphocytes/immunology ; }, abstract = {Targeting the gut microbiota is a promising strategy to enhance the efficiency of cancer immunotherapy; however, success has been limited. Here we combined metagenomic analysis and in silico prediction to identify bacterial species associated with immunotherapy response in patients with non-small-cell lung cancer. We constructed a defined consortium (RCom) of 15 bacterial species, most of which were isolated from responder patient faeces, associated with improved clinical response to anti-programmed cell death protein 1 (PD-1) treatment. Metabolic models and in vitro experiments revealed that RCom is a stable and cooperative community, and in vivo experiments showed that RCom engrafts and produces immunomodulatory metabolites. Oral administration of RCom improved the anti-tumour activity of anti-PD-1 by increasing the intratumoural infiltration and cytotoxic function of CD8[+] T cells in syngeneic tumour models and across mice with heterogeneity in baseline gut microbiota composition. RCom supplementation also limited anti-PD-1 resistance in mice conferred by faecal microbiota transplantation from individual non-responsive patients. These findings suggest that RCom is a potential adjuvant to improve responsiveness to anti-PD-1 therapy in cancer.}, }
@article {pmid41803682, year = {2026}, author = {Shen, Z and Zhang, Z and Gao, J and Chen, J and Xu, Q and Li, D and Zeng, L and Cheng, D and Wang, K and Zhang, J and Wong, JWC}, title = {Microbial succession accompanies increased antibiotic resistance risk during grass carp (Ctenopharyngodon idella) spoilage under ambient household conditions.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41803682}, issn = {1471-2180}, support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 22206107//National Natural Science Foundation of China/ ; 2023ZT10L060//Program for Guangdong Introducing Innovative and Entrepreneurial Teams of China/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; }, mesh = {Animals ; *Carps/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Drug Resistance, Microbial/genetics ; Biogenic Amines/analysis ; *Microbiota/genetics ; Food Microbiology ; Food Safety ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Food Storage ; Food Packaging ; }, abstract = {Understanding fish spoilage mechanisms under household storage conditions is critical for food safety in regions with limited cold chain infrastructure, where ambient storage remains common practice. This study investigated the spoilage dynamics, microbial succession, and antibiotic resistance gene (ARG) proliferation in grass carp stored under simulated household conditions at 13.0 ± 3.4 °C using three packaging scenarios. The biogenic amine index (BAI) of fish exceeded 50 mg/kg within 16 h, marking early spoilage onset. After 64 h, K-values surpassed 60%, TVB-N exceeded the safety limit of 20 mg/100 g, and BAI reached over 220 mg/kg, indicating advanced spoilage. 16S rRNA amplicon sequencing demonstrated dramatic microbial community shifts from Cyanobacteriota-dominated fresh samples to Pseudomonadota-dominated spoilage communities, with Aeromonas emerging as the primary specific spoilage organism (SSO), increasing from 0.001% to 67.2% at 64 h. Pathogen abundance escalated from 0.06% to 72.2% in muscle tissues, posing substantial food safety risks. Distinct microbial community structures were observed across tissue types (muscle vs. gut) and packaging treatments, with storage time exerting the strongest selective pressure on community composition. Metagenomic analysis revealed progressive ARG enrichment, with surface samples exhibiting 2.6-fold higher total ARG abundance and 3.8-fold greater ARG type richness compared to the fresh gut baseline by 24 ~ 64 h. Rapid ARG enrichment was detected during early spoilage (24 h), representing a critical food safety concern. Notably, carbapenem resistance genes (e.g., OXA-12, cphA6) were substantially enriched, underscoring the high risk posed by these clinically relevant resistance genes. These findings demonstrate that grass carp stored under ambient household conditions maintain acceptable quality for < 16 h, necessitating immediate consumption or cold chain implementation to ensure food safety and minimize ARG dissemination.}, }
@article {pmid41803907, year = {2026}, author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM}, title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41803907}, issn = {2049-2618}, support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundaci&#xf3;n Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracci&#xf3;n de talento investigador C&#xe9;sar Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Feces/microbiology ; Metagenomics/methods ; French Guiana ; *Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Metagenome ; }, abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.<br><br>RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs&#x2009;+&#x2009;BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs&#x2009;+&#x2009;BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p&#x2009;<&#x2009;0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.<br><br>CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.}, }
@article {pmid41804664, year = {2026}, author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B}, title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70278}, doi = {10.1111/1462-2920.70278}, pmid = {41804664}, issn = {1462-2920}, support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; }, mesh = {Biodegradation, Environmental ; *Microplastics/metabolism ; *Composting ; *Polymers/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Polyesters/metabolism ; *Microbiota ; Soil Microbiology ; }, abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.}, }
@article {pmid41804674, year = {2026}, author = {Liu, D and Luo, M and Li, M and Chen, C and Chen, S and Wu, Y and Zhang, G and Gao, Y and Hong, Y and Zhou, Q and Li, X and Zhou, S and Wu, Y and Zhao, Y and Zhang, Y and Yin, J}, title = {Dynamic interaction between Escherichia coli enterotoxins and bacteriocins.}, journal = {The FEBS journal}, volume = {293}, number = {16}, pages = {4860-4881}, pmid = {41804674}, issn = {1742-4658}, support = {2023YFD1401400//the National Key R&amp;D Program of China/ ; 32471200//the National Natural Science Foundation of China/ ; kq2208167//the Natural Science Foundation of Changsha/ ; xjt [2021] 346//the postgraduate joint training base project in Hunan Province/ ; 2023JJ10029//the Natural Science Foundation for Distinguished Young Scholars of Hunan Province/ ; }, mesh = {Animals ; *Enterotoxins/metabolism/genetics ; *Enterotoxigenic Escherichia coli/metabolism/genetics/pathogenicity ; *Bacteriocins/metabolism/genetics ; Mice ; *Escherichia coli Proteins/metabolism/genetics ; Colicins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; *Bacterial Toxins/metabolism/genetics ; Signal Transduction ; Swine ; Escherichia coli/metabolism ; Gene Expression Regulation, Bacterial ; Coculture Techniques ; }, abstract = {The intestinal microbiota constitutes a crucial defense barrier against pathogenic invasion; however, the molecular mechanisms enabling pathogens to evade or modulate this defense remain poorly understood. Here, we established a coculture model combining the commensal Escherichia coli Y18J, isolated from the piglet gut, and the enterotoxigenic E. coli (ETEC) strain W25K to investigate microbe-pathogen interactions. Our findings reveal a bidirectional regulatory mechanism between Y18J and W25K mediated by bacteriocin and toxin signaling. Colicin B/M produced by Y18J upregulates the expression of heat-stable enterotoxin (ST) in W25K during the early phase of coculture, while ST suppresses colicin B/M synthesis in Y18J. At later stages, colicin B/M stimulates heat-labile enterotoxin (LT) expression, which in turn enhances colicin B/M production. Notably, LT markedly reduces intestinal colonization of W25K(ST[-]LT[+]) in murine hosts. Leveraging metagenomic and bioinformatic analyses, we further identified a Ligilactobacillus strain within the murine gut microbiota capable of producing multiple bacteriocins that effectively inhibit W25K colonization. Transcriptomic profiling of Y18J revealed glutamine synthetase as a pivotal regulator of colicin B/M-mediated antagonism. Mechanistic investigations demonstrated that ST suppresses colicin B/M expression through the cGMP signaling pathway, whereas LT enhances it via the cAMP signaling pathway. Collectively, these findings uncover a dual regulatory mechanism through which bacterial enterotoxins modulate probiotic antimicrobial activity, providing new insights into the molecular dialog between commensal and pathogenic bacteria. This study establishes a conceptual framework for developing microbiota-based strategies to prevent and control enteric infections.}, }
@article {pmid41805951, year = {2026}, author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM}, title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41805951}, issn = {1432-184X}, mesh = {*Cacao/microbiology/virology ; Colombia ; Fermentation ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; *Fungi/genetics/classification/isolation &amp; purification/metabolism ; Viruses/genetics/classification/isolation &amp; purification ; *Microbiota ; Desiccation ; *Metagenome ; Food, Processed ; Food Microbiology ; }, abstract = {Shotgun metagenomics is an approach increasingly applied to investigate microbial succession and functional potential in complex fermented food systems, including cocoa bean fermentation. In this study, we used Illumina-based shotgun metagenomic sequencing to characterize microbial community dynamics and metabolic potential across two post-harvest cocoa processing routes (R1 and R2) in Boyacá, Colombia, encompassing both fermentation and drying stages. Cocoa beans were sampled at defined time points during fermentation and subsequent natural drying, and non-host metagenomic reads were subjected to taxonomic classification and functional annotation to assess fungi, bacteria, and viruses. A clear multi-ecological succession was observed throughout post-harvest processing. Fungal communities shifted from a yeast-dominated profile, mainly Saccharomyces and Pichia during fermentation, to the emergence of the filamentous fungus Aspergillus during drying. Bacterial populations transitioned from diverse Enterobacteriaceae in early fermentation to a near-complete dominance of Acetobacter, which persisted throughout the drying phase. Viral communities also displayed structured successional patterns, with Lambdavirus and Punavirus prevalent in early fermentation, followed by Spbetavirus, Lafunavirus, and Pemunavirus during later stages and drying. Functional analyses revealed high metabolic potential for carbohydrate, energy, and amino acid metabolism during early fermentation, followed by a marked reduction in later stages, indicating a metabolic slowdown. Core metabolic functions were retained during drying at substantially lower activity levels. This integrated metagenomic analysis links microbial structure to functional potential and provides a scientific basis for optimizing starter cultures and post-harvest processing strategies to enhance cocoa quality and safety.}, }
@article {pmid41807604, year = {2026}, author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L}, title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41807604}, issn = {2045-2322}, mesh = {*Bacillus/genetics/isolation &amp; purification/classification ; Italy ; Phylogeny ; Microbiota ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.}, }
@article {pmid41808169, year = {2026}, author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J}, title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.}, journal = {Microbial cell factories}, volume = {25}, number = {1}, pages = {}, pmid = {41808169}, issn = {1475-2859}, support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Humans ; *Metabolome ; Multiomics ; Recurrence ; *Calcium Oxalate/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; *Kidney Calculi/microbiology/metabolism ; *Nephrolithiasis/microbiology/metabolism ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Caffeine/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {BACKGROUND: The incidence and recurrence rate of nephrolithiasis have been increasing annually. Recent evidence highlights a close association between the composition and function of the gut microbiome and the occurrence and recurrence of kidney stones. We performed a multi-omic study to investigate changes in gut microbiota and their metabolites during nephrolithiasis development and recurrence, and to explore the underlying molecular mechanisms. Stool samples from 37 recurrent stone patients, 38 first-episode stone patients, and 39 healthy controls were collected for 16S rDNA amplicon sequencing and liquid chromatography-mass spectrometry. Ten samples from each group were randomly selected for metagenomic sequencing. RESULTS: Compared to incident cases, recurrent stone patients exhibited further reduced gut microbial richness and diversity, with enrichment of Enterobacterales, Pseudomonadota, Gammaproteobacteria, Enterobacteraceae, Escherichia-Shigella, and Bacillia. In the recurrent kidney stone group, 9 metabolites were upregulated and 86 downregulated, with enrichment of genes in purine and caffeine metabolism pathways. We identified 10 metabolites as recurrence biomarkers and significant correlations between Escherichia-Shigella and Asn-Tyr, Leu-Ala-Ile, Tyrosyl-Alanine, or 3'-hydroxyhexobarbital. Additionally, gender-specific gut microbiota signatures were observed. Oxalate decarboxylase and short-chain fatty acid-related enzymes decreased during stone formation but rebounded with recurrence. Caffeine and its metabolites were significantly downregulated in recurrent patients, suggesting a potential association with stone formation and recurrence that merits further investigation. CONCLUSIONS: Our study comprehensively characterizes gut microbiome and metabolome signatures associated with nephrolithiasis recurrence. The findings reveal that recurrent nephrolithiasis is characterized by impaired gut microbial evenness, enrichment of specific taxa including Escherichia-Shigella, and dysregulated metabolic pathways such as purine metabolism and caffeine metabolism. The 10 identified metabolites show promise as potential recurrence biomarkers, with notable correlations between Escherichia-Shigella and key metabolites. These results highlight the critical association of the gut microbiome-metabolome axis with renal stone recurrence, providing novel microbial and metabolic targets for early prediction, with potential implications for prevention and personalized treatment that require further validation.}, }
@article {pmid41808525, year = {2026}, author = {Jiménez, DJ and Rosado, AS}, title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70272}, pmid = {41808525}, issn = {1462-2920}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Polyethylene Terephthalates/metabolism ; *Microbiota ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biodegradation, Environmental ; *Bacteria/enzymology/genetics/metabolism ; Biocatalysis ; Protein Engineering ; }, abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.}, }
@article {pmid41811526, year = {2026}, author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S}, title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.}, journal = {Cancer causes &amp; control : CCC}, volume = {37}, number = {4}, pages = {}, pmid = {41811526}, issn = {1573-7225}, support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; }, mesh = {Humans ; *Life Style ; Female ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; Male ; Adult ; *Gastrointestinal Microbiome/genetics ; Risk Factors ; Metagenomics/methods ; Finland/epidemiology ; Metagenome ; Diet ; }, abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.<br><br>METHODS: Our data included 1,228 adults aged 25-64&#xa0;years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.<br><br>RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p&#x2009;<&#x2009;0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (&#x3b2; 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (<&#x2009;0.0001).<br><br>CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.}, }
@article {pmid41811805, year = {2026}, author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L}, title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344050}, pmid = {41811805}, issn = {1932-6203}, mesh = {Humans ; *Adenoma/microbiology/metabolism ; *Colorectal Neoplasms/microbiology/metabolism/diagnosis ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Colonoscopy ; Male ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Aged ; }, abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.<br><br>OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.<br><br>MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.<br><br>RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K&#x2082;) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.<br><br>CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K&#x2082; biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.}, }
@article {pmid41812751, year = {2026}, author = {Prabhakar, S and Rajeev, AC and Sankappa, NM and Harsha, R}, title = {High-throughput metagenomic profiling of functional and resistome features in estuarine microplastic microbiomes.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124159}, doi = {10.1016/j.envres.2026.124159}, pmid = {41812751}, issn = {1096-0953}, mesh = {*Estuaries ; *Microplastics/analysis ; *Microbiota ; India ; Metagenomics ; *Water Pollutants, Chemical/analysis/toxicity ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Bacteria/genetics ; }, abstract = {Microplastics (MPs) are now recognized as persistent pollutants in aquatic ecosystems, providing unique surfaces for microbial colonization and acting as vectors for the spread of pathogens, antibiotic resistance, and virulence factors. Estuarine systems, due to their dynamic hydrology and proximity to anthropogenic activity, are particularly vulnerable to MP accumulation and associated microbial risks. This study presents the first comprehensive metagenomic investigation of MP-associated microbial communities across five estuaries spanning the northern and southern coastal regions of Karnataka, India. MPs were isolated, characterized, and the extracted total DNA from the MPs was subjected to high-throughput sequencing and comprehensive bioinformatic analyses. Taxonomic, functional, and resistance gene profiling were performed to evaluate microbial diversity, ecological roles, and potential public health implications. The findings revealed distinct regional differences in microbial community structure and functional potential, with evidence of clinically relevant pathogens, antibiotic resistance genes, and virulence determinants within the plastisphere. These results highlight the role of MPs as reservoirs and vectors for microbial risks in estuarine ecosystems. By linking microbial diversity of MPs with environmental and anthropogenic influences, this work provides crucial baseline data for monitoring and managing estuarine health. It also underscores the urgent need for integrated strategies to mitigate plastic pollution and its cascading ecological and public health impacts.}, }
@article {pmid41814006, year = {2026}, author = {Baldanzi, G and Larsson, A and Sayols-Baixeras, S and Dekkers, KF and Hammar, U and Nguyen, D and Graells, T and Ahmad, S and Gazolla Volpiano, C and Meric, G and Järhult, JD and Tängdén, T and Ludvigsson, JF and Lind, L and Sundström, J and Michaëlsson, K and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.}, journal = {Nature medicine}, volume = {32}, number = {4}, pages = {1351-1361}, pmid = {41814006}, issn = {1546-170X}, support = {20230687//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2023-0380//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2019-01471//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2025-02673//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-01460//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-00243//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-02784//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Strategic Research Area Exodiab 2009-1039//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-00989//Svenska Forskningsr&#xe5;det Formas (Swedish Research Council Formas)/ ; IRC-0067//Stiftelsen f&#xf6;r Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/microbiology ; Female ; Clindamycin/adverse effects ; Sweden ; Metagenome/drug effects ; Male ; Penicillin V/adverse effects ; Fluoroquinolones/adverse effects ; Adult ; Floxacillin/adverse effects ; Nitrofurantoin/adverse effects ; Middle Aged ; }, abstract = {Disruptions in gut microbiome are implicated in cardiometabolic disorders and other health outcomes. Antibiotics are known gut microbiome disruptors, but their long-term consequences remain underexplored. Here we combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. In multivariable confounder-adjusted regression models, antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1-4 and 4-8 years earlier. Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4-8 years earlier was associated with altered abundance of 10-15% of the species studied; penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Similar results were found comparing one antibiotic course 4-8 years before sampling versus none in the past 8 years. These findings indicate that antibiotics may have long-lasting consequences for the gut microbiome.}, }
@article {pmid41814421, year = {2026}, author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41814421}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/immunology ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Animals, Wild/microbiology/immunology ; }, abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.<br><br>RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.<br><br>CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.}, }
@article {pmid41816992, year = {2026}, author = {Rao, B and Jiang, J and Zhang, R and Zhang, D and Zhang, C and Li, A and Lu, H and Zhang, H and Zhou, L and Guo, W and Wen, P and Xue, J and Pan, J and Aji, T and Lan, Z and Jiang, X and Zheng, S and Yu, Z and Ren, Z}, title = {Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {27}, pages = {e17658}, pmid = {41816992}, issn = {2198-3844}, support = {82470654//National Natural Science Foundation of China/ ; 232300421124//Natural Science Foundation Key Project of Henan Province/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; ZYYC202301ZD//Henan Zhongyuan Medical Science and Technology Innovation and Development Foundation/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, mesh = {Humans ; *Cholangiocarcinoma/diagnosis/microbiology ; *Bile Duct Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; *Bifidobacterium ; Feces/microbiology ; Male ; Dysbiosis/microbiology ; Female ; Metagenomics ; China ; Middle Aged ; }, abstract = {Growing evidence suggests a role for the gut microbiome in progression of cholangiocarcinoma (CCA), however, its diagnostic and therapeutic potential remains incompletely characterized. Here, metagenomic sequencing was performed on fecal samples (n = 785) from individuals across East, Central, and Northwestern China. Gut microbial dysbiosis in CCA was characterized by depletion of short-chain fatty acids-producing species and enrichment of potential pathobionts (Klebsiella aerogenes, Clostridium symbiosum). Diagnostic models built using species-level markers demonstrated superior performance, compared to pathway-based models, achieving area under the curve (AUC) values of 98.63% and 99.42% in the discovery cohort, with robust cross-regional validation (AUC = 80.89% and 80.43%). The model effectively distinguished CCA from hepatocellular carcinoma (AUC = 97.86%) and liver fibrosis (AUC = 98.73%) and nonalcoholic fatty liver disease (mean AUC = 96.86%). Analysis of public datasets encompassing 6847 samples across 31 studies and 11 disease states revealed moderate disease specificity influenced by biomarker overlap across conditions. Mechanistically, depleted Bifidobacterium pseudocatenulatum suppressed CCA progression, associated with inhibition of the PI3K-AKT-mTOR pathway. Collectively, this study supports the potential of fecal metagenomic signatures as a complementary noninvasive aid for CCA detection, and provides functional evidence for a candidate protective microbe.}, }
@article {pmid41816995, year = {2026}, author = {Zhao, F and Zhang, R and Wei, R and Fan, H and Hu, Y and Shi, W and Wang, J}, title = {Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {29}, pages = {e16916}, pmid = {41816995}, issn = {2198-3844}, support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; 32370053//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; }, mesh = {Animals ; *Polysaccharides/pharmacology/metabolism ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects/physiology ; *Bacteriophages/physiology/genetics ; Mice ; *Bacteria/virology ; Humans ; Metagenome ; Virome ; }, abstract = {Phages dominate the human gut virome and are known for their ability to prey on bacteria and shape microbiota. However, their response to diet has only been elucidated using small-scale studies. By integrating a massive meta-analysis of 6932 diet-associated metagenomes with a time-resolved mouse model of a high-fat diet and polysaccharide intake, the impact of diet on the gut virome and phage-bacterial interactions was systematically characterized. Diet types, particularly high-fat and polysaccharide-rich diets, exert the strongest shaping force on the gut virome, enhancing the crosstalk between phages and bacteria. High-fat diets promote changes in phage abundance across a broad taxonomic range, from 34.21% to 50.00%, drive phages of diet-associated bacteria toward a lytic lifestyle, and remarkably enrich auxiliary metabolic genes related to amino acid metabolism. Conversely, fucoidan reversed HFD-induced dysbiosis and enhanced phage-mediated horizontal gene transfer by 8.5-fold relative to the baseline. crAssphages and Parabacteroides phages may be important contributors, broadly supporting horizontal gene transfer and auxiliary metabolism or strengthening phage-host interactions in polysaccharide interventions, including fucoidan supplementation. These findings provide a comprehensive landscape of diet-driven cross-kingdom interactions and phage-mediated gene exchange in the gut, offering new insights into potential strategies for precise nutritional interventions targeting the intestinal microbiota.}, }
@article {pmid41818685, year = {2026}, author = {Qu, Q and Jia, Y and Wang, S and Hu, K and Liu, C and Hu, X and Mu, L}, title = {Responses of Microbial Communities in River to Atmospheric Deposition.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {11}, pages = {8583-8592}, doi = {10.1021/acs.est.6c01648}, pmid = {41818685}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; Bacteria ; Atmosphere ; Fungi ; *Microbiota ; }, abstract = {Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.}, }
@article {pmid41819166, year = {2026}, author = {Zhao, X and Zhang, J and Li, Y and Wang, Q and Li, J and Xia, Y and Zha, M and Chen, Y}, title = {Elucidating the microbiota-metabolite interplay in Hurood and Chula: An integrated multiomics investigation.}, journal = {Journal of dairy science}, volume = {109}, number = {8}, pages = {7965-7980}, doi = {10.3168/jds.2025-28134}, pmid = {41819166}, issn = {1525-3198}, mesh = {Volatile Organic Compounds/analysis/metabolism ; *Microbiota ; *Cheese/microbiology/analysis ; Multiomics ; Gas Chromatography-Mass Spectrometry ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {The differences in flavor and quality between Hurood and Chula, two traditional Xilingol cheeses, are primarily due to variations in their production processes. Therefore, how heating and kneading affect their microbial, nonvolatile metabolite, and volatile organic compound (VOC) composition warrants exploration. In this study, shotgun metagenomic sequencing revealed the differential micro-organisms between Hurood and Chula. Ultra-performance liquid chromatography-tandem MS identified 47 differential metabolites. Among these, organic acids and their derivatives, benzene and substituted derivatives, free fatty acids (FFA), and lysophosphatidylcholines showed the highest content in Chula, whereas lactose, melibiose, and histamine were significantly enriched in Hurood, suggesting that the heating and kneading process affected galactose and histidine metabolic pathways. In contrast, headspace solid-phase microextraction GC-MS identified 4 differential VOC with elevated levels in Hurood. These compounds functioned as key aroma contributors, imparting richer and more complex aroma characteristics that included creamy, oily, fatty, caramel, coconut, woody, spice, and maple notes. Correlation analysis indicated that the differential micro-organisms were involved in metabolite dynamics and VOC accumulation and further revealed that they drove the directed accumulation of VOC through regulating FFA release and transformation and by regulating the Maillard reaction of small peptides, thereby underpinning their distinct flavor profiles. This study provides important insights into the heating- and kneading-induced formation of flavor and quality in traditional Xilingol cheeses, thereby facilitating the precise control of traditional processes and subsequent product quality improvement.}, }
@article {pmid41819204, year = {2026}, author = {Qi, Y and Zheng, X and He, X and Huang, K and Wang, D and Zhang, XX}, title = {Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124241}, doi = {10.1016/j.envres.2026.124241}, pmid = {41819204}, issn = {1096-0953}, mesh = {*Triazoles/metabolism ; Biodegradation, Environmental ; *Microbiota ; *Microbial Consortia ; *Bacteria/metabolism/genetics ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {The escalating prevalence of benzotriazole (BTR), an emerging refractory organic pollutant, has drawn significant attention for the development of efficient bioremediation solutions. Although the construction of microbial consortia represents a promising strategy, the intrinsic relationship between community succession and functional features during artificial selection remains poorly understood. To address this, this study engineered two distinct microbial consortia from activated sludge using a top-down selection strategy in sequencing batch reactors fed with increasing BTR concentrations. While the two consortia evolved along divergent taxonomic pathways, they exhibited remarkable functional convergence, maintaining consistently high BTR transformation (>96%) and chemical oxygen demand (>75%) removal efficiencies. This robust performance under the stringent condition of BTR as the sole carbon source highlighted their significant adaptive potential. Metagenomic analysis further attributed this functional stability to the principle of functional redundancy, wherein taxonomically distinct keystone species (e.g., Nocardioides and Methylobacterium) harbored functionally analogous gene clusters. Additionally, multiple congeneric species (e.g., MAG.480 and MAG.17) within the Bacteroidota phylum exhibited significant divergence in their degradation gene repertoires. These findings not only advance ecological understanding of microbiome-mediated BTR biodegradation but also provide a foundation for the rational design and optimization of high-performance bioremediation consortia.}, }
@article {pmid41821330, year = {2026}, author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M}, title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {2}, pages = {202-214}, doi = {10.3967/bes2025.162}, pmid = {41821330}, issn = {2214-0190}, mesh = {*Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Species Specificity ; Bacteria/classification ; }, abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.<br><br>METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.<br><br>RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).<br><br>CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.}, }
@article {pmid41823302, year = {2026}, author = {Al, KF and Jia, S and Silverman, M and Reid, G and Burton, JP and Parvathy, SN}, title = {Prebiotic modulation of FMT donor microbiota enhances MASLD-relevant taxa and functions in an in vitro gut model.}, journal = {Journal of applied microbiology}, volume = {137}, number = {4}, pages = {}, doi = {10.1093/jambio/lxag074}, pmid = {41823302}, issn = {1365-2672}, support = {//Lawson/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Prebiotics/analysis ; Humans ; Inulin/metabolism ; *Gastrointestinal Microbiome/drug effects ; Oligosaccharides/pharmacology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Glucuronates ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.<br><br>METHODS AND RESULTS: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 h with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.<br><br>CONCLUSIONS: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.}, }
@article {pmid41823694, year = {2026}, author = {Pessi, IS and Eronen-Rasimus, E and Näkki, P and Thomas, DN and Kaartokallio, H}, title = {Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41823694}, issn = {1751-7370}, support = {332174//Research Councils of Finland/ ; }, mesh = {*Seawater/microbiology ; Metagenomics ; Biodegradation, Environmental ; *Bacteria/metabolism/classification/genetics ; *Microbiota ; *Biodegradable Plastics/metabolism ; Gene Expression Profiling ; *Plastics/metabolism ; Cellulose/metabolism/analogs &amp; derivatives ; }, abstract = {Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.}, }
@article {pmid41824271, year = {2026}, author = {Singh, K and Sambyal, D and Julka, JM}, title = {Metagenomic exploration of bacterial community shifts before, during, and after passage through earthworm Eutyphoeus waltoni.}, journal = {Biologia futura}, volume = {77}, number = {2}, pages = {387-399}, pmid = {41824271}, issn = {2676-8607}, mesh = {Animals ; *Oligochaeta/microbiology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Understanding the transformation of soil microbial communities during their passage through the earthworm gut provides essential insights into soil health and ecosystem functioning. In this study, we employed 16S rRNA gene sequencing to investigate the bacterial community dynamics in the surrounding soil, gut, and casts of anecic earthworm Eutyphoeus waltoni, an important ecosystem engineer. This research aims to elucidate the microbial selection and transformation processes that occur as microorganisms pass through the earthworm’s alimentary canal. E. waltoni was selected for its significant role in organic matter decomposition and nutrient cycling within Indian soils. While species like Eisenia fetida and Lumbricus terrestris are well-studied, E. waltoni remains understudied despite its ecological importance. We observed notable shifts in microbial communities across the three microhabitats, primarily composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria. The gut environment selectively enriched Firmicutes, particularly Clostridioides, and reduced Proteobacteria. In the cast, microbial recovery was partial, with the presence of genera such as Azospira and Nitrospira, which are linked to nutrient turnover. These findings demonstrate that E. waltoni selectively restructures microbial assemblages, promoting taxa that enhance nutrient cycling and biogeochemical processes.}, }
@article {pmid41825203, year = {2026}, author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T}, title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106607}, doi = {10.1016/j.clnu.2026.106607}, pmid = {41825203}, issn = {1532-1983}, mesh = {Humans ; *Obesity/metabolism/blood/microbiology ; Male ; Female ; Multiomics ; Postprandial Period/physiology ; Adult ; *Nutrients ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Diet ; Metabolomics ; Overweight/metabolism ; Proteomics ; Feeding Behavior/physiology ; }, abstract = {BACKGROUND&amp; AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.<br><br>METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.<br><br>RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 &#xb1; 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).<br><br>CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.}, }
@article {pmid41825563, year = {2026}, author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G}, title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134417}, doi = {10.1016/j.biortech.2026.134417}, pmid = {41825563}, issn = {1873-2976}, mesh = {Anaerobiosis ; Methane/biosynthesis/metabolism ; Bioreactors/microbiology ; *Microbial Consortia/physiology ; Fatty Acids, Volatile/metabolism ; Food Loss and Waste ; }, abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.}, }
@article {pmid41825740, year = {2026}, author = {Alvarado, DA and Holthaus, TA and Martell, S and Southey, NL and Atallah, M and Sarma, R and Revilla, D and Brown, M and Mehta, T and Khan, NA and Holscher, HD}, title = {Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.}, journal = {The Journal of nutrition}, volume = {156}, number = {5}, pages = {101473}, pmid = {41825740}, issn = {1541-6100}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Cognition/drug effects ; Cross-Over Studies ; *Dietary Fiber/pharmacology/administration &amp; dosage ; Double-Blind Method ; *Executive Function/drug effects ; Feces/microbiology ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; *Zea mays/chemistry ; }, abstract = {BACKGROUND: Dietary fiber may support cognition through gastrointestinal-microbiota mechanisms, but clinical evidence is limited.<br><br>OBJECTIVES: We aimed to determine whether soluble corn fiber (SCF) improved cognition and altered fecal microbiota and fermentation end products in adults.<br><br>METHODS: In a randomized, double-blind, crossover trial, 42 healthy adults (45-75 y) consumed SCF (18 g/d) or a maltodextrin placebo control (CON: 22 g/d) for 4 wk, separated by a washout. Cognitive outcomes included executive function with event-related potentials, relational memory, neuropsychological performance, and mood. Secondary outcomes included fecal microbiota, metabolomics, and gastrointestinal tolerance. Tertiary analyses related microbial and metabolite changes to cognitive improvements using correlation, mediation, and moderation models, and explored SCF fermentation pathways with 16S-predicted functional profiling, shotgun metagenomics, and in vitro culturing.<br><br>RESULTS: SCF improved reaction times (RT) during congruent (&#x3b2; = -9.8 ms, 95% confidence interval (CI): -18.4, -1.2, false discovery rate (FDR) P = 0.01) and incongruent (&#x3b2; = -14.2 ms, 95% CI: -22.8, -5.6, FDR P = 0.003) flanker trials and increased Parabacteroides (&#x223c;4-fold, &#x3b2; = 1.44 log, 95% CI: 1.01, 1.88, FDR P < 0.001). At the SCF endpoint, congruent RT tended to be inversely associated with fecal acetate (&#x3c1; = -0.33) and propionate (&#x3c1; = -0.36), whereas Parabacteroides was marginally positively associated with acetate (&#x3c1; = 0.34) (all FDR P < 0.1). Moderation analyses indicated that SCF-RT relation varied by Parabacteroides magnitude change. At endpoint, SCF increased the predicted functional potential of carbohydrate-related KEGG Orthologs and pathways (FDR P < 0.05). In vitro culturing confirmed Parabacteroides distasonis ferments SCF.<br><br>CONCLUSIONS: SCF consumption improved attentional inhibition, altered the gut microbiota, and selectively enriched Parabacteroides. Although mediation analyses did not support a direct microbiota-to-cognition pathway, moderation analyses suggested that SCF-related cognitive effects may depend in part on Parabacteroides abundance. Collectively, these findings suggest that certain cognitive benefits of SCF consumption may be partly underpinned by the gut microbiota. This study was registered at clinicaltrials.gov as NCT05066425 (https://clinicaltrials.gov/study/NCT05066425).}, }
@article {pmid41826874, year = {2026}, author = {Wang, H and Fu, Y and Xu, H and Song, X and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W}, title = {Viromic profiling of amniotic fluid reveals distinct viral communities associated with maternal health status.}, journal = {BMC pregnancy and childbirth}, volume = {26}, number = {1}, pages = {}, pmid = {41826874}, issn = {1471-2393}, support = {No. 2023YFD1801300//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; JSYGY-1-2023-03(03)//Hospital Management Innovation Research Project of Jiangsu Provincial Hospital Association/ ; Nos. SH2023058, SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; }, mesh = {Humans ; Female ; *Amniotic Fluid/virology ; Pregnancy ; *Virome/genetics ; Phylogeny ; Adult ; China ; Metagenomics ; *Maternal Health ; Case-Control Studies ; Health Status ; }, abstract = {BACKGROUND: Amniotic fluid is a critical compartment in pregnancy; however, its virome remains poorly characterized, and potential associations with maternal–fetal health are largely unexplored. This study aimed to comprehensively profile the human amniotic fluid virome and explore its association with maternal health status during pregnancy. METHODS: We performed viral metagenomic sequencing of 515 amniotic fluid samples from 515 pregnant women in Changzhou, China, including healthy pregnancies (n = 275) and pregnancies with complications (n = 240). Viral sequences were identified using a bioinformatics pipeline, and phylogenetic analyses were used to assess genetic relationships. RESULTS: We identified diverse viral sequences, including members of viral families such as Anelloviridae and Paramyxoviridae. BLAST-based nucleotide comparisons showed high nucleotide identity to previously reported viruses, indicating that many detected sequences are closely related to known viruses. Phylogenetic analyses further supported their placement within established viral taxa. Community-level analyses indicated differences in virome composition profiles between the healthy control and disease groups. CONCLUSIONS: Our findings describe a previously undercharacterized virome in human amniotic fluid. This study establishes a basis for future investigations into the origins and potential associations of these viral signatures with pregnancy health, highlighting the importance of assessing their clinical relevance for both maternal and neonatal outcomes. Because metagenomic sequencing detects viral nucleic acids, these findings do not establish viral infectivity or causality.}, }
@article {pmid41827056, year = {2026}, author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T}, title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41827056}, issn = {2049-2618}, support = {T21-705/20-N//University Grants Committee/ ; }, mesh = {*Bacteria/growth &amp; development/genetics/classification ; *Metagenome ; Software ; *Metagenomics/methods ; *Computational Biology/methods ; Microbiota ; }, abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.<br><br>RESULTS: We introduce Pilea&#xa0;(https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.<br><br>CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.}, }
@article {pmid41828538, year = {2026}, author = {Chen, J and Xu, Y and Liu, Z}, title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828538}, issn = {1422-0067}, mesh = {Animals ; Biotransformation ; *Stress, Physiological ; *Gastrointestinal Microbiome/physiology ; Fermentation ; Mice ; *Metabolic Networks and Pathways ; Metabolomics/methods ; Lactiplantibacillus plantarum/metabolism ; }, abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.}, }
@article {pmid41829938, year = {2026}, author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW}, title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829938}, issn = {2072-6643}, support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Dietary Supplements ; Male ; Whey Proteins/administration &amp; dosage ; Oryza ; Pea Proteins/administration &amp; dosage ; *Plant Proteins/administration &amp; dosage ; Young Adult ; *Athletes ; Animals ; Resistance Training ; Adult ; Bacteria/classification/metabolism ; Soccer ; RNA, Ribosomal, 16S/genetics ; *Football ; }, abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.<br><br>METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.<br><br>RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.<br><br>CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.}, }
@article {pmid41831863, year = {2026}, author = {Patel, SS and Shree, T and Kumar, A}, title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.}, journal = {Pesticide biochemistry and physiology}, volume = {219}, number = {}, pages = {106993}, doi = {10.1016/j.pestbp.2026.106993}, pmid = {41831863}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Pesticides/metabolism ; *Microbial Consortia ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).}, }
@article {pmid41833387, year = {2026}, author = {Han, Z and Wang, Y and Yang, J}, title = {Physiological and biochemical changes and microbial community succession during the postharvest rot process of Stropharia rugosoannulata.}, journal = {The Journal of general and applied microbiology}, volume = {72}, number = {1}, pages = {}, doi = {10.2323/jgam.2026.03.001}, pmid = {41833387}, issn = {1349-8037}, mesh = {Metagenomics ; *Microbiota ; Superoxide Dismutase/metabolism ; Food Microbiology ; Glycosyltransferases/genetics/metabolism ; Bacteria/genetics/classification/isolation &amp; purification ; Pseudomonas/genetics ; Malondialdehyde/metabolism ; }, abstract = {This study systematically elucidated the microbial community succession and functional gene dynamics during the postharvest spoilage process of Stropharia rugosoannulata by integrating physiological and biochemical indicators with metagenomic analysis. The experimental results demonstrated that as storage time extended, the activities of antioxidant enzymes (superoxide dismutase, peroxidase) in S. rugosoannulata significantly declined, while the content of membrane lipid peroxidation product malondialdehyde increased, leading to compromised cell membrane integrity and creating favorable conditions for microbial colonization. Metagenomic analysis revealed that during the spoilage phase (post-harvest day 14), the relative abundance of Pseudomonadota increased to 85.7%, with Pseudomonas replacing Ewingella as the absolutely dominant microbial population. Further functional gene analysis showed that the post-harvest day 14 exhibited significant enrichment of glycosyltransferases (GT0, GT1, GT2, GT4) and carbohydrate-binding modules (CBM10, CBM16, CBM50), along with pectinase (GH78), chitinase (GH19), and polysaccharide-modifying enzymes (CE4, CE11). This indicated a metabolic shift towards cell wall synthesis and substrate recognition. In contrast, the post-harvest day 7, prior to fruiting body softening, demonstrated high expression of glycoside hydrolases (GH1, GH2, GH4, GH94) and carbohydrate esterase CE8, focusing on the degradation of cellulose and starch. These findings, for the first time from a molecular ecology perspective, clarify that the essence of postharvest spoilage in S. rugosoannulata is a quality deterioration process driven by a Pseudomonas-dominated microbial community. The study provided a basis for the development of targeted antibacterial preservation strategies.}, }
@article {pmid41833938, year = {2026}, author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L}, title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41833938}, issn = {2055-5008}, support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Zea mays/microbiology ; Soil Microbiology ; Rhizosphere ; Fusarium/physiology ; *Stress, Physiological ; *Bacteria/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Metagenomics/methods ; DNA, Bacterial/genetics ; Plant Stems/microbiology ; }, abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.}, }
@article {pmid41834217, year = {2026}, author = {Yuan, X and Gong, H and Zhang, L and Liu, Y and Zhou, M and Liu, Y and Tang, J and Pan, S and Xu, X and Wang, Y and Zhang, X and Zhang, T and Song, J}, title = {T2DM-Induced Gut Dysbiosis Exacerbates Periodontitis Through Intestinal Barrier Disruption and Redox Imbalance.}, journal = {Journal of clinical periodontology}, volume = {53}, number = {5}, pages = {821-833}, doi = {10.1111/jcpe.70116}, pmid = {41834217}, issn = {1600-051X}, support = {U22A20314//National Natural Science Foundation of China/ ; 82170968//National Natural Science Foundation of China/ ; 82301082//National Natural Science Foundation of China/ ; 2022YFC2504200//National Key Research and Development Program of China/ ; 2025MD774176//China Postdoctoral Science Foundation/ ; YXQN202401//Chongqing Youth Talent Support Program/ ; }, mesh = {Animals ; *Dysbiosis/complications ; *Periodontitis/microbiology/etiology/metabolism ; *Diabetes Mellitus, Type 2/complications ; Mice ; Mice, Inbred C57BL ; Oxidation-Reduction ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Intestinal Barrier Function ; Oxidative Stress ; Male ; Disease Models, Animal ; }, abstract = {AIM: To investigate the potential role and underlying mechanisms of gut microbiota in type 2 diabetes mellitus (T2DM)-exacerbated periodontitis.<br><br>MATERIALS AND METHODS: A T2DM-associated periodontitis model was established in C57BL/6 mice and analysed using multi-omics sequencing (16S rRNA, metagenomics and metabolomics). Faecal microbiota transplantation (FMT) from T2DM donors was carried out in recipient mice to investigate the impact of gut dysbiosis on periodontitis. FMT from healthy donors, supplementation of intestinal barrier protectant or the metabolite oleic acid (OA) was administered to mice with T2DM-associated gut dysbiosis to examine their ameliorative effects on periodontal damage.<br><br>RESULTS: T2DM-associated gut dysbiosis, independent of hyperglycaemia, triggered intestinal barrier disruption, which disturbed systemic redox-related metabolisms and elevated oral oxidative stress, thereby aggravating periodontitis. Restoring gut microbiota via FMT from a healthy donor or protecting the intestinal barrier ameliorated periodontitis. Exogenous supplementary metabolite OA rescued periodontal damage by activating the SIRT1/FoxO1 pathway and enhancing antioxidant enzymes in mice with T2DM-associated gut dysbiosis.<br><br>CONCLUSIONS: T2DM-induced gut dysbiosis exacerbates periodontitis through intestinal barrier disruption and redox imbalance. These findings provide new adjunctive therapeutic perspectives including microbiota restoration, intestinal barrier protection and antioxidant supplementation for managing patients with T2DM-induced periodontitis.}, }
@article {pmid41834952, year = {2026}, author = {Tu, Y and Niu, C and Huang, Z}, title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {65-72}, pmid = {41834952}, issn = {1672-173X}, mesh = {Humans ; *Saliva/virology ; *Virome/genetics ; Female ; Male ; *Dental Plaque/virology ; *Mouth/virology ; *Fatty Liver/virology ; Case-Control Studies ; Middle Aged ; Adult ; *Non-alcoholic Fatty Liver Disease/virology ; }, abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.<br><br>METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.<br><br>RESULTS: The &#x3b1;-diversity and &#x3b2;-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the &#x3b1;-diversity (Shannon index) and &#x3b2;-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.<br><br>CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.}, }
@article {pmid41836173, year = {2026}, author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL}, title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20880}, pmid = {41836173}, issn = {2167-8359}, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Brazil ; *Metagenomics ; *Culicidae/virology ; Phylogeny ; Female ; Genome, Viral ; *Virome/genetics ; High-Throughput Nucleotide Sequencing ; *Mosquito Vectors/virology ; }, abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.}, }
@article {pmid41837716, year = {2026}, author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E}, title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0011426}, pmid = {41837716}, issn = {2379-5077}, support = {PRG1414//Estonian Research Council Grant/ ; 3573//EMBO Installation grant/ ; 16-0125//Estonian Center of Genomics/Roadmap II/ ; }, mesh = {Humans ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Cohort Studies ; Genetic Variation ; *Bacteria/genetics/classification ; Genome, Bacterial ; }, abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.<br><br>IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.}, }
@article {pmid41839407, year = {2026}, author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D}, title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134433}, doi = {10.1016/j.biortech.2026.134433}, pmid = {41839407}, issn = {1873-2976}, mesh = {*Composting/methods ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Lignin/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.}, }
@article {pmid41840154, year = {2026}, author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A}, title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41840154}, issn = {1678-4405}, support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; CAR-21861//Universidad Aut&#xf3;noma de Yucat&#xe1;n/ ; }, mesh = {Animals ; Bees/microbiology/classification ; *Gastrointestinal Microbiome ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; Sympatry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.}, }
@article {pmid41840625, year = {2026}, author = {Zhang, Y and Zhang, Q and Luo, Y and Li, X and Zhao, R and Xu, Y and Zhang, S and Bai, X and Chen, H and Li, H and Hong, Y and Xie, Z}, title = {Bifidobacterium breve inhibits colorectal cancer via extracellular vesicles containing formate acetyltransferase.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {}, pmid = {41840625}, issn = {1477-3155}, support = {82574649//National Natural Science Foundation of China/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; }, mesh = {*Extracellular Vesicles/metabolism ; Animals ; Humans ; *Colorectal Neoplasms/pathology/microbiology/drug therapy/metabolism/therapy ; *Bifidobacterium breve/enzymology/metabolism ; Mice ; *Probiotics/pharmacology ; Apoptosis/drug effects ; *Acetyltransferases/metabolism ; Cell Line, Tumor ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. The gut microbiota exerts unique therapeutic advantages against CRC, and the probiotic Bifidobacterium breve (B. breve) has been extensively documented to suppress CRC initiation in murine models. Although the role of B. breve in CRC has been established, whether its extracellular vesicles (EVs), as key mediators of bacteria-host crosstalk, exert a functional impact remains undefined. Here, we aim to explore the therapeutic potential of B. breve-derived EVs (B.breEVs) and their active cargo, formate acetyltransferase (pflB), in CRC.<br><br>RESULTS: Integrative analysis of the curated database of human gut metagenomes cohort (GMrepo) database and an MC38 subcutaneous tumor model revealed a significant reduction of B. breve abundance in faecal samples from CRC patients and tumor-bearing mice. Administration of live B. breve or its cell-free supernatant markedly inhibited tumor growth, whereas pasteurized bacteria or GW4869-mediated EVs blockade abolished this effect, indicating that EVs are the critical effector entities. Isolated B.breEVs selectively accumulated within tumor tissue, directly triggered apoptosis of colorectal cancer cells, and elevated the proportion of IFN-&#x3b3;&#x207a; CD8&#x207a; cytotoxic T lymphocytes (CTLs) in tumor while concurrently ameliorating gut microbial structure and function. Mass-spectrometric profiling identified the pflB as an important active protein within B.breEVs. Recombinant pflB selectively inhibited MC38 cell viability in vitro and significantly reduced CRC burden in vivo. RNA sequencing of tumor issue demonstrated that pflB up-regulated granzyme B, perforin1 and CTL/NK-associated transcripts, and activated the intrinsic apoptotic pathway. Immuno-combination studies further revealed that pflB plus anti-PD1 therapy markedly increased the infiltration of CD8&#x207a; CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.<br><br>CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8&#x207a; CTL/NK anti-tumor immunity, directly induce mitochondrial apoptosis in malignant cells, and enhance the effects of immune checkpoint blockers to overcome drug resistance, offering a precision "probiotic-EVs-active protein" triadic intervention strategy for CRC.}, }
@article {pmid41840712, year = {2026}, author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z}, title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41840712}, issn = {2049-2618}, support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; }, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metabolome ; Age Factors ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Police ; Male ; Aging ; Metagenome ; Female ; Feces/microbiology ; }, abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.<br><br>RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (&#x3b3;-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.<br><br>CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.}, }
@article {pmid41840729, year = {2026}, author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T}, title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41840729}, issn = {2049-2618}, support = {JPMJND2206//Japan Science and Technology Agency/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Metadata ; Molecular Sequence Annotation ; *Microbiota/genetics ; *Databases, Genetic ; *Bacteria/classification/genetics ; Computational Biology/methods ; Biocuration ; }, abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.<br><br>RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were&#x2009;>95% completeness and&#x2009;<1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and&#x2009;~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.<br><br>CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.}, }
@article {pmid41841491, year = {2026}, author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A}, title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.}, journal = {Nucleic acids research}, volume = {54}, number = {5}, pages = {}, pmid = {41841491}, issn = {1362-4962}, support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette &amp; Yersin PhD Grant/ ; }, mesh = {*Metagenomics/methods ; Autoencoder ; Humans ; *Software ; Microbiota/genetics ; Generative Adversarial Networks ; Algorithms ; Generative Artificial Intelligence ; Metagenome ; }, abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.}, }
@article {pmid41841524, year = {2026}, author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y}, title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2645267}, pmid = {41841524}, issn = {1949-0984}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R03 OD039979/OD/NIH HHS/United States ; }, mesh = {Animals ; *Mucins/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; Cell Cycle Proteins/metabolism ; Cohesins ; Bacterial Proteins/metabolism/genetics ; *Eubacteriales/metabolism/genetics/isolation &amp; purification/classification ; Animals, Domestic/microbiology ; }, abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.}, }
@article {pmid41841712, year = {2026}, author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE}, title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.}, journal = {Biomeditsinskaia khimiia}, volume = {72}, number = {1}, pages = {62-74}, doi = {10.18097/PBMCR1644}, pmid = {41841712}, issn = {2310-6972}, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology ; *Microbiota ; *Vagina/microbiology ; Adult ; Case-Control Studies ; Lactobacillus/isolation &amp; purification/genetics ; Recurrence ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.}, }
@article {pmid41841737, year = {2026}, author = {Cruz, MC and Ruhal, R and Lavin, J and Bridwell, S and Maghboli Balasjin, N and Raasch, B and Melton, R and Mayer, BK and Marshall, CW and Hristova, K}, title = {Acinetobacter spp. with lower susceptibility to quaternary ammonium compounds enriched in microbial communities of frequently used sinks.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0196825}, pmid = {41841737}, issn = {1098-5336}, support = {W9132T-22-2-0001//U.S. Department of Defense/ ; }, mesh = {*Quaternary Ammonium Compounds/pharmacology ; *Acinetobacter/drug effects/genetics/isolation &amp; purification/physiology ; *Disinfectants/pharmacology ; Biofilms/drug effects ; *Microbiota/drug effects ; Seasons ; Drug Resistance, Bacterial ; }, abstract = {Sanitary environments that undergo frequent cleaning and disinfection may harbor microbial communities with potential health risks. While biofilms in healthcare settings are well studied, comparatively less is known about sink-drain microbiomes in public and educational buildings, where hundreds of people may interact with shared sink fixtures. This study characterized the spatial and temporal heterogeneity of sink-drain biofilm microbiomes in academic buildings. We sampled 16 sinks from two buildings (four floors each, with sinks closest and furthest to the bathroom entrance), which are cleaned daily with quaternary ammonium compound (QAC) disinfectants, during periods of low and high student traffic (during and after academic breaks, respectively) across winter, spring, and summer. We observed significant spatial and temporal variations in microbial assemblages. Individual sinks accounted for 43% (PERMANOVA, P < 0.0001) of the variation in microbial communities. Microbiomes in each building were dominated by two genera, which together accounted for 30% of the community composition: Acinetobacter and Enhydrobacter (also classified as Moraxella) in the newer building, and Sphingomonas and Mycobacterium in the older building. Acinetobacter abundance varied seasonally and showed higher relative abundance during periods of high traffic. Metagenomic analysis of selected sinks revealed a high prevalence of qac genes and metagenome-assembled genomes (MAGs) harboring antimicrobial resistance genes (ARGs), including A. parvus. Notably, 34%-53% of qac genes were co-localized on contigs associated with mobile genetic elements. These findings suggest that disinfected sink drains serve as persistent reservoirs of diverse microorganisms and potentially mobile resistance elements.IMPORTANCESink drains are recognized as environmental reservoirs for multidrug-resistant bacteria and have been linked to healthcare-associated outbreaks. In public and educational buildings, these microbiomes are shaped by frequent human activity, making them potential sources of exposure and contributors to the environmental dissemination of antibiotic resistance genes. Quaternary ammonium compound (QAC) disinfectants are widely used on surfaces; however, they can select for resistant taxa and co-select for antibiotic resistance. In this study, despite routine cleaning of sink surfaces with QACs, public restroom sink drains remain colonized by resilient biofilms, posing a potential risk to multiple users. Additionally, factors such as human traffic and seasonal variation may influence drain usage and microbial community composition. Elucidating how seasonal dynamics and human activity shape sink-drain biofilms is essential for understanding their role in the environmental transmission of antimicrobial resistance and informing mitigation strategies in nonclinical settings.}, }
@article {pmid41841761, year = {2026}, author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L}, title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0231325}, pmid = {41841761}, issn = {2165-0497}, support = {2021-I4201010-221801//Fondation Saint Luc/ ; HC01020F//Fonds De La Recherche Scientifique - FNRS/ ; ARC 25/30-151//Fonds Sp&#xe9;ciaux de Recherche/ ; WELBIO-CR-2022A-02P//Walloon excellence in life sciences and biotechnology/ ; EOS 40007505//Fonds De La Recherche Scientifique - FNRS/ ; FRC//Fondation Saint Luc/ ; 2021//Fonds Sp&#xe9;ciaux de Recherche/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Actinobacteria/isolation &amp; purification/genetics/classification ; *Corynebacterium/isolation &amp; purification/genetics/classification ; *COVID-19/microbiology/complications ; Longitudinal Studies ; Microbiota ; *Nasopharynx/microbiology ; *Post-Acute COVID-19 Syndrome/microbiology ; SARS-CoV-2/physiology ; }, abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.}, }
@article {pmid41842880, year = {2026}, author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G}, title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.}, journal = {Puerto Rico health sciences journal}, volume = {45}, number = {1}, pages = {3-10}, pmid = {41842880}, issn = {2373-6011}, support = {K23 NR020039/NR/NINR NIH HHS/United States ; P50 GM133807/GM/NIGMS NIH HHS/United States ; R21 CA288925/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Pilot Projects ; *Rectal Neoplasms/microbiology/therapy ; Cross-Sectional Studies ; *Diet/standards ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Aged ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.<br><br>METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.<br><br>RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.<br><br>CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.}, }
@article {pmid41843957, year = {2026}, author = {Zhu, L and Huang, C and Tian, Y and Zuo, W and Shan, G}, title = {Targeted enhancement of ammonia assimilation and microbial community metabolic synergy in chicken manure aerobic composting mediated by tricarboxylic acid cycle modulators.}, journal = {Waste management (New York, N.Y.)}, volume = {216}, number = {}, pages = {115471}, doi = {10.1016/j.wasman.2026.115471}, pmid = {41843957}, issn = {1879-2456}, mesh = {*Ammonia/metabolism ; Animals ; *Citric Acid Cycle ; *Composting/methods ; Chickens ; Nitrogen/metabolism ; Isocitrate Dehydrogenase/metabolism ; *Microbiota ; }, abstract = {Reducing nitrogen loss during composting is essential. To investigate the effects of directly modulating the tricarboxylic acid (TCA) cycle on microbial ammonia assimilation during composting, this study employed paired stable isotope labeling combined with metagenomic analysis to assess the role of the TCA cycle regulator citric acid (CA) in enhancing ammonia assimilation efficiency and regulating carbon-nitrogen metabolism within the microbial community. CA markedly reduced NH3 emissions (0.5-2265 ppm) and increased organic nitrogen retention (4.2%-17.7%), primarily through improved ammonia assimilation efficiency (0.06-0.22 mg N·kg[-1]·d[-1]) rather than weakened mineralization. Mechanistically, CA upregulated IDH1 (5.4%-18.5%) and increased IDH enzyme activity (0.35-0.66 IU/g), combined with NH3 uptake, balancing oxoglutarate and ammonium supply. Moreover, CA strengthened the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway (3.4%-23.4%) and enzyme activity (0.08-0.74 IU/g), particularly in the initial and thermophilic phases. In addition, CA induced an upregulation (14.8%-28.4%) of genes encoding succinyl-CoA synthetase, providing sufficient energy to support the ammonia assimilation process. Furthermore, CA enhanced microbial diversity and metabolic cooperation while reducing competition, thereby promoting NH3 assimilation and glutamate synthesis. Inorganic and amino acid metabolism emerged as critical cooperative processes within core microbial populations.}, }
@article {pmid41844673, year = {2026}, author = {Singh, NK and Garg, P and Kumari, S and Banda, L and Patel, AM and Sindhuja, RH and Bhandari, Y and Khan, NA and Tandon, S and Jain, R and Rajesh, T and Qureshi, A and Vodapalli, A and Singha, B and Esari, D and Annan, MO and Nagabandi, T and Panda, A and Kapley, A and Nandicoori, VK and Mishra, RK and Sowpati, DT and Siva, AB and Tallapaka, KB}, title = {Metagenomic profiling of antimicrobial resistance in wastewater from metropolitan cities of India.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41844673}, issn = {2041-1723}, support = {2021 HTH 018//Rockefeller Foundation/ ; }, mesh = {India ; *Wastewater/microbiology ; *Metagenomics/methods ; Cities ; *Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; }, abstract = {Wastewater-based surveillance has emerged as a powerful tool for monitoring microbial diversity, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). In this study, wastewater samples collected from March 2022 to March 2024 from 19 locations in four metropolitan cities of India were profiled using shotgun metagenomics. Taxonomic abundance and beta diversity analyses revealed significant differences in microbial community compositions, with city-specific clustering; suggesting distinct local environmental influences. However, such distinct clusters were not evident with the ARGs. A high proportion of potentially novel metagenome-assembled genomes (MAGs) (53-70%) were identified on reconstructing the microbial genomes from the metagenomic data. ARGs conferring resistance to antibiotics such as tetracyclines and beta-lactams showed higher association with MGEs in contrast to macrolide resistance genes. Microbial co-occurrence network analysis revealed a city-specific structure and higher contribution of ARGs from specific communities of microbes. These findings underscore the complex interplay between microbial diversity, ARG dissemination, and MGEs in wastewater environments, emphasizing the need for continued surveillance, for designing appropriate mitigation strategies towards curbing the spread of antimicrobial resistance.}, }
@article {pmid41845390, year = {2026}, author = {Sung, H and Hyun, DW and Whon, TW and Kim, PS and Kim, HS and Lee, JY and Lee, SY and Choi, JW and Yoo, JH and Jung, MJ and Yun, JH and Lee, JY and Tak, EJ and Jeong, YS and Kim, SW and Baeg, M and Eun, YG and Lee, YC and Bae, JW}, title = {Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.}, journal = {BMC biology}, volume = {24}, number = {1}, pages = {}, pmid = {41845390}, issn = {1741-7007}, support = {RS-2020-NR049315//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; }, mesh = {Humans ; *Microbiota ; Prognosis ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Mouth/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; }, abstract = {BACKGROUND: Head and neck cancer, predominantly squamous cell carcinoma, has emerged as a significant global health concern. Growing evidence has established a strong association between dysbiosis of the oral microbiota and both oral and systemic diseases. However, the association between the oral microbiota and head and neck cancer has not yet been fully described. This study aimed to investigate the distinct profiles of the oral microbiota in patients with head and neck cancer and their potential as diagnostic and prognostic biomarkers for head and neck cancer.<br><br>RESULTS: Comparative analyses revealed that compared to controls, the oral microbiota of patients with head and neck squamous cell carcinoma (HNSCC) exhibited an increased abundance of anaerobic, biofilm-forming bacteria, and potential pathogens. A machine learning model successfully differentiated HNSCC patients from controls with an area under the curve of 0.902. Key features of this model, such as Peptostreptococcus and Capnocytophaga, were found to be candidate biomarkers for HNSCC, with certain taxa, such as Abiotrophia, serving as prognostic indicators. Although pronounced differences in oral microbiota among HNSCC patients primarily resulted from inter-individual variations, distinct community types were identified, with the type dominated by Proteobacteria being associated with the lowest probability of survival.<br><br>CONCLUSIONS: Our findings indicate that the oral microbiota may predict HNSCC and may act as a therapeutic target to improve the prognosis of HNSCC. This investigation underscores the crucial role of oral microbial dysbiosis in the etiopathogenesis and clinical prognosis of HNSCC, making a case for further integrative metagenomic and clinical research.}, }
@article {pmid41845494, year = {2026}, author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P}, title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41845494}, issn = {2049-2618}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Animals ; Female ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; *Extracellular Vesicles/metabolism/genetics ; Cattle ; *MicroRNAs/genetics/metabolism ; Metabolome ; *Heat-Shock Response/physiology ; Milk/metabolism/chemistry ; Multiomics ; *Mammary Glands, Animal/metabolism/physiology ; Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fermentation ; }, abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.<br><br>RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.<br><br>CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.}, }
@article {pmid41845564, year = {2026}, author = {Zhang, Y and Wang, DD}, title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644682}, pmid = {41845564}, issn = {1949-0984}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; U54 AG089325/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; Multiomics ; Metagenomics ; *Gastrointestinal Microbiome/physiology ; Animals ; Diet ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.}, }
@article {pmid41846078, year = {2026}, author = {Li, Q and Yuan, J and Sun, Y and Wang, Y and Li, Y and Ni, A and Zong, Y and Yang, H and Li, X and Huang, X and Ma, H and Chen, J}, title = {Multi-omics analysis revealed that oxidative phosphorylation contributed to the heterosis for feed efficiency in laying chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106658}, pmid = {41846078}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/physiology/microbiology ; *Hybrid Vigor ; Female ; *Oxidative Phosphorylation ; Multiomics ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; }, abstract = {Improving feed efficiency has been the top priority in animal husbandry. Host genetics and gut microbiota synergistically regulate feed efficiency in laying chicken. However, the role of gut microbiota in heterosis for feed efficiency was rarely investigated. Herein, we used multi-omics data to elucidate the regulatory mechanisms of heterosis for feed efficiency in White Leghorn, Beijing-You chicken, and their reciprocal crosses. We observed divergent heterosis for residual feed intake (RFI) between two crossbreds during the laying period from 43 to 46 weeks of age. Metagenomic analysis showed the significant difference in richness and function of cecal microbiota among crossbreds and purebreds (P < 0.05), and the differential functional pathways were mainly related to metabolism. Most microorganisms (>90 %) were non-additive in crossbreds. Weighted gene co-expression network analysis and LDA effect size analysis revealed seven non-additive RFI-associated microorganisms, such as Leyella, Paraprevotella, and Zongyangia. We also identified 544 RFI-associted metabolites, which were mainly overrepresented in glycerophospholipid metabolism and oxidative phosphorylation. Integrative analysis further revealed the interactions among non-additive microorganisms, genes, and metabolites. Specifically, the non-additive expression of Zongyangia was positively correlated with UQCR10 and Ubiquinone-1 levels within the oxidative phosphorylation pathway. These factors were negatively correlated with RFI, contributing to the RFI heterosis. Our study highlighted that key microorganisms, genes, and metabolites involved in oxidative phosphorylation interact to regulate negative heterosis for RFI in laying hens. The findings established a theoretical and practical foundation for further exploring the molecular mechanisms that drive heterosis for feed efficiency.}, }
@article {pmid41846103, year = {2026}, author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J}, title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1872}, number = {5}, pages = {168216}, doi = {10.1016/j.bbadis.2026.168216}, pmid = {41846103}, issn = {1879-260X}, mesh = {Animals ; *Lacticaseibacillus rhamnosus ; Mice ; *Probiotics/pharmacology ; *Liver/metabolism/pathology/drug effects ; Mice, Knockout ; Disease Models, Animal ; *Liver Cirrhosis, Biliary/pathology/microbiology/genetics/drug therapy/metabolism/therapy ; *Transcription Factors/genetics/deficiency ; *Ribonucleases/genetics/deficiency ; *Gastrointestinal Microbiome/drug effects ; Bile Acids and Salts/blood/metabolism ; }, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.<br><br>METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15&#xa0;mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10&#xa0;mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.<br><br>RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.<br><br>CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.}, }
@article {pmid41850677, year = {2026}, author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J}, title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {20}, number = {7}, pages = {101770}, pmid = {41850677}, issn = {2352-345X}, mesh = {Animals ; *Neutrophils/metabolism/immunology/drug effects ; *Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism ; *Propionates/metabolism/pharmacology ; Mice ; Mice, Knockout ; *Gastrointestinal Microbiome/immunology ; Transforming Growth Factor beta1/metabolism ; *Liver/pathology/immunology/metabolism ; Fecal Microbiota Transplantation ; Copper-Transporting ATPases/genetics ; Disease Models, Animal ; Male ; Humans ; Hydroxamic Acids ; }, abstract = {BACKGROUND &amp; AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.<br><br>METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-&#x3b2;1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.<br><br>RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-&#x3b2;1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-&#x3b2;1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-&#x3b2;1.<br><br>CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-&#x3b2;1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.}, }
@article {pmid41851530, year = {2026}, author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E}, title = {Advances and opportunities in measuring dietary intake: from omics to AI.}, journal = {Nature metabolism}, volume = {8}, number = {4}, pages = {795-809}, pmid = {41851530}, issn = {2522-5812}, mesh = {Humans ; *Artificial Intelligence ; Proteomics ; *Eating ; *Diet ; Gastrointestinal Microbiome ; Nutrition Assessment ; }, abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.}, }
@article {pmid41852664, year = {2026}, author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H}, title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748638}, pmid = {41852664}, issn = {2235-2988}, mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Urine/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics ; Middle Aged ; Aged ; Microscopy, Electron, Transmission ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; }, abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.}, }
@article {pmid41852665, year = {2026}, author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L}, title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1728182}, pmid = {41852665}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Urologic Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; Male ; *Urinary Tract/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Urine/microbiology ; }, abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.<br><br>METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.<br><br>RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.<br><br>CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.}, }
@article {pmid41853994, year = {2026}, author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C}, title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70245}, pmid = {41853994}, issn = {1758-2229}, support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; }, mesh = {*Ecosystem ; *Fresh Water/microbiology ; Metagenome ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; *Lakes/microbiology ; Transcriptome ; Water Microbiology ; }, abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.}, }
@article {pmid41854352, year = {2026}, author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J}, title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.}, journal = {Lupus}, volume = {35}, number = {7}, pages = {667-677}, doi = {10.1177/09612033261432163}, pmid = {41854352}, issn = {1477-0962}, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Pilot Projects ; Female ; India ; Adult ; Saliva/microbiology ; Male ; Killer Cells, Natural/immunology ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Middle Aged ; *Gastrointestinal Microbiome/immunology ; Case-Control Studies ; Feces/microbiology ; *Microbiota ; Young Adult ; CD8-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/immunology ; }, abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.}, }
@article {pmid41854683, year = {2026}, author = {Wang, J and Shi, Y and Jia, Y and Peng, J}, title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71679}, doi = {10.1096/fj.202503650RRR}, pmid = {41854683}, issn = {1530-6860}, support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Pancreatitis/drug therapy/metabolism/microbiology/chemically induced/blood ; Mice ; *Flavonoids/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Metabolomics/methods ; Mice, Inbred C57BL ; Metagenomics/methods ; Ceruletide/toxicity ; *Metabolome/drug effects ; Acute Disease ; Pancreas/drug effects/metabolism ; Fecal Microbiota Transplantation ; }, abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.}, }
@article {pmid41855987, year = {2026}, author = {Demaria, F and Suleiman, M and Bargiela, R and Ferrer, M and Hernández, SB and Núñez, AE and Petchey, OL and Corvini, PF and Junier, P}, title = {Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141801}, doi = {10.1016/j.jhazmat.2026.141801}, pmid = {41855987}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; Pharmaceutical Preparations/metabolism ; *Bacteria/metabolism/genetics ; Microbial Consortia ; Waste Disposal, Fluid ; Adaptation, Physiological ; }, abstract = {Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 µg/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation.}, }
@article {pmid41856620, year = {2026}, author = {Lan, HY and Yang, XY and Zhang, YH and Lyu, YW and Bao, LL and Yu, YY}, title = {[Study on the characteristics and differences of intestinal microbiota in children with allergic diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {3}, pages = {346-358}, doi = {10.3760/cma.j.cn112150-20251015-00988}, pmid = {41856620}, issn = {0253-9624}, support = {GSWS2024031//Research Project of the Gusu Talent Program of Suzhou City/ ; }, mesh = {Humans ; Child, Preschool ; *Gastrointestinal Microbiome ; Case-Control Studies ; Infant ; Child ; Male ; Female ; *Hypersensitivity/microbiology ; Dermatitis, Atopic/microbiology ; Feces/microbiology ; Food Hypersensitivity/microbiology ; Rhinitis, Allergic/microbiology ; }, abstract = {Objective: Based on metagenomic sequencing technology, this study aims to investigate the characteristics and differences of the intestinal microbiota in children with different allergic diseases, providing a theoretical basis for the early prevention and treatment of allergic diseases. Methods: The study adopted a case-control research method. 214 children with allergic diseases (Group A) who visited the Suzhou Hospital Affiliated to Nanjing Medical University from March 2023 to June 2024 were selected. According to age matching, 93 healthy controls (Group H) who participated in physical examinations during the same period were also included. Fecal samples and clinical data of the subjects were collected. The subjects were grouped according to age and type of allergic disease, and the fecal samples of the subjects were analyzed using metagenomic sequencing technology to study the characteristics and differences of the gut microbiota in different groups. The subjects were divided into 0-1 year old group (A1 and H1), 1-3 year old group (A2 and H2), and≥3 year old group (A3). According to the disease type, A1 was divided into food allergy without atopic dermatitis (F1) group and food allergy with atopic dermatitis (F2) group, A2 was divided into atopic dermatitis (AD) group, allergic rhinitis (AR) group and AD with AR group. A3 was divided into AR group, AD with AR group and AR with asthma (AS) group. Results: With age increase, the number of species annotated at the genus level in the microbiota showed a gradually increasing trend. There were significant differences in the diversity and composition of the intestinal microbiota between the allergic disease group and the control group. In the diversity analysis, it was found that there were differences in species richness between group A and group H (chao index, group A: 955.2±226.1, group H: 762.3±260.9, W=5 664, P<0.000 1), and significant differences in β-diversity between group A2 and group H2, and between group A3 and group AD-AR and group AR-AS (R=0.045, P=0.018, R=0.044, P=0.011). At the species level, the allergic disease group was mainly enriched with Bifidobacterium, Enterococcus, Escherichia, Mediterraneibacter and Blautia, while the control group was mainly enriched with Bifidobacterium. By age group analysis, the relative abundance of Mediterraneibacter and Blautia in group A1 (0-1 years old) was significantly higher than that in group H1 (Mediterraneibacter: A1: 5.2±9.4, H1: 0.9±2.1, W=718, P=0.000 8; Blautia: A1: 3.5±6.0, H1: 1.3±3.2, W=701, P= 0.000 5). In group A2 (1-3 years old), the relative abundance of Bacteroides and Faecalibacterium was significantly higher than that in group H2 (Bacteroides: A2: 5.6±8.7, H2: 3.1±5.8, W=456, P=0.020 8; Faecalibacterium: A2: 2.6±2.8, H2: 1.2±1.9, W=395, P=0.002 8). In the clinical subtype analysis, the relative abundance of Blautia and Fusicatenibacter was significantly increased in AR children (Blautia: AD: 8.0±7.9, AD-AR: 13.5±8.3, AR: 20.2±7.8, H=9.300 8, P=0.009 6; Fusicatenibacter: AD: 0.5±0.9, AD-AR: 1.2±1.6, AR: 2.2±2.4, H=7.878 3, P=0.019 5), and the relative abundance of Escherichia was significantly increased in AD children (AD: 3.3±4.3, AD-AR: 1.8±4.5, AR: 0.8±2.0, H=9.476 6, P=0.008 8). In group A3 (≥3 years old), Mediterraneibacter was significantly enriched (A3: 6.3±6.9, H3: 2.9±1.9, W=571, P=0.039 7), and the relative abundance of Anaerostipes was significantly increased in AR children (AD-AR: 2.9±2.9, AR: 5.2±4.9, AR-AS: 3.2±3.5, H=7.269, P=0.026 4). Conclusion: In infancy, the species of intestinal flora gradually increase with age. There are significant differences in the composition of intestinal flora among children with different allergic diseases. Bifidobacterium, as the main dominant species in infancy, has a lower relative abundance in the allergic disease group at different ages than in the healthy control group, suggesting that the lack of Bifidobacterium may be related to the occurrence and development of allergic diseases.}, }
@article {pmid41857857, year = {2026}, author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G}, title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e115290}, pmid = {41857857}, issn = {2044-6055}, mesh = {Humans ; *Conjunctivitis, Allergic/diet therapy/immunology ; Young Adult ; Adult ; *Gastrointestinal Microbiome ; Quality of Life ; Randomized Controlled Trials as Topic ; Adolescent ; *Brassica ; Female ; Biomarkers/blood ; Male ; *Fermented Foods ; }, abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.<br><br>METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.<br><br>ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charit&#xe9;-Universit&#xe4;tsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.<br><br>TRIAL REGISTRATION NUMBER: DRKS00036475.}, }
@article {pmid41860568, year = {2026}, author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J}, title = {Klebsiella enrichment is associated with disease severity in ulcerative colitis.}, journal = {Journal of applied microbiology}, volume = {137}, number = {4}, pages = {}, doi = {10.1093/jambio/lxag079}, pmid = {41860568}, issn = {1365-2672}, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; Feces/microbiology ; Prospective Studies ; *Klebsiella/isolation &amp; purification/genetics/physiology ; Female ; Severity of Illness Index ; Male ; Adult ; Middle Aged ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; }, abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.<br><br>METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (&#x2265;18 years) from the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.<br><br>RESULTS: Fecal microbiota &#x3b1;-diversity was significantly lower in UC vs. controls (Shannon index 4.15&#xa0;vs. 5.44, P&#xa0;=&#xa0;0.005); mucosal diversity showed no difference (P&#xa0;=&#xa0;0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in &#x3b1;-diversity (fecal: 3.99&#xa0;vs. 4.37, P&#xa0;=&#xa0;0.14; mucosal: 3.40&#xa0;vs. 3.72, P&#xa0;=&#xa0;0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g. allopurinol, histidine), enriching tyrosine, and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g. quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.<br><br>CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.}, }
@article {pmid41860897, year = {2026}, author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S}, title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {3}, pages = {e0014118}, pmid = {41860897}, issn = {1935-2735}, mesh = {Humans ; Metagenomics ; *Microbiota/genetics ; *Noma/microbiology ; *Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Child ; Female ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; *Mouth/microbiology ; Dysbiosis/microbiology ; Treponema/genetics/isolation &amp; purification ; Shotgun Sequencing ; Child, Preschool ; }, abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.}, }
@article {pmid41861238, year = {2026}, author = {Loop Yao, M and Dai, Y and Zhang, W}, title = {Natural Products from the Oral Microbiome.}, journal = {Annual review of biochemistry}, volume = {95}, number = {1}, pages = {569-593}, doi = {10.1146/annurev-biochem-051024-050248}, pmid = {41861238}, issn = {1545-4509}, mesh = {Humans ; *Biological Products/metabolism/chemistry ; *Microbiota ; *Mouth/microbiology ; Peptide Synthases/metabolism/genetics ; Polyketide Synthases/metabolism/genetics ; Multigene Family ; *Bacteria/metabolism/genetics ; }, abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.}, }
@article {pmid41861946, year = {2026}, author = {Wang, ST and Li, L and Yang, Q and Zhang, GF}, title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124314}, doi = {10.1016/j.envres.2026.124314}, pmid = {41861946}, issn = {1096-0953}, mesh = {*Sulfur/metabolism ; *Microbiota ; *Nitrogen Cycle ; *Coral Reefs ; Bacteria/genetics/metabolism ; China ; Archaea/genetics/metabolism ; *Nitrogen/metabolism ; Seawater/microbiology ; }, abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.}, }
@article {pmid41862052, year = {2026}, author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P}, title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.}, journal = {Life sciences}, volume = {393}, number = {}, pages = {124336}, doi = {10.1016/j.lfs.2026.124336}, pmid = {41862052}, issn = {1879-0631}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/microbiology/genetics ; Male ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Renal Insufficiency, Chronic/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Feces/microbiology ; Adult ; Real-Time Polymerase Chain Reaction/methods ; Diabetic Nephropathies/microbiology ; Aged ; }, abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.<br><br>METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.<br><br>KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p&#xa0;<&#xa0;0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.<br><br>SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.}, }
@article {pmid41862737, year = {2026}, author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY}, title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41862737}, issn = {1420-9071}, support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; }, mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Humans ; *Tryptophan/metabolism ; *Wnt Signaling Pathway ; Rats ; Fibrosis/metabolism ; Male ; Mice ; beta Catenin/metabolism ; *Kidney/pathology/metabolism ; Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; *Kidney Diseases/metabolism/pathology ; Female ; Middle Aged ; }, abstract = {Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.}, }
@article {pmid41862790, year = {2026}, author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H}, title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41862790}, issn = {1471-2180}, support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; *Ursidae/microbiology ; Seasons ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Feces/microbiology ; *Diet/veterinary ; Plant Leaves ; Metagenomics ; }, abstract = {The nutritional changes of giant pandas (Ailuropoda melanoleuca) in response to the seasonal variations from bamboo shoots (rich in proteins) to fibrous leaves trigger significant alterations in the structure and functions of the gut microbiome. However, the effect these dietary changes have on the gut resistome, especially in older adults, is not well characterized. In this study, shotgun metagenomic sequencing and quantitative PCR (qPCR) were used to investigate the microbial composition, functional potential, and profiles of antibiotic- and metal-resistance genes (ARG and MRG) in feces of adult (n = 11) and geriatric captive pandas (n = 11) that were fed on bamboo shoots or leaves. The microbes varied considerably among diet and age groups, with diet becoming the main source of taxonomic and functional disparity (P < 0.05). Shoot-fed pandas exhibited higher alpha diversity at the genus level and distinct clustering in principal coordinate analyses, whereas leaf-fed groups showed enrichment of taxa associated with fiber degradation and stress tolerance (P < 0.05). Functional annotation of bacterial responses to diet showed changes in carbohydrate processing pathway, carbohydrate transport, and cellular process pathways by changes in the KEGG pathway (P < 0.05). Changes depending on diet were also identified with significant changes in carbohydrate-active enzyme (CAZy) family during changes in the composition of the bamboo parts. Metagenomics and qPCR revealed that several antibiotic resistance genes, such as aac(3)-Xa, bcrA, tet44, sul2 and macB, were highly interacting between diet and age and the most diverse resistome was found in geriatric pandas (P < 0.05). Correlation analysis demonstrated that there is a positive co-occurrence pattern of Enterobacteriaceae and several ARGs. Collectively, our findings demonstrate that seasonal dietary shifts and host aging jointly restructure the gut microbiome and resistome of giant pandas, suggesting diet-mediated modulation of microbial adaptation, resistance dissemination, and ecological resilience in captivity.}, }
@article {pmid41863981, year = {2026}, author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C}, title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106706}, pmid = {41863981}, issn = {1525-3171}, mesh = {Animals ; *Polyphenols/metabolism/administration &amp; dosage ; *Antioxidants/metabolism ; Male ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Tea/chemistry ; *Geese/microbiology/physiology/metabolism ; Cecum/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Random Allocation ; *Intestines/drug effects/physiology/anatomy &amp; histology ; *Camellia sinensis/chemistry ; }, abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.}, }
@article {pmid41864063, year = {2026}, author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J}, title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106224}, pmid = {41864063}, issn = {2352-3964}, mesh = {Humans ; *Parkinson Disease/blood/microbiology/diagnosis ; Disease Progression ; Cross-Sectional Studies ; Female ; Aged ; Male ; Whole Genome Sequencing ; Biomarkers ; *Microbiota ; Middle Aged ; Bacteria/genetics/classification ; Metagenomics/methods ; }, abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.<br><br>METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.<br><br>FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.<br><br>INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.<br><br>FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.}, }
@article {pmid41865546, year = {2026}, author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C}, title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129432}, doi = {10.1016/j.jenvman.2026.129432}, pmid = {41865546}, issn = {1095-8630}, mesh = {*Fertilizers ; Nitrogen ; Soil/chemistry ; *Microbiota ; *Ammonia ; *Soil Microbiology ; *Nitrous Oxide ; Animals ; }, abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.}, }
@article {pmid41865575, year = {2026}, author = {Xie, H and Zhou, J and Shi, Y}, title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141830}, doi = {10.1016/j.jhazmat.2026.141830}, pmid = {41865575}, issn = {1873-3336}, mesh = {*Petroleum/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Saccharomyces cerevisiae/metabolism/genetics ; *Soil Microbiology ; *Hydrocarbons/metabolism ; Microbial Consortia ; }, abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.}, }
@article {pmid41865866, year = {2026}, author = {Wang, Y and Wang, D and Wang, H}, title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {316}, number = {}, pages = {111996}, doi = {10.1016/j.cbpa.2026.111996}, pmid = {41865866}, issn = {1531-4332}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Larva/microbiology/metabolism ; *Ranidae/microbiology/metabolism/growth &amp; development ; Metagenomics ; Sympatry ; }, abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.}, }
@article {pmid41866358, year = {2026}, author = {Deepthi, M and Vadakkadath Meethal, K}, title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41866358}, issn = {2045-2322}, mesh = {Animals ; *Aedes/microbiology/drug effects ; Larva/microbiology/drug effects ; Recombinant Proteins/pharmacology/genetics ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; Insecticides/pharmacology ; *Antimicrobial Peptides/genetics/pharmacology ; Mosquito Control/methods ; Oligopeptides ; }, abstract = {Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).}, }
@article {pmid41866421, year = {2026}, author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R}, title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866421}, issn = {1573-0972}, mesh = {*Rhizosphere ; India ; *Soil Microbiology ; *Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Piper/microbiology ; Phylogeny ; Soil/chemistry ; Plants, Medicinal/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Proteobacteria/genetics ; }, abstract = {The rhizosphere of medicinal plants harbors complex microbial communities that plays a key role in nutrient cycling, plant growth, and environmental adaptation. Piper longum L., an important medicinal plant, remains poorly explored with respect to its rhizospheric microbiome. In this study, rhizospheric soil samples of P. longum were collected at the spike stage from the Herbal Garden of Dayalbagh Educational Institute, Agra, India, and analyzed using metagenomic approach. Soil physicochemical analysis revealed a neutral to slightly alkaline pH with moderate nutrient availability, indicating favorable conditions for microbial activity. High-throughput Illumina sequencing generated ~ 19.94 million paired-end reads (~ 5.92 Gb), which were assembled into 97,432 scaffolds (52.26 Mb total length), and 45,876 protein-coding genes were predicted. Taxonomic profiling revealed dominance of Proteobacteria (42%), followed by Actinobacteria (13.9%), Thaumarchaeota (13.16%), Chloroflexi (8.21%), and Acidobacteria (7.28%). At the genus level, Nitrososphaera was the most abundant (23.58%), with Candidatus Nitrososphaera gargensis as the predominant species (11.21%), indicating an active microbial community of ammonia-oxidizing archaea involved in nitrogen fixation. Functional annotation using COG, KEGG, Pfam, GO, and FIGfams databases revealed enrichment of genes associated with amino acid transport and metabolism, carbohydrate metabolism, energy production, and environmental adaptation. Overall, this study provides the first metagenomic baseline of the P. longum rhizosphere microbiome and highlights its potential role in nutrient cycling and sustainable cultivation.}, }
@article {pmid41869825, year = {2026}, author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G}, title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {33}, number = {5-6}, pages = {643-659}, doi = {10.1177/15578666261428562}, pmid = {41869825}, issn = {1557-8666}, mesh = {*RNA Editing/genetics ; Humans ; *Computational Biology/methods ; *Microbiota/genetics ; Escherichia coli/genetics ; Genome, Bacterial ; *RNA, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.}, }
@article {pmid41869887, year = {2026}, author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J}, title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {29}, pages = {e20332}, pmid = {41869887}, issn = {2198-3844}, support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Mice ; *Colorectal Neoplasms/immunology/microbiology ; *Bacterial Proteins/immunology/genetics/metabolism ; *Cytokines/immunology/genetics/metabolism ; *Immunologic Factors/immunology ; Escherichia coli/genetics ; }, abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.}, }
@article {pmid41870088, year = {2026}, author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S}, title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0010426}, pmid = {41870088}, issn = {2379-5077}, support = {NRF-2019R1G1A1002215//Ministry of Science and ICT, South Korea/ ; NRF-2019R1G1A1002215, NRF-2023R1A2C2002674//Ministry of Science and ICT, South Korea/ ; 2023-ER2105-02//Korea National Institute of Health/ ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification ; Cyclosporine/therapeutic use/administration &amp; dosage ; *Dry Eye Syndromes/microbiology/drug therapy ; *Eye/microbiology ; Meibomian Gland Dysfunction/microbiology/drug therapy ; Meibomian Glands/microbiology ; *Microbial Interactions ; *Microbiota/drug effects ; Tears/microbiology ; }, abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.}, }
@article {pmid41871943, year = {2026}, author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB}, title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.}, journal = {Gut}, volume = {75}, number = {9}, pages = {1711-1725}, pmid = {41871943}, issn = {1468-3288}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; IK6 BX004477/BX/BLRD VA/United States ; P40 OD010995/OD/NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; I01 BX005730/BX/BLRD VA/United States ; IS1 BX004777/BX/BLRD VA/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; U01 CA280829/CA/NCI NIH HHS/United States ; R01 DK139587/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice ; *Cholangitis, Sclerosing/complications/microbiology ; Mice, Knockout ; *Dysbiosis/complications/microbiology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; *Colitis-Associated Neoplasms/microbiology/metabolism/etiology ; *Colorectal Neoplasms/microbiology/etiology ; *Colitis, Ulcerative/microbiology/complications ; Male ; Mice, Inbred C57BL ; Colitis/microbiology ; Humans ; }, abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.<br><br>OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.<br><br>DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] &#xd7; interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.<br><br>RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7&#x3b1;-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.<br><br>CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.}, }
@article {pmid41872600, year = {2026}, author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E}, title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.}, journal = {Nature medicine}, volume = {32}, number = {5}, pages = {1884-1894}, pmid = {41872600}, issn = {1546-170X}, mesh = {Humans ; *Diet ; Phenotype ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; Metagenomics ; Male ; Streptococcus thermophilus ; Yogurt/microbiology ; *Precision Medicine ; Adult ; Coffee/microbiology ; Milk/microbiology ; Bifidobacterium/genetics ; }, abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.}, }
@article {pmid41874416, year = {2026}, author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI}, title = {The role of the gut microbiome in nicotine withdrawal and dependence.}, journal = {Nicotine &amp; tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {28}, number = {9}, pages = {1573-1579}, pmid = {41874416}, issn = {1469-994X}, support = {P30DA033934/DA/NIDA NIH HHS/United States ; P30 CA016059//NIH-NCI Cancer Center Support/ ; }, mesh = {Animals ; *Substance Withdrawal Syndrome/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Nicotine/adverse effects/administration &amp; dosage ; Fecal Microbiota Transplantation ; Male ; *Tobacco Use Disorder/microbiology ; Mice, Inbred C57BL ; Feces/microbiology ; }, abstract = {INTRODUCTION: Smoking is considered a global pandemic, with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.<br><br>METHODS: We used osmotic minipumps (MPs) as an application of chronic nicotine for 15&#xa0;days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24&#xa0;h and 1&#xa0;week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.<br><br>RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of MPs. The shotgun metagenomic results of the fecal samples from 24&#xa0;h after MP removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine-treated and its homologous FMT treatment.<br><br>CONCLUSIONS: Our results indicate that under our experimental conditions, fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.<br><br>IMPLICATIONS: This report shows for the first time that the gut microbiome may modulate nicotine withdrawal intensity in mice. Homologous fecal material transplants (FMT) prevented nicotine-induced gut microbiome dysbiosis and consequently reduced withdrawal severity in mice. These results may have important implications in the management of smoking cessation.}, }
@article {pmid41874457, year = {2026}, author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP}, title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {330}, number = {5}, pages = {E606-E626}, pmid = {41874457}, issn = {1522-1555}, support = {W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; T32 DK137525/DK/NIDDK NIH HHS/United States ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; }, mesh = {Adult ; Humans ; Male ; Young Adult ; *Androgens/administration &amp; dosage ; *Energy Intake/drug effects ; *Energy Metabolism/drug effects ; Fatty Acids, Volatile/metabolism ; Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Testosterone/administration &amp; dosage/analogs &amp; derivatives/analogs &amp; derivatives ; }, abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically active men were randomized to receive 200 mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ∼2,000 kcal/day SED. Multiomic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting the effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.NEW &amp; NOTEWORTHY This study is the first to demonstrate that testosterone administration partially preserves gut microbiota composition and metabolic function during severe energy deficit in healthy men. Using a multiomic approach, we show that testosterone modulates short-chain fatty acid-producing taxa and microbial pathways linked to host energy metabolism. These findings reveal a novel role for androgens in shaping host-microbiome interactions during catabolic stress and may inform strategies to maintain metabolic resilience.}, }
@article {pmid41874663, year = {2026}, author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C}, title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41874663}, issn = {1432-184X}, support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; }, mesh = {*Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Nitrogen/metabolism ; *Aquaculture ; RNA, Ribosomal, 16S/genetics ; Denitrification ; Nitrification ; Biofilms ; Metagenomics ; *Microbiota ; }, abstract = {The composition and function of bacterial communities in recirculating aquaculture systems (RAS) vary significantly across operational phases and treatment units. Yet the causal links between these bacterial dynamics and nitrogen removal mechanisms remain obscure. In this study, we demonstrated dynamic shifts in bacterial community composition and nitrogen removal function within RAS throughout cultivation and in each unit, by water quality monitoring, 16 S rRNA gene sequencing, metagenomics, 15N isotope tracing and kinetic modeling. Bacterial community composition shifted temporally, marked by a decline in r-strategists and increases in both α- and β-diversity from the start-up to the culture phase, a succession primarily driven by salinity, total dissolved solids, and conductivity. Ecologically, this transition is indicative of a shift in dominant life-history strategies, from an r-selected pioneer community to a K-selected, more stable and resilient community. Denitrification, anammox, and nitrification dominated nitrogen removal pathways, collectively representing 45.2% of the nitrogen-cycling functional genes. In addition, there was significant spatiotemporal heterogeneity in bacterial nitrogen removal. Spatially, aquatic bacteria exhibited higher denitrification activity, while biofilm-attached anammox bacteria of K-strategist demonstrated disproportionately high metabolic activity relative to their low abundance; this was probably regulated by biofilm-associated quorum sensing. Temporally, the ammonia-oxidizing bacteria (AOB) enabled an initial rapid ammonia degradation, whereas nitrite-oxidizing bacteria (NOB) and denitrifiers dominated later-stage decreases in nitrite and nitrate, indicating that the bacterial nitrogen removal function responded to nutrient dynamics. This study demonstrated the coupling mechanisms between ecological adaptation strategies of bacterial communities and nitrogen removal function in RAS, thereby establishing a basis for precision management technologies targeting functional bacteria.}, }
@article {pmid41874734, year = {2026}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM}, title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41874734}, issn = {1573-0972}, mesh = {Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Plant Roots/microbiology ; *Calotropis/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Brazil ; *Extremophiles ; Soil/chemistry ; Phylogeny ; Ecosystem ; DNA, Bacterial/genetics ; }, abstract = {This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.}, }
@article {pmid41875555, year = {2026}, author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S}, title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120059}, doi = {10.1016/j.ecoenv.2026.120059}, pmid = {41875555}, issn = {1090-2414}, mesh = {*Wastewater/microbiology/chemistry ; *Fluorocarbons/analysis ; *Water Pollutants, Chemical/analysis ; *Disinfection ; Bacteria/genetics ; *Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Water Purification/methods ; China ; Environmental Monitoring ; Caprylates/analysis ; }, abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.}, }
@article {pmid41875745, year = {2026}, author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J}, title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.}, journal = {Water research}, volume = {297}, number = {}, pages = {125768}, doi = {10.1016/j.watres.2026.125768}, pmid = {41875745}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Sulfur/metabolism ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Oxidation-Reduction ; Anaerobic Ammonia Oxidation ; *Microbial Consortia ; }, abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.}, }
@article {pmid41876513, year = {2026}, author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE}, title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41876513}, issn = {2041-1723}, support = {1026-00159B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Methane/metabolism ; Cytochromes/metabolism/genetics ; Phylogeny ; Methanosarcina/genetics/metabolism ; Genome, Bacterial ; *Microbial Consortia/genetics ; Electric Conductivity ; }, abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.}, }
@article {pmid41878266, year = {2026}, author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B}, title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1598786}, pmid = {41878266}, issn = {2235-2988}, mesh = {Humans ; *Infant, Premature ; *Virome ; *Metagenomics/methods ; Infant, Newborn ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Bacteriophages/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Enterococcus faecalis ; Staphylococcus epidermidis ; Metagenome ; Gastrointestinal Tract/microbiology/virology ; Klebsiella pneumoniae/isolation &amp; purification ; Feces/microbiology/virology ; }, abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.<br><br>METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.<br><br>RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).<br><br>DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.}, }
@article {pmid41878990, year = {2026}, author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B}, title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {32}, pages = {e17444}, pmid = {41878990}, issn = {2198-3844}, support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; }, mesh = {Animals ; China/epidemiology ; *Herbivory ; Humans ; *Animals, Domestic/virology ; *Virome/genetics ; *Viruses/genetics/classification ; }, abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.}, }
@article {pmid41880538, year = {2026}, author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, &#xc1;}, title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.}, journal = {Medical mycology}, volume = {64}, number = {4}, pages = {}, pmid = {41880538}, issn = {1460-2709}, support = {2019-2020//Programmatic Health Sciences Call/ ; //Universidad de Antioquia/ ; }, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology ; *Vagina/microbiology ; Adult ; *Microbiota ; Middle Aged ; Colombia ; Young Adult ; Recurrence ; Lactobacillus/isolation &amp; purification ; Dysbiosis/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, G. swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed a greater abundance of L. crispatus and L. gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system, fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.}, }
@article {pmid41881444, year = {2026}, author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML}, title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, pmid = {41881444}, issn = {2052-4439}, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; Bronchoscopy ; *Anti-Bacterial Agents/therapeutic use ; Aged ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Drug Resistance, Microbial/genetics ; *Lung Diseases/microbiology/drug therapy ; Idiopathic Pulmonary Fibrosis/microbiology ; Asthma/microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.<br><br>METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.<br><br>RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95%&#x2009;CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics &#x2264;3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).<br><br>CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.}, }
@article {pmid41881873, year = {2026}, author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N}, title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120044}, doi = {10.1016/j.ecoenv.2026.120044}, pmid = {41881873}, issn = {1090-2414}, mesh = {Humans ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Schools ; China ; *Genes, Bacterial ; Nasal Cavity/microbiology ; Hand/microbiology ; Bacteria/genetics ; }, abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.}, }
@article {pmid41882035, year = {2026}, author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK}, title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41882035}, issn = {2045-2322}, support = {2020//Centre for Agricultural Bioinformatics/ ; }, mesh = {*Triticum/microbiology/genetics/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Genotype ; *Microbiota/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification ; Metagenomics ; Phylogeny ; }, abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.}, }
@article {pmid41882401, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M}, title = {Microbial Omics.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {333-366}, pmid = {41882401}, issn = {0079-6484}, mesh = {*Metabolomics/methods ; Multiomics ; *Proteomics/methods ; *Genomics/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Transcriptome ; }, abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.}, }
@article {pmid41882608, year = {2026}, author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J}, title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41882608}, issn = {1472-6831}, mesh = {Humans ; Adolescent ; *Dental Caries/microbiology/etiology ; Risk Assessment/methods ; Female ; Male ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota ; Dental Plaque/microbiology ; }, abstract = {OBJECTIVE: This study aimed to develop and initially validate a caries risk assessment scale for adolescents undergoing fixed orthodontic treatment, and to exploratorily analyze the potential association between oral microbiota and caries risk levels. METHODS: Clinical examinations and questionnaires were conducted on 210 adolescent orthodontic patients before orthodontic treatment and at 1st, 3rd, and 6th month, and the caries risk assessment scale was constructed according to the correlation statistics. Six patients in low-risk group and middle-risk group were randomly selected. Dental plaque samples were collected before orthodontic treatment and 1st month, respectively. Bioinformatics analyses were performed to explore differences in microbial community composition and function. RESULTS: The caries risk assessment scale involves 7 factors, such as simplified debris index (DI-S), brushing time, and frequency of sugar intake. Differences in scale scores before and during orthodontic treatment at the 1st, 3rd, and 6th months correlated with the presence of caries at the corresponding orthodontic stages (P < 0.001). Differences in scores at 1st month correlated with the presence or absence of caries at 3rd and 6th month (P < 0.05). The differences in scores at 3rd month correlated with the caries status at 6th month (P < 0.001). The caries risk related Glycan biosynthesis and metabolism pathways were positively correlated with Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). The Carbohydrate Metabolism pathways were positively correlated with Prevotella_melaninogenica, Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). CONCLUSIONS: A practical caries risk assessment scale for orthodontic adolescents was established and shows promise for cross-sectional risk stratificationthroughout the orthodontic treatment cycle. Its longitudinal predictive efficacy requires further validation with appropriate statistical models. The microbial findings, particularly the involvement of Candidatus_Nanosynbacter_sp._HMT-352 in relevant metabolic pathways, are preliminary and hypothesis-generating. These results are constrained by the study's limited sample size and the lack of a high-risk comparator group, necessitating confirmation in larger, more comprehensive future studies.}, }
@article {pmid41882673, year = {2026}, author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C}, title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41882673}, issn = {1479-5876}, mesh = {Humans ; *Psoriasis/microbiology/virology ; Biomarkers/metabolism ; Case-Control Studies ; *Gastrointestinal Microbiome ; Female ; *Virome ; Male ; *Environment ; Feces/microbiology ; Middle Aged ; Adult ; Bacteria ; }, abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.<br><br>METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.<br><br>RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.<br><br>CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.<br><br>TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.}, }
@article {pmid41886955, year = {2026}, author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ}, title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158089}, doi = {10.1016/j.phymed.2026.158089}, pmid = {41886955}, issn = {1618-095X}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Hyperuricemia/drug therapy/complications ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism/pharmacology ; *Kidney Diseases/drug therapy ; Kidney/drug effects ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; Feces/microbiology ; }, abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.<br><br>OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.<br><br>METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.<br><br>RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.<br><br>CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.}, }
@article {pmid41887041, year = {2026}, author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z}, title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101810}, doi = {10.1016/j.cbd.2026.101810}, pmid = {41887041}, issn = {1878-0407}, mesh = {Animals ; Female ; Male ; *Mucus/microbiology ; *Microbiota ; *Fishes/microbiology/genetics ; *Metagenomics ; *Epidermis/microbiology ; *Metagenome ; *Bacteria/genetics/classification ; }, abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.}, }
@article {pmid41887297, year = {2026}, author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S}, title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108461}, doi = {10.1016/j.micpath.2026.108461}, pmid = {41887297}, issn = {1096-1208}, mesh = {Animals ; *Cryptosporidiosis/parasitology/microbiology ; Sheep ; *Cryptosporidium/genetics/isolation &amp; purification ; Feces/parasitology/microbiology ; *Metagenomics ; *Sheep Diseases/parasitology/microbiology ; Tibet ; *Gastrointestinal Microbiome/genetics ; Polymerase Chain Reaction ; Bacteria/classification/genetics ; }, abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.}, }
@article {pmid41887505, year = {2026}, author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y}, title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.}, journal = {Journal of dairy science}, volume = {109}, number = {5}, pages = {4811-4825}, doi = {10.3168/jds.2025-27796}, pmid = {41887505}, issn = {1525-3198}, mesh = {Animals ; Goats ; Mongolia ; Metagenomics ; *Cultured Milk Products/microbiology/analysis ; Fermentation ; *Milk/microbiology/chemistry ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbiota ; Food Microbiology ; }, abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.}, }
@article {pmid41887507, year = {2026}, author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM}, title = {Microbiota changes in rumen and milk corresponding to dietary protein intake in transition dairy cows.}, journal = {Journal of dairy science}, volume = {109}, number = {6}, pages = {6287-6300}, doi = {10.3168/jds.2025-27576}, pmid = {41887507}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology ; Female ; Cattle/microbiology/physiology ; *Milk/microbiology/chemistry ; Lactation ; *Dietary Proteins/metabolism/administration &amp; dosage ; Diet/veterinary ; Animal Feed/analysis ; *Microbiota ; Postpartum Period ; }, abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively affected milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in MP supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (MP80) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (MP100) for an additional 14 d. Control cows (n = 6) were fed MP100 for the entire experiment. Samples of rumen content and milk were taken in the immediate postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental recovery phase on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated with the effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the MP100 compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.}, }
@article {pmid41887859, year = {2026}, author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z}, title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {409-419}, doi = {10.1016/j.jes.2025.05.033}, pmid = {41887859}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Thiazolidines/toxicity ; Soil/chemistry ; *Soil Pollutants/toxicity ; Ecosystem ; *Microbiota/drug effects ; Pesticides/toxicity ; RNA, Ribosomal, 16S ; Bacteria/drug effects ; Organophosphorus Compounds ; }, abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.}, }
@article {pmid41888125, year = {2026}, author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C}, title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41888125}, issn = {2055-5008}, support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Aging ; *Metagenomics/methods ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenome ; }, abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.}, }
@article {pmid41888223, year = {2026}, author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K}, title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41888223}, issn = {2045-2322}, support = {4020052//Center for International Scientific Studies &amp; Collaborations (CISSC)/ ; }, mesh = {*Metagenome ; Metagenomics/methods ; Microbiota/genetics ; }, abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.}, }
@article {pmid41888360, year = {2026}, author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ}, title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41888360}, issn = {1573-0972}, mesh = {*Wastewater/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Mining ; Cyanides/metabolism ; Metagenome ; Gold ; Phylogeny ; Bioreactors/microbiology ; *Microbial Consortia/genetics ; Lakes/microbiology ; Metagenomics ; Aerobiosis ; Whole Genome Sequencing ; Water Purification/methods ; Denitrification ; Sequence Analysis, DNA ; }, abstract = {Biological treatment of cyanide-contaminated wastewater is mediated by microbial consortia in which different organisms perform distinct, functionally specialized roles. This study investigated microbial communities involved in gold mine wastewater treatment with integrated aerobic-anoxic reactors seeded with consortia from an alkaline soda lake, Lake Chitu. Whole-genome sequencing of isolates (WGS) and metagenomic sequencing of the bioreactor were performed to characterize the consortia, resulting in the identification of 23 non-redundant genomes, comprising 14 whole-genome sequencing isolates and 19 metagenome-assembled genomes (MAGs). Most isolated genomes were similar to the recovered metagenomes of MAGs. Except for Alkalibacterium, all isolates possessed one or more genes potentially involved in cyanide or cyanate transformation, along with at least one type of terminal oxygenase; however, the gene encoding cynD, which is required for the direct hydrolysis of free cyanide (CN[-]), was not detected. Three representative Halomonas isolates harboured the nitrate reductase narGHI, nitrite reductase nirS, nitric oxide reductase norB/norC, and nitrous-oxide reductase nosZ genes for full denitrification. All of the isolates possessed several gene clusters associated with different heavy metal resistances. This study suggests that the microbial inoculum sourced from Lake Chitu harbors diverse microorganisms possessing genes potentially involved in cyanide-related metabolic pathways. The findings of this study add to our understanding of the alkaliphilic microbial population that degrades cyanide and cyanide intermediates and provide insight into how these organisms break down cyanide and resist cyanide and heavy metal inhibitory effects.}, }
@article {pmid41888912, year = {2026}, author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH}, title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41888912}, issn = {2049-2618}, support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; }, mesh = {*Diatoms/metabolism/chemistry ; *Mannans/metabolism/chemistry ; *Microbiota ; Oceans and Seas ; *Seawater/microbiology ; Sulfates/metabolism/chemistry ; Metagenome ; Metagenomics ; Bacteria/genetics/classification/metabolism ; }, abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.<br><br>RESULTS: We discovered that diatoms exude a C6-sulfated &#x3b1;-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.<br><br>CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome. Video Abstract.}, }
@article {pmid41889037, year = {2026}, author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS}, title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109518}, pmid = {41889037}, issn = {1875-595X}, mesh = {Humans ; Female ; Pilot Projects ; Middle Aged ; *Microbiota/physiology ; Aged ; Adult ; *Menopause ; Saliva/microbiology/chemistry ; *Mouth/microbiology ; Aged, 80 and over ; *Nitrates/metabolism ; Cross-Sectional Studies ; Retrospective Studies ; Young Adult ; Adolescent ; *Bacteria/metabolism ; Estradiol/analysis/metabolism ; Nitrites/metabolism ; }, abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.<br><br>METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.<br><br>RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.<br><br>CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.}, }
@article {pmid41891399, year = {2026}, author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK}, title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71738}, pmid = {41891399}, issn = {2045-7634}, support = {R21CA293626/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; *Liver Neoplasms/drug therapy/microbiology/immunology/complications ; *Gastrointestinal Microbiome/immunology/drug effects ; Fecal Microbiota Transplantation ; Dysbiosis/immunology/microbiology ; *Liver Diseases/microbiology ; }, abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.}, }
@article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41892593}, issn = {1751-7370}, mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Bacteria/classification/metabolism/genetics ; Sulfides/metabolism ; Sequence Analysis, DNA ; *Microbiota ; Methylglucosides ; }, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, }
@article {pmid41894043, year = {2026}, author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J}, title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41894043}, issn = {1573-7446}, support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology/blood/growth &amp; development/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; Metabolome ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; }, abstract = {The rumen microbial community is influenced by various factors such as diet, age, genetics, and breed. This study employs metagenomics and untargeted metabolomics to investigate the characteristics of rumen microbiota and plasma metabolite changes in crossbred beef cattle (Simmental♀× Belgian Blue♂) as they age, as well as their regulatory effects on growth performance. The LEfse analysis results indicated that the dominant microorganisms in the 12-month-old crossbred beef cattle group were Stomatobaculum sp., Succiniclasticum ruminis, and uncultured Succiniclasticum sp., etc., while the dominant microorganisms in the 18-month-old crossbred beef cattle group were Succinivibrio sp., Oceanobacillus sp., and uncultured Holdemanella sp., etc. The differentially expressed metabolites in the rumen and plasma were significantly enriched in the Pyrimidine metabolism pathway and the Valine, leucine and isoleucine biosynthesis pathway. Through GSEA analysis, it was found that the rumen metabolites Thymidine, 4,5-Dihydroorotic acid, Uracil, and Uridine were more abundant at 12 months of age (P < 0.05), while the plasma metabolite 2s-Amino-3s-methylpentanoic acid was more abundant at 18 months of age (P < 0.05). As the age increases, the rumen microbiota of crossbred beef cattle tends to mature and stabilize, and the ability of rumen metabolites and plasma metabolites to provide protein for the host gradually enhances. In summary, our research results aim to provide basic information on the regulatory role of microorganisms and metabolites in the growth performance of crossbred beef cattle, and also offer targets for precise nutritional regulation of beef cattle.}, }
@article {pmid41895941, year = {2026}, author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y}, title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118860}, doi = {10.1016/j.foodres.2026.118860}, pmid = {41895941}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Milk/microbiology ; *Food Microbiology ; *Microbiota ; *Metabolome ; China ; Amino Acids ; }, abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.}, }
@article {pmid41895971, year = {2026}, author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M}, title = {Microbiota of foods: a comprehensive review of diversity and potential implications.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118899}, doi = {10.1016/j.foodres.2026.118899}, pmid = {41895971}, issn = {1873-7145}, mesh = {*Food Microbiology/methods ; *Microbiota/genetics ; *Fermented Foods/microbiology ; Fermentation ; Metagenomics ; *Bacteria/classification/genetics ; Multiomics ; Humans ; }, abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.}, }
@article {pmid41896490, year = {2026}, author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A}, title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.}, journal = {Translational stroke research}, volume = {17}, number = {2}, pages = {}, pmid = {41896490}, issn = {1868-601X}, support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Intracranial Arteriosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Case-Control Studies ; Biomarkers ; Middle Aged ; Aged ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; *Eubacteriales ; }, abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.}, }
@article {pmid41896639, year = {2026}, author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP}, title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41896639}, issn = {2399-3642}, support = {RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; NIH R35 GM144276//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Animals ; *Foxes/microbiology/physiology ; *Behavior, Animal ; Phenotype ; *Gastrointestinal Microbiome ; Domestication ; *Bacteria/classification/genetics ; }, abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.}, }
@article {pmid41896653, year = {2026}, author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L}, title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41896653}, issn = {2045-2322}, support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; }, mesh = {Animals ; *Pancreatic Neoplasms/drug therapy/metabolism/pathology ; Humans ; *Scutellaria/chemistry ; Mice ; Cell Line, Tumor ; Network Pharmacology/methods ; Apoptosis/drug effects ; *Plant Extracts/pharmacology ; Xenograft Model Antitumor Assays ; Multiomics ; Mice, Nude ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; *Antineoplastic Agents, Phytogenic/pharmacology ; Proteomics ; Cell Movement/drug effects ; Gastrointestinal Microbiome/drug effects ; Male ; }, abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.}, }
@article {pmid41896698, year = {2026}, author = {Jung, S and Militsi, E and Huck, O}, title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.}, journal = {Oral diseases}, volume = {32}, number = {5}, pages = {1237-1272}, pmid = {41896698}, issn = {1601-0825}, mesh = {Humans ; *Microbiota ; *Autoimmune Diseases/microbiology/immunology ; *Mouth/microbiology ; Dysbiosis/microbiology ; Sjogren's Syndrome/microbiology ; Saliva/microbiology ; Arthritis, Rheumatoid/microbiology ; }, abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.<br><br>METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).<br><br>RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sj&#xf6;gren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct &#x3b2;-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.<br><br>CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.}, }
@article {pmid41898386, year = {2026}, author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y}, title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898386}, issn = {1422-0067}, mesh = {Humans ; Female ; *Microbiota ; *Precision Medicine/methods ; Probiotics ; *Women's Health ; Pregnancy ; }, abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.}, }
@article {pmid41898595, year = {2026}, author = {Makiel, K}, title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898595}, issn = {1422-0067}, support = {//University of Physical Education, 31-571 Cracow, Poland/ ; }, mesh = {Humans ; *Metabolic Syndrome/diet therapy/metabolism/microbiology/genetics ; *Obesity/diet therapy/metabolism/microbiology/genetics ; *Adipokines/metabolism/genetics ; *DNA Methylation ; Multiomics ; *Gastrointestinal Microbiome ; Animals ; *Diet ; *Anti-Inflammatory Agents ; Inflammation/diet therapy ; Nutrigenomics ; }, abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.}, }
@article {pmid41898625, year = {2026}, author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA}, title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898625}, issn = {1422-0067}, support = {24-75-10100//Russian Science Foundation/ ; }, mesh = {Humans ; Phylogeny ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation &amp; purification/metabolism ; Animals ; Genome, Bacterial ; Mice ; Fatty Acids/metabolism ; *Extracellular Vesicles/metabolism ; }, abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.}, }
@article {pmid41898646, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ}, title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898646}, issn = {1422-0067}, support = {DP1 DA048493/DA/NIDA NIH HHS/United States ; DA048493/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Herpesvirus 4, Human/isolation &amp; purification/genetics ; Female ; Torque teno virus/isolation &amp; purification/genetics ; Viral Load ; Parvovirus/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Male ; }, abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.}, }
@article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898837}, issn = {2073-4425}, mesh = {Multiomics ; *Soil Microbiology ; Rhizosphere ; *Plants/microbiology/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Genomics/methods ; Soil ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, }
@article {pmid41901100, year = {2026}, author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A}, title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901100}, issn = {2072-6643}, support = {2022R1A2C1005235//National Research Foundation of Korea/ ; }, mesh = {Animals ; *Thioctic Acid/pharmacology/administration &amp; dosage ; *Carnitine/pharmacology/administration &amp; dosage ; Male ; *Obesity/microbiology/metabolism/blood ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; *Betaine/pharmacology/administration &amp; dosage ; Disease Models, Animal ; Bacteria/classification ; }, abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.}, }
@article {pmid41901112, year = {2026}, author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF}, title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901112}, issn = {2072-6643}, support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; }, mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Metagenome ; *Transcriptome ; *Colitis/chemically induced/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/genetics ; *Vegetables ; *Dietary Supplements ; Swine ; *Diet ; Colon/pathology ; Disease Models, Animal ; }, abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.}, }
@article {pmid41901695, year = {2026}, author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P}, title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901695}, issn = {2076-0817}, mesh = {Humans ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; India ; Sepsis ; Cytokines/metabolism ; Feces/microbiology ; Hospitalization ; Aged ; Metagenome ; }, abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.}, }
@article {pmid41902210, year = {2026}, author = {Zhang, Y and Ding, X and Tao, X and Tuohuti, N and Wang, X and Maimaiti, A and Su, Z and Ma, X}, title = {Viral Metagenomic Analysis Reveals High Prevalence of Dromedary Camel Bocavirus and Porcine Astrovirus in Bactrian Camel Intestinal Tissue.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902210}, issn = {1999-4915}, support = {2022KY025//Autonomous Region Science and Technology Commissioner Project of Xinjiang Uygur Autonomous Region, China/ ; }, mesh = {Animals ; *Camelus/virology ; Phylogeny ; Metagenomics ; *Bocavirus/genetics/isolation &amp; purification/classification ; Prevalence ; *Astroviridae Infections/veterinary/epidemiology/virology ; Swine ; *Parvoviridae Infections/veterinary/epidemiology/virology ; *Intestines/virology ; China/epidemiology ; *Mamastrovirus/genetics/isolation &amp; purification/classification ; Swine Diseases/virology ; Virome ; }, abstract = {Bactrian camels (Camelus bactrianus) are economically vital livestock in arid regions; however, their intestinal virome is poorly understood. We employed viral metagenomics to analyze intestinal tissue samples from deceased camels at a breeding facility in Urumqi, Xinjiang, China, and uncovered a diverse viral population dominated by dromedary camel bocavirus (DBoV1) and porcine astrovirus (PoAstV5). A molecular epidemiological survey of 261 anal swab samples collected across Xinjiang revealed prevalence rates of 36.40% (95/261) for DBoV1 and 26.44% (69/261) for PoAstV5, indicating their widespread circulation. Phylogenetic analyses of the DBoV1 NS1 and PoAstV5 ORF1a genes showed close relationships with known strains, with no evidence of recombination. This study expands the known viral spectrum of Bactrian camels, marking the first report of PoAstV5 in this species, a finding suggestive of cross-species transmission. These results enhance our understanding of camel viral diversity and provide critical data for managing enteric diseases in camel populations, with potential implications for livestock health and surveillance of zoonotic risks.}, }
@article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; *Penaeidae/microbiology/growth &amp; development ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Aquaculture ; *Microbiota/genetics ; *Water Microbiology ; Metagenome ; Larva/microbiology/growth &amp; development ; Phylogeny ; }, abstract = {Enhancing our understanding of the role of microbial life strategies and their trade-offs in the functioning of microbial communities is essential for improving the management of microbial communities. In aquaculture microbiomes, management aimed at increasing the dominance of K-strategists has experimentally been shown to influence cultivation performance. To understand the mechanisms behind such observations, we need to improve our understanding of the typical properties and behaviour of r- and K-strategists. Several studies have advanced our understanding of theoretical trade-offs that may shape these life strategies, but our understanding of which trade-offs are relevant under natural conditions is still limited. In this study, we investigated the in situ growth strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture by reconstructing 67 high quality metagenome assembled genomes (MAGs), which covered between 31 and 85% of the sampled communities. We found evidence for niche separation between r- and K-biased strategists residing in these communities, with r-biased strategists typically encoding more and more versatile transport and metabolism pathways, and having a higher fitness for exploitation of spatially structured nutrient hotspots. We further increased the knowledge regarding the influence of r- and K-biased strategistson aquaculture cultivation performance by showing that the in situ growth activity of r-biased strategists could be linked better with cultivation performance than the relative abundance of r- and K-biased strategists.}, }
@article {pmid41903026, year = {2026}, author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S}, title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {2}, pages = {}, pmid = {41903026}, issn = {1573-3890}, mesh = {Humans ; *Machine Learning ; *Inflammatory Bowel Diseases/blood/diagnosis/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism/microbiology ; *Metabolomics/methods ; Biomarkers/blood ; *Gastrointestinal Microbiome/physiology ; Metabolome ; Mass Spectrometry/methods ; Crohn Disease ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.<br><br>OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.<br><br>METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.<br><br>RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.<br><br>CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.}, }
@article {pmid41903463, year = {2026}, author = {Rathnayake, M and Shaik, NA and Palkumbura, A and Ranaraja, A and Basnayake, Y and Basyouni, R and Taylor, A and Ambrose, N and Popowich, S and Ayalew, LE and Tikoo, S and Gomis, S}, title = {Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106823}, pmid = {41903463}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; *Infectious bursal disease virus/physiology ; *Jejunum/microbiology ; *Poultry Diseases/virology/microbiology ; *Birnaviridae Infections/veterinary/virology ; *Animal Husbandry/methods ; *Anti-Bacterial Agents/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; RNA, Ribosomal, 16S/analysis ; RNA, Bacterial/analysis ; }, abstract = {Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.}, }
@article {pmid41904207, year = {2026}, author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W}, title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41904207}, issn = {2045-2322}, support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; }, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; Humans ; Animals ; Male ; *Lipid Metabolism ; *Glycemic Control ; Blood Glucose/metabolism ; Female ; *Lactobacillus johnsonii/physiology ; *Circadian Rhythm ; Mice ; Middle Aged ; Gastrointestinal Microbiome ; Feces/microbiology ; *Probiotics/administration &amp; dosage ; }, abstract = {Although most patients with type 2 diabetes mellitus (T2DM) and circadian rhythm disruption have poor blood glucose control, a fraction of patients with T2DM and circadian rhythm disruption who still have good blood glucose control. Previous studies have shown that individuals with circadian rhythm disruption are more prone to developing T2DM, and the occurrence of T2DM is associated with the gut microbiota. However, the role of gut microbiota in patients with T2DM and circadian rhythm disruption remains unclear. Stool samples were collected from 6 patients with poorly controlled type 2 diabetes mellitus (T2DM) and circadian rhythm disruption, as well as from 6 patients with well-controlled T2DM and circadian rhythm disruption. Metagenomic sequencing was performed on the stool samples. Compared to the well-controlled group, the abundance of Lactobacillus johnsonii(L. johnsonii) was significantly decreased in the poorly controlled group. To investigate the effects of L. johnsonii supplementation on glucose and lipid metabolism, diabetic mice with circadian rhythm disruption were administered L. johnsonii and their metabolic indicators were measured. Metagenomic sequencing of the gut microbiota revealed a higher microbial diversity in the well blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (W-T2D-RD). Additionally, a significant decrease in the abundance of L. johnsonii was observed in patients with poor blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (P-T2D-RD) when compared to those with W-T2D-RD. Following supplementation of L. johnsonii to the mice in the type 2 diabetes mellitus rhythm disruption Lactobacillus johnsonii group (T2DM-RD-L), the fasting blood glucose levels and postprandial blood glucose levels were significantly reduced. Additionally, total cholesterol and low-density lipoprotein levels decreased, high-density lipoprotein levels increased in the T2DM-RD-L group. Lactobacillus johnsonii has a positive impact on both glucose and lipid metabolism in patients with type 2 diabetes mellitus and circadian rhythm disruption.}, }
@article {pmid41904418, year = {2026}, author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S}, title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41904418}, issn = {2730-6844}, mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; Adult ; Feces/microbiology ; Bacteria/genetics/classification ; }, abstract = {OBJECTIVE: Microbiome being a potential biomarker holds the future hope for insight into GD pathogenesis, diagnosis and cure. Many factors such as diet, lifestyle, environment, host genetics shape the diversity and composition of human microbiome. Although recent studies have indicated that gut microbiome dysbiosis was significantly associated with the onset of gestational diabetes mellitus (GDM). Information on the alteration of gut microbiota composition in Pakistani women is limited. Therefore, present study was designed to elucidate gut microbiota taxonomic composition and relative abundance of taxa in local GD women. DATA DESCRIPTION: 16S Metagenomics data revealed variation in bacterial community structure in gestational diabetic (GD), pregnant non-diabetic (PND), non-pregnant diabetic (NPD) and non-pregnant non-diabetic (NPND) women. Predominant bacterial phyla residing faecal sample of GD, NPD, PND included Firmicutes, Bacteriodota, Proteobacteria accounting for 95.07%, 97.1% and 97.04%, of relative abundance respectively. While Predominant phyla inhabiting faecal sample of NPND included firmicutes, Bacteriodota, and Actinobacteriodota accounting for 98.4%. Simpson’s Reciprocal Index showed great variability, the value ranged between 11.655 and 16.17. The distance matrix depicted dissimilarity between samples with dissimilarity coefficient values ranging between 0.381 and 0.588. These findings would pave the way for future studies, which will aid in early diagnosis, management and treatment. CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41904571, year = {2026}, author = {Kolenda, R and Hassan, MM and Arrieta-Gisasola, A and Kamara, A and Ansorge, R and Sidorczuk, K and Acton, L and Thilliez, G and Baker, DJ and Burdukiewicz, M and Stares, MD and Browne, HP and Le Gall, G and Torres, RC and Chavez-Arroyo, A and Garrett, J and Stevens, MP and Lawley, TD and Bäumler, AJ and La Ragione, R and Hildebrand, F and Kingsley, RA}, title = {Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41904571}, issn = {2049-2618}, support = {BB/W003155/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Salmonella typhimurium/drug effects/genetics/physiology ; Swine ; *Copper/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenomics/methods ; Genomic Islands ; Salmonella Infections, Animal/microbiology ; Whole Genome Sequencing ; Intestines/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34.<br><br>RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche.<br><br>CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.}, }
@article {pmid41904606, year = {2026}, author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H}, title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649435}, pmid = {41904606}, issn = {1949-0984}, mesh = {Animals ; *Dietary Fiber/metabolism/administration &amp; dosage ; *Colitis/prevention &amp; control/microbiology/chemically induced ; *Gastrointestinal Microbiome ; Mice ; Feces/microbiology ; Dextran Sulfate/adverse effects ; Colon/pathology/microbiology ; Mice, Inbred C57BL ; Male ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Intestinal Mucosa/metabolism ; Intestinal Barrier Function ; Diet ; Disease Models, Animal ; }, abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.}, }
@article {pmid41905375, year = {2026}, author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS}, title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.}, journal = {The Lancet. Microbe}, volume = {7}, number = {4}, pages = {101294}, doi = {10.1016/j.lanmic.2025.101294}, pmid = {41905375}, issn = {2666-5247}, mesh = {Adolescent ; Adult ; Female ; Humans ; Young Adult ; Anti-Bacterial Agents ; Double-Blind Method ; *Dysbiosis/therapy/microbiology ; Lactobacillus/physiology ; *Microbiota ; Treatment Outcome ; *Vagina/microbiology ; *Biological Therapy ; }, abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.<br><br>METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.<br><br>FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26&#xb7;1 years [SD 3&#xb7;8]) and 12 to the placebo group (27&#xb7;3 years [4&#xb7;8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0&#xb7;65; 95% CI 0&#xb7;20-2&#xb7;16, p=0&#xb7;49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.<br><br>INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.<br><br>FUNDING: Freya Biosciences.}, }
@article {pmid41905742, year = {2026}, author = {Wu, Z and Duan, A and Liu, Y and Chen, R and Md Din, MF and Sanjaya, EH and Ali, EAE and Saad, A and Liu, Z and Chen, H}, title = {Mechanistic insights into sulfate-driven performance adaptation and membrane fouling in a UASB-SBR-AXMBR system: metabolic network reconstruction and microbial community succession.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124374}, doi = {10.1016/j.envres.2026.124374}, pmid = {41905742}, issn = {1096-0953}, mesh = {*Bioreactors/microbiology ; *Sulfates/metabolism ; *Waste Disposal, Fluid/methods ; Membranes, Artificial ; Wastewater ; Metabolic Networks and Pathways ; *Microbiota ; Bacteria/metabolism ; }, abstract = {Sulfate-rich wastewater poses considerable challenges to the operational stability of biological treatment systems. This study investigated the long-term (294 days) response of a combined UASB-SBR-AXMBR process to stepwise increases in sulfate concentration from 100 to 2000 mg/L. The system maintained stable carbon and nitrogen removal performance under sulfate stress, with COD removal exceeding 90.3% and total nitrogen removal stabilizing at 85.5% via a partial nitritation-anammox (PN/A) pathway. However, high sulfate loading significantly intensified membrane fouling, with the primary driving factor likely being the co-deposition of elemental sulfur (S[0]) and soluble extracellular polymeric substances (S-EPS). Microbial analysis revealed persistent enrichment of Bacteroidota and Proteobacteria in the SBR, alongside a marked increase in Anammoxoglobus (from 17.1% to 51.2%) in the Anaerobic Ammonia Oxidation Membrane Bioreactor (AXMBR), underpinning system resilience. Metagenomic profiling further indicated adaptive shifts in key nitrogen-cycling genes (hao, amoA) and sulfur metabolism pathways. Notably, sulfate-reducing bacteria (SRB) outcompeted methanogens, redirecting carbon flow from methanogenesis to sulfur reduction, while niche diversification in the AXMBR expanded nitrogen removal pathways. These findings provide new mechanistic insights into the adaptive responses of integrated bioprocesses under sulfate stress and provide practical guidance for the treatment of high-sulfate industrial wastewaters such as monosodium glutamate effluent.}, }
@article {pmid41905975, year = {2026}, author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC}, title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41905975}, issn = {2045-2322}, mesh = {Humans ; *Rubus ; *Gastrointestinal Microbiome ; Metagenomics ; Feces/microbiology ; C-Reactive Protein/metabolism ; Metagenome ; Triglycerides/blood ; }, abstract = {Red raspberries have been shown to exert beneficial effects on immunometabolic health in numerous studies; however, these effects are subject to interindividual variability. Building on a previous transcriptomic-based clustering analysis from an 8-week randomized controlled trial in which 24 individuals consumed 280 g of red raspberries daily, we investigated whether functional metagenomic profiling may enhance our understanding of the observed interindividual variability in metabolic responses. Participants were classified as responders (n = 13) or non-responders (n = 11) based on prior clustering approaches, which identified significant reductions in plasma levels of C-reactive protein (CRP), triglycerides, and total cholesterol in responders. Microbial DNA extracted from fecal samples collected before and after the intervention was sequenced, and carbohydrate-active enzyme (CAZyme) counts were generated using a bioinformatics pipeline. Differential analysis revealed distinct functional metagenomic profiles between responders and non-responders. Multiple linear regressions identified potential associations between baseline CAZyme levels and changes in CRP, with contrasting trends observed between responders and non-responders. CBM8 and CBM49 were among the highlighted CAZymes. GH5 and several GH5 subfamilies were also identified as candidate CAZymes associated with interindividual variability observed in metabolic responses. These findings support the integration of microbiome-derived functional data alongside other omics to improve precision nutrition strategies.}, }
@article {pmid41909847, year = {2026}, author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L}, title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779296}, pmid = {41909847}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/virology/microbiology ; *Metagenomics/methods ; *Sputum/virology/microbiology ; *Bronchoalveolar Lavage Fluid/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Female ; Bacteria/virology ; Computational Biology ; Male ; Metagenome ; Middle Aged ; Microbiota ; Aged ; }, abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.<br><br>METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.<br><br>RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.<br><br>CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.}, }
@article {pmid41910132, year = {2026}, author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A}, title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0019126}, pmid = {41910132}, issn = {2379-5077}, mesh = {Animals ; *Chickens/virology ; *Virome/genetics ; *Gastrointestinal Tract/virology ; Genome, Viral ; Metagenome ; Bacteriophages/genetics/classification ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; }, abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.<br><br>IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.}, }
@article {pmid41910214, year = {2026}, author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J}, title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649440}, pmid = {41910214}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; *Prenatal Exposure Delayed Effects/microbiology/psychology ; Rats ; Oxytocin/metabolism ; *Gastrointestinal Microbiome ; *Social Behavior ; Fecal Microbiota Transplantation ; Male ; Paraventricular Hypothalamic Nucleus/metabolism ; *Stress, Psychological ; Rats, Sprague-Dawley ; }, abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.}, }
@article {pmid41910252, year = {2026}, author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y}, title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0252325}, pmid = {41910252}, issn = {1098-5336}, support = {2024CXPT056//Key R&amp;D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; 32170093//National Natural Science Foundation of China/ ; }, mesh = {*Volatile Organic Compounds/metabolism ; Acetoin/metabolism ; Rhizosphere ; *Bacillus/metabolism/genetics ; Butylene Glycols/metabolism ; *Bacillus subtilis/metabolism/genetics ; Metagenomics ; Metabolomics ; *Solanum lycopersicum/microbiology/growth &amp; development/metabolism ; Microbiota ; Soil Microbiology ; *Host Microbial Interactions ; }, abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.}, }
@article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0179025}, pmid = {41910273}, issn = {2379-5077}, support = {407270017/RTG2530//Deutsche Forschungsgemeinschaft/ ; GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; 03F0864C//Bundesministerium f&#xfc;r Bildung und Forschung/ ; Core Funding//ETH Z&#xfc;rich Foundation/ ; }, mesh = {*Estuaries ; *Carbon/metabolism ; Salinity ; *Microbiota ; Metagenome ; Bacteria/metabolism/genetics/classification ; Water Microbiology ; }, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.<br><br>IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, }
@article {pmid41910342, year = {2026}, author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D}, title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.}, journal = {mSphere}, volume = {11}, number = {4}, pages = {e0085625}, pmid = {41910342}, issn = {2379-5042}, mesh = {Humans ; Multiomics ; Metagenomics ; *Glutens/metabolism/adverse effects ; Irritable Bowel Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metabolomics ; Metabolome ; Archaea/classification/genetics ; Bacteria/classification/genetics ; }, abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.<br><br>IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.}, }
@article {pmid41910593, year = {2026}, author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, MS and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , }, title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.}, journal = {Pancreas}, volume = {55}, number = {5}, pages = {e458-e468}, pmid = {41910593}, issn = {1536-4828}, support = {R01 CA282786/CA/NCI NIH HHS/United States ; U01 DK108327/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Pancreatitis, Chronic/microbiology/diagnosis ; Feces/microbiology ; Female ; *Metagenomics/methods ; *Machine Learning ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Adult ; Prospective Studies ; Saliva/microbiology ; Predictive Learning Models ; Case-Control Studies ; Random Forest ; }, abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.<br><br>OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).<br><br>METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP), and 148 recurrent acute pancreatitis (RAP). In addition, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.<br><br>RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared with HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve-AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.<br><br>CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.}, }
@article {pmid41910796, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D}, title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41910796}, issn = {1573-7446}, mesh = {Animals ; *Ponds/microbiology ; *Aquaculture/methods ; Egypt ; *Penaeidae/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; *Water Microbiology ; }, abstract = {Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.}, }
@article {pmid41910822, year = {2026}, author = {Kumar, V and Nautiyal, CS}, title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41910822}, issn = {1573-0972}, mesh = {*Endophytes/genetics/physiology/classification ; *Symbiosis ; *Agroecology ; Genomics ; *Plants/microbiology ; Multiomics ; Agriculture ; Ecosystem ; Microbiota ; Metagenomics ; Bacteria/genetics/classification ; }, abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.}, }
@article {pmid41910951, year = {2026}, author = {Dasgupta, S}, title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.}, journal = {Omics : a journal of integrative biology}, volume = {30}, number = {4}, pages = {191-202}, doi = {10.1177/15578100261419483}, pmid = {41910951}, issn = {1557-8100}, mesh = {Humans ; *Metagenomics/methods ; *Dysbiosis/microbiology ; *Host Microbial Interactions/genetics ; *Lung/microbiology ; *Gastrointestinal Microbiome ; Animals ; *Lung Diseases, Obstructive/microbiology ; }, abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.}, }
@article {pmid41911519, year = {2026}, author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R}, title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {2}, pages = {}, pmid = {41911519}, issn = {1536-2442}, support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; *Grasshoppers/microbiology ; Female ; Bacteria ; }, abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.}, }
@article {pmid41912071, year = {2026}, author = {Zhang, PP and Cui, MY and Shen, Y and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF}, title = {Ophiopogon japonicus polysaccharide ameliorates pulmonary fibrosis via gut microbiota-metabolite crosstalk.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108464}, doi = {10.1016/j.micpath.2026.108464}, pmid = {41912071}, issn = {1096-1208}, mesh = {Animals ; *Ophiopogon/chemistry ; *Polysaccharides/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Metabolomics ; Metagenomics ; Lung/pathology/drug effects ; *Plant Extracts/pharmacology ; Saponins/pharmacology ; Flavonoids/pharmacology ; Mice, Inbred C57BL ; *Idiopathic Pulmonary Fibrosis/drug therapy/chemically induced ; Male ; }, abstract = {Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log2FC = 2.17) and Duncaniella muricolitica (log2FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log2FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.}, }
@article {pmid41912361, year = {2026}, author = {Rathwell, C and Fuchsman, CA and Rocap, G}, title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70274}, pmid = {41912361}, issn = {1462-2920}, support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; }, mesh = {Phylogeny ; *Bacteria/virology/genetics/classification/metabolism ; Pacific Ocean ; *Chlorophyll/analysis/metabolism ; *Seawater/microbiology/virology/chemistry ; *Bacteriophages/genetics/classification/physiology ; Metagenomics ; *Microbiota ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; }, abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.}, }
@article {pmid41914171, year = {2026}, author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN}, title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39439}, doi = {10.31083/FBE39439}, pmid = {41914171}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Female ; Cattle ; High-Throughput Nucleotide Sequencing ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metagenomics ; }, abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.<br><br>METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.<br><br>RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).<br><br>CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.}, }
@article {pmid41914733, year = {2026}, author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D}, title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0235725}, pmid = {41914733}, issn = {1098-5336}, support = {NJ01180//USDA | USDA Rural Development (RD)/ ; 2128073//National Science Foundation/ ; //Schmidt Sciences and FFAR/ ; }, mesh = {*Sargassum/microbiology/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Polysaccharides/metabolism ; Arsenic/metabolism ; Biodegradation, Environmental ; }, abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.}, }
@article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0035926}, pmid = {41914849}, issn = {1098-5336}, support = {2024J010010//Natural Science Foundation of Fujian Province/ ; 20720240092//Headmaster' Faculty Fund/The Fundamental Research Funds for the Central Universities/ ; 423B2603//National Natural Science Foundation of China/ ; 42522607//National Natural Science Foundation of China/ ; 2023YFC3108600//National Key Research and Development Program of China/ ; }, mesh = {*Symbiosis ; *Diatoms/physiology/classification/microbiology ; *Microbiota ; Seawater/microbiology ; Stochastic Processes ; }, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, }
@article {pmid41915167, year = {2026}, author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E}, title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41915167}, issn = {1432-184X}, mesh = {*Microbiota ; Large Language Models ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.}, }
@article {pmid41917812, year = {2026}, author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W}, title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41917812}, issn = {1471-2180}, support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; }, mesh = {Animals ; *Virome/genetics ; Mice ; Liver/virology/parasitology ; Phylogeny ; *Echinococcosis/virology/parasitology ; Lung/virology/parasitology ; Metagenomics ; *Echinococcus/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; Female ; }, abstract = {The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.}, }
@article {pmid41918091, year = {2026}, author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J}, title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41918091}, issn = {1471-2180}, support = {2022YFC26023002//National Key Research and Development Program of China/ ; }, mesh = {*Hot Springs/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; China ; Metagenomics/methods ; Hot Temperature ; Temperature ; *Microbiota/genetics/physiology ; Phylogeny ; Metagenome ; }, abstract = {BACKGROUND: Understanding microbial adaptation to extreme environments remains a key challenge in microbial ecology. Geothermal hot springs, characterized by temperature gradients and varying geochemical conditions, represent valuable natural laboratories for studying microbial diversity, adaptive strategies, and evolutionary mechanisms. However, despite many studies of hot spring communities, how temperature gradients shape key microbial adaptation strategies remains insufficiently understood, limiting our ability to explain survival and function in extreme environments. RESULTS: Our study investigated microbial community composition and functional profiles across a natural thermal gradient (50–93 °C) in six hot springs on the Western Sichuan Plateau using optimized contig- and MAG-based metagenomic strategies. Enhanced annotation approaches significantly improved taxonomic resolution in these extreme environments. Metagenomic analyses revealed distinct shifts in microbial communities along the thermal gradient: moderate-temperature springs (50–70 °C) were dominated by Pseudomonadota and Bacteroidota, exhibiting heterotrophic flexibility and utilizing the Calvin–Benson–Bassham cycle and diverse nitrogen reduction pathways; high-temperature springs (70–90 °C) were enriched in Chloroflexota, which primarily employed the Wood–Ljungdahl pathway coupled with enhanced sulfur metabolism; and extreme-temperature springs (≥ 90 °C) were characterized by Aquificota and Thermoproteota, relying on specialized autotrophic pathways (rTCA, DH/HH cycles), streamlined nitrogen assimilation, and sulfur oxidation pathways. These thermophilic lineages showed genome streamlining, reduced regulatory complexity, and specialized metabolic strategies, reflecting narrower ecological niches and deeper phylogenetic branches. CONCLUSIONS: This metagenomic investigation across a temperature gradient in western Sichuan hot springs highlights temperature as an essential driver of microbial community structure, genome evolution, and adaptive specialization. Thermophilic lineages in extreme-temperature environments exhibited streamlined genomes, specialized metabolic functions, and narrower ecological niches, consistent with adaptation to persistent thermal stress. The findings enhance understanding of microbial evolutionary strategies and underscore the ecological significance of temperature-driven adaptation in extreme environments.}, }
@article {pmid41918874, year = {2026}, author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D}, title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1782744}, pmid = {41918874}, issn = {2235-2988}, mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; *Probiotics/administration &amp; dosage ; Pregnancy ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Metabolomics ; Adult ; Metagenomics ; }, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.<br><br>METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.<br><br>RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-&#x3b1; and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.<br><br>DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.}, }
@article {pmid41919968, year = {2026}, author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C}, title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0039226}, pmid = {41919968}, issn = {1098-5336}, support = {52374051//National Natural Science Foundation of China/ ; U24B2037//National Natural Science Foundation of China/ ; }, mesh = {Biodegradation, Environmental ; China ; *Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Metagenome ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Phylogeny ; Petroleum ; Genome, Bacterial ; }, abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.}, }
@article {pmid41921236, year = {2026}, author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X}, title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.}, journal = {Pathology, research and practice}, volume = {282}, number = {}, pages = {156456}, doi = {10.1016/j.prp.2026.156456}, pmid = {41921236}, issn = {1618-0631}, mesh = {Animals ; *Legionnaires' Disease/immunology/microbiology/pathology ; *Legionella pneumophila/pathogenicity/immunology ; *Gastrointestinal Microbiome/immunology ; Guinea Pigs ; *Bacterial Translocation ; *Immunocompromised Host ; *Liver/pathology/microbiology/immunology ; Apoptosis ; Disease Models, Animal ; Dysbiosis/microbiology ; }, abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.}, }
@article {pmid41921531, year = {2026}, author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, Q}, title = {Feasibility of low-biomass exhaled breath microbiome sequencing using a PDC-sampler in febrile and healthy individuals.}, journal = {Journal of breath research}, volume = {20}, number = {2}, pages = {}, doi = {10.1088/1752-7163/ae5a51}, pmid = {41921531}, issn = {1752-7163}, mesh = {Humans ; Breath Tests/methods/instrumentation ; *Microbiota/genetics ; *Exhalation ; Feasibility Studies ; Female ; Male ; Adult ; *Fever/microbiology ; Middle Aged ; Healthy Volunteers ; }, abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-Omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16 S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated byPseudomonadota, Bacillota, Bacteroidota, andActinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.}, }
@article {pmid41921761, year = {2026}, author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S}, title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.}, journal = {Diabetes research and clinical practice}, volume = {235}, number = {}, pages = {113232}, doi = {10.1016/j.diabres.2026.113232}, pmid = {41921761}, issn = {1872-8227}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Diabetes Mellitus/microbiology/metabolism ; Dysbiosis/microbiology ; }, abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.}, }
@article {pmid41923466, year = {2026}, author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC}, title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70324}, pmid = {41923466}, issn = {1758-2229}, support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; }, mesh = {*Soil Microbiology ; *Phytophthora/genetics/physiology/isolation &amp; purification ; *Metagenome ; Forests ; *Microbiota/genetics ; Shotgun Sequencing ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; New Zealand ; Plant Diseases/microbiology/parasitology ; Bacteria/genetics/classification/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; }, abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.}, }
@article {pmid41923582, year = {2026}, author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A}, title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e9317962}, pmid = {41923582}, issn = {2314-6753}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/blood/complications ; *Dyslipidemias/microbiology/blood ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; Female ; Male ; Middle Aged ; *Bacteria/genetics/classification ; Aged ; }, abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.}, }
@article {pmid41925105, year = {2026}, author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H}, title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71752}, pmid = {41925105}, issn = {2045-7634}, support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; }, mesh = {Female ; Animals ; Humans ; *Gastrointestinal Microbiome ; *Ovarian Neoplasms/drug therapy/microbiology ; Rats ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; Cisplatin/adverse effects/administration &amp; dosage ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Carboplatin/adverse effects/administration &amp; dosage ; Paclitaxel/adverse effects/administration &amp; dosage ; Metabolomics/methods ; Aged ; Feces/microbiology ; }, abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).<br><br>METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n&#x2009;=&#x2009;25) and non-CINV (n&#x2009;=&#x2009;25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.<br><br>RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p&#x2009;<&#x2009;0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p&#x2009;<&#x2009;0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p&#x2009;<&#x2009;0.05) and partially reversed by non-CINV FMT (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.}, }
@article {pmid41925227, year = {2026}, author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y}, title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41925227}, issn = {1751-7370}, support = {32170430//National Natural Science Foundation of China/ ; 32400412//National Natural Science Foundation of China/ ; 2023B10564001//Specific University Discipline Construction Project/ ; }, mesh = {Animals ; *Ursidae/microbiology ; *Cellulase/genetics/metabolism ; *Escherichia coli/enzymology/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/lytic polysaccharide monooxygenase-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution, and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.}, }
@article {pmid41927536, year = {2026}, author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J}, title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.}, journal = {Nutrition &amp; diabetes}, volume = {16}, number = {1}, pages = {}, pmid = {41927536}, issn = {2044-4052}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Cohort Studies ; Middle Aged ; Europe ; Feces/microbiology ; Asia ; Dysbiosis/microbiology ; Adult ; Bacteria/classification/genetics ; Aged ; }, abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.<br><br>METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.<br><br>RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs&#x2009;>&#x2009;0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.<br><br>CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.}, }
@article {pmid41927589, year = {2026}, author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, &#x10c; and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H}, title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41927589}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Antimicrobial Peptides/pharmacology/genetics ; Phylogeny ; *Bacteria/genetics/classification/drug effects ; Multigene Family ; Archaea/genetics/classification ; Genome, Bacterial ; Metagenome ; Genome, Archaeal ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.}, }
@article {pmid41927746, year = {2026}, author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA}, title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41927746}, issn = {2045-2322}, support = {SRUG2204254606//National Research Foundation/ ; }, mesh = {Animals ; *Methane/metabolism ; *Rumen/microbiology/drug effects ; *Plant Extracts/pharmacology/administration &amp; dosage ; Animal Feed/analysis ; Sheep ; Dietary Supplements ; Jatropha/chemistry ; Fermentation/drug effects ; *Gastrointestinal Microbiome/drug effects ; Aloe/chemistry ; }, abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.}, }
@article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {19}, number = {1}, pages = {}, pmid = {41928235}, issn = {1755-8794}, support = {K99 ES034086/ES/NIEHS NIH HHS/United States ; R00 ES034086/ES/NIEHS NIH HHS/United States ; R01 ES027224/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; *Cardiometabolic Risk Factors ; *Cardiovascular Diseases/microbiology/epidemiology ; }, abstract = {BACKGROUND: Alterations to the gut microbiome have been linked to cardiometabolic disease, like type 2 diabetes and hypertension, in adults, but few studies have investigated these associations in adolescents. We examined the relation between the gut microbiome and cardiometabolic risk in adolescence and determined whether sex and race/ethnicity modified these associations. METHODS: In 144 adolescents (age range: 11–14 years) from the Health Outcomes and Measures of the Environment (HOME) Study, we quantified gut microbiome alpha diversity using the Shannon index and species’ relative abundances (i.e., centered log-ratio normalized abundances) in stool DNA that underwent metagenomic sequencing. We assessed adolescent cardiometabolic risk using a cardiometabolic risk summary score, its individual components (i.e., visceral fat, leptin to adiponectin ratio, HOMA-IR, triglyceride to high-density lipoprotein cholesterol ratio, and systolic blood pressure), as well as total cholesterol and hemoglobin A1c. We used linear regression models to estimate covariate-adjusted cross-sectional associations of the Shannon diversity index and species’ relative abundances with cardiometabolic risk, and examine differences in these associations by sex and race/ethnicity. At the species level, the false discovery rate (FDR) correction, with q-value < 0.20, was considered statistically significant. RESULTS: Among all adolescents, a higher Shannon diversity index was associated with lower systolic blood pressure [β: -0.18 (95% CI: -0.35, -0.01)] in covariate-adjusted models. However, the associations of the Shannon diversity index with cardiometabolic risk did not differ significantly by sex or race/ethnicity. Although associations of the relative abundances of species, prevalent in at least 10% of samples, with cardiometabolic risk were not statistically significant tamong all adolescents after correcting for multiple comparisons (qFDR ≥ 0.20), sex modified the association of the relative abundance of Ruminococcus lactaris with HOMA-IR (qinteraction = 0.151), with positive association among females [β: 2.05 (95% CI: 0.93, 3.17), q = 0.155] and suggestive negative association among males [β: -0.84 (95% CI: -1.59, -0.09), q = 0.983]. Associations of the relative abundances of Streptococcus parasanguinis (qinteraction = 0.097), Enterocloster SGB14313 (qinteraction = 0.097), and Alistipes ihumii (qinteraction = 0.097) with total cholesterol also differed between female and male adolescents. We observed differences between adolescents of non-Hispanic black and non-Hispanic white race/ethnicity in the association of the relative abundance of Lachnospira pectinoschiza (qinteraction = 0.028) with total cholesterol. CONCLUSIONS: Our findings suggest that the gut microbiome is associated with cardiometabolic risk in adolescence in a sex-specific manner, and may differ by race and ethnicity.}, }
@article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, mesh = {Animals ; *Feces/microbiology ; *Sus scrofa/microbiology ; *Metagenomics/methods ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Dietary Fiber/metabolism ; Carbohydrate Metabolism ; Sequence Analysis, DNA ; Diet ; Animals, Wild/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.<br><br>RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.<br><br>CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, }
@article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Periodontitis/therapy/microbiology ; Longitudinal Studies ; Male ; *Mouth/microbiology ; Female ; Middle Aged ; *Lung/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Adult ; Dental Plaque/microbiology ; Respiratory Function Tests ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, }
@article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; Humans ; *Asthenozoospermia/metabolism/etiology/microbiology ; *Dysbiosis/complications/metabolism/microbiology ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Adult ; Fecal Microbiota Transplantation ; Case-Control Studies ; Sperm Motility ; Metabolomics ; Spermatozoa ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, }
@article {pmid41930813, year = {2026}, author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S}, title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158039}, doi = {10.1016/j.phymed.2026.158039}, pmid = {41930813}, issn = {1618-095X}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/metabolism ; *Diterpenes/pharmacology ; Humans ; Mice ; Male ; *Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; Signal Transduction/drug effects ; Dextran Sulfate ; Colon/drug effects ; Andrographis/chemistry ; }, abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.<br><br>PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.<br><br>METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-&#x3b3;-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.<br><br>RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1&#x3b2;, IL-6, TNF-&#x3b1;) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-&#x3ba;B signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-&#x3ba;B signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.<br><br>CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-&#x3ba;B signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.}, }
@article {pmid41931897, year = {2026}, author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y}, title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141890}, doi = {10.1016/j.jhazmat.2026.141890}, pmid = {41931897}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Wastewater/microbiology/analysis ; *Fluorocarbons/analysis/toxicity ; RNA, Ribosomal, 16S/genetics ; *Genes, Bacterial ; *Microbiota/drug effects/genetics ; Water Microbiology ; Bacteria/genetics ; }, abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.}, }
@article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, mesh = {*Olea/microbiology ; Fermentation ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/isolation &amp; purification/genetics ; *Food Microbiology ; *Microbiota ; Fermented Foods/microbiology ; Italy ; }, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, }
@article {pmid41932525, year = {2026}, author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J}, title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134546}, doi = {10.1016/j.biortech.2026.134546}, pmid = {41932525}, issn = {1873-2976}, mesh = {Oxidation-Reduction ; *Chromium/metabolism ; *Methane/metabolism ; Electron Transport ; Biodegradation, Environmental ; *Microbial Consortia/physiology ; }, abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-L-Proline, L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.}, }
@article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41932913}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Bacteriocins/pharmacology/metabolism/biosynthesis ; Homeostasis ; *Mouth/microbiology ; Phosphorylation ; Streptococcus salivarius/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects ; Porphyromonas gingivalis/drug effects ; Biofilms/drug effects ; Streptococcus pneumoniae/drug effects ; Metagenomics ; Symbiosis ; Antimicrobial Peptides ; }, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, }
@article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41933095}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; *Pneumonia/microbiology/diagnosis/genetics ; *Lung/microbiology ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Multiomics ; Prospective Studies ; Sputum/microbiology ; Transcriptome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, }
@article {pmid41933601, year = {2026}, author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y}, title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134536}, doi = {10.1016/j.biortech.2026.134536}, pmid = {41933601}, issn = {1873-2976}, mesh = {Food Loss and Waste ; Methane/biosynthesis ; *Temperature ; Anaerobiosis ; Hydrolysis ; *Microbial Consortia/physiology ; Archaea/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism ; *Refuse Disposal/methods ; }, abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.}, }
@article {pmid41933710, year = {2026}, author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {140}, number = {}, pages = {105932}, doi = {10.1016/j.meegid.2026.105932}, pmid = {41933710}, issn = {1567-7257}, mesh = {Animals ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Tibet ; Phylogeny ; Genome, Viral ; *Mammals/virology ; Metagenome ; Virome ; }, abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.}, }
@article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {34}, number = {8}, pages = {820-827}, pmid = {41934012}, issn = {1878-4380}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; Microbial Interactions ; Ecosystem ; Ecology ; Bacteria/genetics ; }, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, }
@article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {7}, pages = {e70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Multiomics ; Metagenomics ; *Microbiota ; Feces/microbiology ; Bacteria/genetics/classification ; Male ; Adult ; Fungi/genetics/classification ; Female ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, }
@article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, mesh = {*Drinking Water ; Animals ; *Chlorine/toxicity ; Halogenation ; *Gastrointestinal Microbiome/drug effects ; Humans ; Mice ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, }
@article {pmid41935109, year = {2026}, author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J}, title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41935109}, issn = {2045-2322}, support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; }, mesh = {*Caves/microbiology ; China ; Humans ; Geologic Sediments/microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; *Human Activities ; Nitrogen/metabolism ; Phosphorus/metabolism ; Metagenomics ; }, abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.}, }
@article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41935274}, issn = {1743-422X}, mesh = {Animals ; Swine ; England/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Swine Diseases/virology/epidemiology ; *Virome ; Feces/virology ; *Viruses/classification/isolation &amp; purification/genetics ; Weaning ; Metagenomics ; Gastrointestinal Tract/virology ; Phylogeny ; *Virus Diseases/veterinary/virology ; }, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.<br><br>METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.<br><br>RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.<br><br>CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, }
@article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {7}, pages = {101848}, pmid = {41935631}, issn = {2589-5559}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; Homeostasis ; Male ; Female ; *Liver Diseases, Alcoholic/metabolism ; Cross-Sectional Studies ; Liver/metabolism ; Middle Aged ; Feces/chemistry ; Adult ; }, abstract = {BACKGROUND &amp; AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.<br><br>METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n = 462), alongside matched healthy controls (n = 148), and validated key findings in two independent ALD cohorts (n = 34 and n = 52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.<br><br>RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F = 69.9, p = 8.6e-66) and feces (inprimis, cholic acid: F = 5.5, p = 1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multistep dehydroxylation pathway (including baiB) increased, whereas those in the reduction arm (baiN) were depleted. In patients with ALD, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.<br><br>CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.<br><br>IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive ALD progression. Additionally, our study identifies specific bacterial species influencing BA concentrations in ALD using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating ALD.}, }
@article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {71}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, mesh = {*Doxycycline/therapeutic use/pharmacology ; Humans ; *Military Personnel ; *Antimalarials/therapeutic use ; Case-Control Studies ; Male ; Germany ; *Gastrointestinal Microbiome/drug effects/genetics ; Adult ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; Young Adult ; Feces/microbiology ; Female ; Malaria/prevention &amp; control ; *Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.<br><br>METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.<br><br>RESULTS: In total, 3770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).<br><br>CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, }
@article {pmid41937718, year = {2026}, author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X}, title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {19}, pages = {14120-14136}, doi = {10.1021/acs.est.5c17817}, pmid = {41937718}, issn = {1520-5851}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; *Horseshoe Crabs/microbiology ; *Drug Resistance, Microbial/genetics ; Diet ; }, abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.}, }
@article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0190325}, pmid = {41940696}, issn = {1098-5336}, support = {21TQ1400210//the Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 32071271//National Natural Science Foundation of China/ ; 32371332//National Natural Science Foundation of China/ ; 92478203//National Natural Science Foundation of China/ ; IPP30140//College Student Innovation and Practice Program of Shanghai Jiao Tong University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenome ; *Colorectal Neoplasms/microbiology ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; *Polysaccharide-Lyases/genetics/metabolism ; Mucins/metabolism ; Female ; Male ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, }
@article {pmid41940802, year = {2026}, author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , }, title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653550}, doi = {10.1080/19490976.2026.2653550}, pmid = {41940802}, issn = {1949-0984}, mesh = {Humans ; *Mouth/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Child, Preschool ; Saliva/microbiology ; Feces/microbiology ; *Growth Disorders/microbiology ; Male ; Cross-Sectional Studies ; Central African Republic ; Female ; Infant ; *Bacterial Translocation ; *Gastrointestinal Tract/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.}, }
@article {pmid41942192, year = {2026}, author = {Xia, Y and Kuda, T and Zhou, Q and He, Q}, title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118924}, doi = {10.1016/j.foodres.2026.118924}, pmid = {41942192}, issn = {1873-7145}, mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; Animals ; Antioxidants/pharmacology ; *Microbiota/drug effects ; Metabolomics ; Biogenic Amines/analysis ; Swine ; }, abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.}, }
@article {pmid41942205, year = {2026}, author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H}, title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118955}, doi = {10.1016/j.foodres.2026.118955}, pmid = {41942205}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Prunus avium/microbiology ; *Food Storage/methods ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/classification/genetics ; *Fruit/microbiology ; }, abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.}, }
@article {pmid41944841, year = {2026}, author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME}, title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41944841}, issn = {1432-072X}, mesh = {*Hevea/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Diseases/microbiology ; Phytoplasma/genetics/isolation &amp; purification ; Plant Bark/microbiology ; Latex/metabolism ; Metagenomics ; }, abstract = {Tapping Panel Dryness (TPD) is a complex physiological disorder in Hevea brasiliensis that leads to the cessation of latex flow, causing significant economic loss, yet its underlying cause remains unclear. Anatomical investigation of bark samples collected from TPD-affected samples exhibited deformed latex vessels, blocked sieve tubes, and DNA-containing bodies within phloem elements. Metagenomic profiling indicated largely similar microbial composition and diversity between healthy and TPD-affected bark samples, except for the presence of low-abundance taxa such as phytoplasma only in affected samples. However, predicted metabolic pathways differed significantly between healthy and TPD samples. The combined anatomical, cytological, and molecular evidences in the current study supports the potential involvement of a biotic factor in the etiology of TPD.}, }
@article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, mesh = {*Chromium/toxicity ; *Wastewater/microbiology ; Reactive Oxygen Species/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Antioxidants/pharmacology ; *Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Plasmids ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, }
@article {pmid41946403, year = {2026}, author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y}, title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134561}, doi = {10.1016/j.biortech.2026.134561}, pmid = {41946403}, issn = {1873-2976}, mesh = {Ammonium Compounds ; Oxidation-Reduction ; *Cephalexin/toxicity ; *Bioreactors ; *Microbial Consortia/drug effects ; Molecular Docking Simulation ; Stress, Physiological ; *Water Purification ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.}, }
@article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; *Lactation/physiology ; Milk/chemistry/metabolism ; Multiomics ; Metagenomics/methods ; Postpartum Period ; Prevotella/isolation &amp; purification/genetics ; Fatty Acids, Volatile/metabolism ; Methanobrevibacter/genetics/isolation &amp; purification ; Metabolomics ; Succinivibrionaceae/isolation &amp; purification/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.<br><br>RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.<br><br>CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, }
@article {pmid41947478, year = {2026}, author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G}, title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {40}, number = {8}, pages = {5016-5029}, pmid = {41947478}, issn = {1099-1573}, support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Saponins/pharmacology ; Humans ; *Triterpenes/pharmacology ; Caco-2 Cells ; *Gastrointestinal Microbiome/drug effects ; *Hypoglycemic Agents/pharmacology ; Mice ; Intestinal Barrier Function/drug effects ; Male ; Diabetes Mellitus, Type 2/drug therapy/metabolism ; Fatty Acids, Volatile/metabolism ; *Glucose/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/drug effects/metabolism ; Feces/chemistry ; Blood Glucose/metabolism/drug effects ; }, abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.}, }
@article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Virome/genetics ; Metagenomics ; Feces/microbiology/virology ; *Fungi/classification/genetics/isolation &amp; purification ; *Constipation/microbiology/virology ; Bacteria/classification/genetics/isolation &amp; purification ; *Mycobiome/genetics ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Metagenome ; Female ; Chronic Disease ; Viruses/classification/genetics/isolation &amp; purification ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, }
@article {pmid41949970, year = {2025}, author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A}, title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.}, journal = {La Tunisie medicale}, volume = {103}, number = {11}, pages = {1707-1717}, doi = {10.62438/tunismed.v103i11.6101}, pmid = {41949970}, issn = {2724-7031}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/therapy/microbiology ; *Dysbiosis/therapy/etiology/microbiology ; Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology/drug effects ; Prebiotics/administration &amp; dosage ; Diet, Mediterranean ; }, abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.}, }
@article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/drug therapy ; Multiomics ; *Gastrointestinal Microbiome/genetics ; Drug Monitoring/methods ; Dysbiosis/microbiology ; Feces/microbiology ; Metagenomics ; Metabolomics ; Proteomics ; }, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, }
@article {pmid41951175, year = {2026}, author = {Rana, N and Tiewsoh, K and Ray, P and Angrup, A}, title = {Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease.}, journal = {Indian journal of medical microbiology}, volume = {61}, number = {}, pages = {101110}, doi = {10.1016/j.ijmmb.2026.101110}, pmid = {41951175}, issn = {1998-3646}, mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Workflow ; Phylogeny ; Computational Biology/methods ; Bacteria/classification/genetics ; Software ; }, abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.<br><br>METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.<br><br>RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.<br><br>CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.}, }
@article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41951635}, issn = {2052-4463}, mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Sus scrofa/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Archaea/genetics/classification ; Bacteria/genetics/classification ; }, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, }
@article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {58}, number = {9}, pages = {911-922}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, mesh = {Humans ; Female ; Cross-Sectional Studies ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Adult ; Sensitivity and Specificity ; *Respiratory Tract Infections/diagnosis/microbiology ; Microbiota ; }, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.<br><br>METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.<br><br>RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n&#x2009;=&#x2009;18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.<br><br>CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, }
@article {pmid41955799, year = {2026}, author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G}, title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141956}, doi = {10.1016/j.jhazmat.2026.141956}, pmid = {41955799}, issn = {1873-3336}, mesh = {*Cadmium/metabolism ; Mining ; *Sulfates/metabolism ; Biodegradation, Environmental ; Metagenomics ; Bioreactors ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; Sewage/microbiology ; Microbial Consortia ; Oxidation-Reduction ; Wastewater ; }, abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.}, }
@article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology ; *Inhalation Exposure/adverse effects ; *Air Pollutants/adverse effects ; }, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.<br><br>METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.<br><br>RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.<br><br>CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, }
@article {pmid41957950, year = {2026}, author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A}, title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.}, journal = {Oncoimmunology}, volume = {15}, number = {1}, pages = {2656514}, pmid = {41957950}, issn = {2162-402X}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Actinobacteria/genetics/metabolism ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Neoplasms/therapy ; *Oncolytic Virotherapy/methods ; *Oncolytic Viruses/genetics ; Clinical Trials, Phase I as Topic ; }, abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.}, }
@article {pmid41961352, year = {2026}, author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H}, title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41961352}, issn = {1573-6903}, mesh = {Animals ; *Toll-Like Receptor 4/metabolism ; Male ; *Depression/drug therapy/metabolism ; *Isoflavones/therapeutic use/pharmacology ; Signal Transduction/drug effects ; *Myeloid Differentiation Factor 88/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *NF-kappa B/metabolism ; Rats ; Rats, Sprague-Dawley ; *Antidepressive Agents/therapeutic use/pharmacology ; Hippocampus/metabolism/drug effects ; }, abstract = {Depression is a highly prevalent mental disorder in which dysfunction of the gut microbiota is implicated as a significant factor in its pathogenesis. Puerarin has been suggested to alleviate depression via the microbe-gut-brain axis (MGBA), although the precise mechanisms remain elusive. This study aimed to elucidate the association between the antidepressant effects of puerarin and its role in regulating intestinal flora imbalance and inhibiting subsequent activation of the LPS/TLR4 inflammatory pathway from metabolomics and metagenomics perspectives. A rat model of depression was established using a 6-week chronic unpredictable mild stress (CUMS) protocol. Depressive-like behaviors were assessed through the sucrose preference test (SPT), forced swim test (FST), and open field test (OFT). Inflammatory cytokines (TNF-α, IL-1β, IL-6), LPS, corticosterone, and 5-HT were measured via ELISA. Hippocampal and colonic protein expression of TLR4, MyD88, IκBα, and NF-κB was analyzed by western blot. Colon tissue integrity was evaluated using H&amp;E staining, PAS staining, and transmission electron microscopy. Immunofluorescence was employed to detect Iba-1+ microglia, TLR4+ cells, and ZO-1 expression. Fecal metabolomics and metagenomics were conducted to identify differential metabolites and microbial composition, followed by KEGG and KO enrichment analyses to predict relevant pathways. Spearman correlation analysis was used to explore relationships among gut microbiota, metabolites, and behavioral indices. Puerarin markedly ameliorated depression-like behaviors in CUMS rats. Concurrently, puerarin inhibited the LPS/TLR4 signaling pathway and its downstream pro-inflammatory mediators in both the hippocampus and colon, resulting in a significant reduction in inflammatory responses across these regions, as well as in the serum. Metagenomic sequencing revealed that puerarin suppressed inflammation-associated bacteria, enhanced the abundance of Firmicutes, and induced alterations in the microbial community structure and composition. Metabolomic analysis demonstrated that puerarin could counteract dysregulated fecal metabolism, identifying 17 metabolites as potential key mediators in restoring metabolic homeostasis in CUMS rats. These biomarkers were implicated in several metabolic pathways, including Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, Alanine, Aspartate, and Glutamate metabolism. Puerarin may exert its antidepressant effects by modulating the gut microbial structure and metabolite profiles, thereby alleviating inflammatory stress in the colon, bloodstream, and hippocampus, potentially through inhibition of the LPS/TLR4 signaling pathway.}, }
@article {pmid41961886, year = {2026}, author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T}, title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0345919}, pmid = {41961886}, issn = {1932-6203}, mesh = {*Computational Biology/methods ; Machine Learning ; *Models, Biological ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.}, }
@article {pmid41963033, year = {2026}, author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I}, title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105049}, doi = {10.1016/j.fm.2026.105049}, pmid = {41963033}, issn = {1095-9998}, mesh = {*Cheese/microbiology/classification ; Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; Milk/microbiology ; High-Throughput Nucleotide Sequencing ; Greece ; }, abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.}, }
@article {pmid41963036, year = {2026}, author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y}, title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105055}, doi = {10.1016/j.fm.2026.105055}, pmid = {41963036}, issn = {1095-9998}, mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Seeds/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Phylogeny ; Microbiota ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Soil Microbiology ; }, abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.}, }
@article {pmid41963048, year = {2026}, author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M}, title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105075}, doi = {10.1016/j.fm.2026.105075}, pmid = {41963048}, issn = {1095-9998}, mesh = {Animals ; *Meat Products/microbiology/analysis ; Metagenomics ; Swine ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; Cooking ; Food Microbiology ; Food Storage ; Food Handling ; }, abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.}, }
@article {pmid41963512, year = {2026}, author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y}, title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41963512}, issn = {2045-2322}, mesh = {Humans ; *Stomach Neoplasms/microbiology/metabolism/pathology ; Male ; Aged ; *Gastrointestinal Microbiome ; Female ; *Metabolic Networks and Pathways ; Metagenome ; Middle Aged ; Bacteria/genetics/classification ; Aged, 80 and over ; Metagenomics ; }, abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.}, }
@article {pmid41964024, year = {2026}, author = {Sosef, NP and Boxman, ILA and Dirks, RAM}, title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41964024}, issn = {1743-422X}, support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; }, mesh = {*Nucleic Acid Hybridization/methods ; *Food Safety/methods ; Animals ; Humans ; Ostreidae/virology ; *Virome ; Norovirus/genetics/isolation &amp; purification ; Food Microbiology ; *Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.}, }
@article {pmid41964077, year = {2026}, author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ}, title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41964077}, issn = {2049-2618}, support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; }, mesh = {*Soil Microbiology ; California ; *Carbon/analysis/metabolism ; *Grassland ; *Soil/chemistry ; *Rain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/growth &amp; development/metabolism ; Seasons ; *Microbiota ; Carbon Dioxide/analysis/metabolism ; Carbon Cycle ; Metagenome ; }, abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.<br><br>RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by&#x2009;~1 order of magnitude, yielding decreased community growth efficiency (CGE&#x2009;=&#x2009;new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.<br><br>CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.}, }
@article {pmid41964107, year = {2026}, author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W}, title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657047}, pmid = {41964107}, issn = {1949-0984}, mesh = {Humans ; *Aldosterone/metabolism/blood ; *Hyperaldosteronism/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Mice ; Ruminococcus/metabolism/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Eubacteriales/metabolism/isolation &amp; purification/genetics ; Essential Hypertension/microbiology ; Blood Pressure ; }, abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.}, }
@article {pmid41965517, year = {2026}, author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H}, title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41965517}, issn = {1471-2180}, support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Silicon Dioxide/adverse effects/toxicity ; *Arginine/metabolism ; Mice ; *Pulmonary Fibrosis/chemically induced/metabolism/microbiology ; *Dysbiosis/microbiology/metabolism ; Disease Models, Animal ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; Lung/pathology ; Akkermansia ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.<br><br>RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.<br><br>CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.}, }
@article {pmid41966291, year = {2026}, author = {Ashango, ZA and Seyum, EG and Nwogha, JS}, title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {141}, number = {}, pages = {105941}, doi = {10.1016/j.meegid.2026.105941}, pmid = {41966291}, issn = {1567-7257}, mesh = {*Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Plant Breeding/methods ; *Microbiota ; }, abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.}, }
@article {pmid41966300, year = {2026}, author = {Bojko, J and Abd-Alla, A}, title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108623}, doi = {10.1016/j.jip.2026.108623}, pmid = {41966300}, issn = {1096-0805}, mesh = {Animals ; *Invertebrates/virology ; *Virome ; *Viruses/genetics ; }, abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.}, }
@article {pmid41966472, year = {2026}, author = {Merkhan, K and Chaudhry, AS}, title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.}, journal = {Anaerobe}, volume = {98}, number = {}, pages = {103046}, doi = {10.1016/j.anaerobe.2026.103046}, pmid = {41966472}, issn = {1095-8274}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Methane/metabolism/biosynthesis ; Fermentation ; *Animal Feed/analysis ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; Archaea/metabolism ; Bacteria/classification/genetics/metabolism ; *Food Additives ; }, abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.<br><br>METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72&#xa0;h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20&#xa0;g&#xa0;kg[-1] DM) for each PFA.<br><br>RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20&#xa0;g&#xa0;kg[-1] DM, followed by GBL with a 28.5% reduction at 10&#xa0;g&#xa0;kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.<br><br>CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.}, }
@article {pmid41966829, year = {2026}, author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, S&#xc1; and Ferenczi, S and Szőke, Z}, title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104498}, pmid = {41966829}, issn = {2666-1667}, mesh = {Animals ; Glyphosate ; *Mycotoxins/analysis/toxicity ; *Glycine/analogs &amp; derivatives/analysis/blood ; *Deer/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/chemistry/microbiology ; Metagenome/drug effects ; Computational Biology/methods ; Shotgun Sequencing ; Chromatography, Liquid ; }, abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].}, }
@article {pmid41967167, year = {2026}, author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB}, title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101830}, doi = {10.1016/j.cbd.2026.101830}, pmid = {41967167}, issn = {1878-0407}, mesh = {Animals ; *Aquaculture/methods ; Metabolomics ; *Microbiota ; *Multiomics ; }, abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.}, }
@article {pmid41968748, year = {2026}, author = {Hilpert, K}, title = {Peptidomics: A New Dimension in Microbiome Research.}, journal = {Protein and peptide letters}, volume = {33}, number = {2}, pages = {488-496}, doi = {10.2174/0109298665436241260327111926}, pmid = {41968748}, issn = {1875-5305}, mesh = {*Proteomics/methods ; *Microbiota/genetics/physiology ; Alzheimer Disease/microbiology ; Parkinson Disease/microbiology ; Depression/microbiology ; Cardiovascular Diseases/microbiology ; Humans ; Metagenome ; Biomarkers ; Metagenomics ; }, abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.}, }
@article {pmid41972755, year = {2026}, author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB}, title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.}, journal = {mSphere}, volume = {11}, number = {5}, pages = {e0011326}, pmid = {41972755}, issn = {2379-5042}, support = {//Flu Lab/ ; }, mesh = {Humans ; *Machine Learning ; *Biomarkers/analysis ; *Metagenome ; *Mouth/virology/microbiology ; *Viruses/genetics/isolation &amp; purification/classification ; *Environmental Monitoring/methods ; Microbiota ; *Nose/virology ; Saliva/virology ; Metagenomics ; }, abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.}, }
@article {pmid41973308, year = {2026}, author = {Aydin, F and Çek, &#x15e;}, title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.}, journal = {Veterinary research communications}, volume = {50}, number = {4}, pages = {}, pmid = {41973308}, issn = {1573-7446}, mesh = {Animals ; *Aquaculture ; *Fishes/microbiology/physiology ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects/physiology ; *Minerals/metabolism/administration &amp; dosage ; Diet/veterinary ; Animal Nutritional Physiological Phenomena ; Gastrointestinal Tract/microbiology ; }, abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.}, }
@article {pmid41973542, year = {2026}, author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S}, title = {Functional gut microbiomes enhance performance in house fly larvae.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0001126}, pmid = {41973542}, issn = {1098-5336}, support = {NNF21OC0070910//Novo Nordisk Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Houseflies/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.<br><br>IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.}, }
@article {pmid41974712, year = {2026}, author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y}, title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974712}, issn = {2041-1723}, support = {R21 AI180737/AI/NIAID NIH HHS/United States ; R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; Humans ; Male ; Mice ; Disease Models, Animal ; *Dysbiosis/diet therapy/immunology/microbiology ; *Faecalibacterium prausnitzii/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology/genetics ; *Lupus Erythematosus, Systemic/diet therapy/immunology/microbiology ; Metabolomics ; Metagenome ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration &amp; dosage ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; }, abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.}, }
@article {pmid41975031, year = {2026}, author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE}, title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41975031}, issn = {2399-3642}, support = {DairyBio//Dairy Australia/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Methane/metabolism ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Australia ; }, abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.}, }
@article {pmid41975041, year = {2026}, author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , }, title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.}, journal = {British journal of cancer}, volume = {135}, number = {1}, pages = {139-151}, pmid = {41975041}, issn = {1532-1827}, support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy/methods ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; Treatment Outcome ; }, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).<br><br>METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.<br><br>RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa&#xa0;-notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.<br><br>CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.<br><br>PROSPERO: CRD42023433704.}, }
@article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology ; *Vagina/microbiology ; Case-Control Studies ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Rectum/microbiology ; Aged ; Metagenomics/methods ; Endometrium/microbiology ; Adult ; Shotgun Sequencing ; }, abstract = {BACKGROUND: The human microbiome plays an emerging role in cancer biology, yet its contribution to endometrial cancer (EC) remains poorly defined. This study investigates the microbial composition of the vaginal, rectal, and endometrial sites in women with and without EC, aiming to uncover microbial signatures associated with the disease. RESULTS: We performed shotgun metagenomic sequencing on vaginal, rectal, and endometrial samples from 25 patients with EC and 27 control women undergoing hysterectomy for benign conditions. Vaginal and rectal swabs were collected before surgery, while endometrial swabs were obtained post-hysterectomy using a sterile brushing technique to prevent cross-contamination. Vaginal microbiota in patients with EC showed significantly higher microbial diversity and distinct community composition compared to controls. These differences remained significant after adjusting for age and body mass index. Several bacterial species, including Peptococcus niger, Anaerococcus murdochii, Mobiluncus, Porphyromonas, and Prevotella, were more abundant in the vaginal microbiota of patients with cancer. In contrast, Lactobacillus spp. were more abundant in vaginal and rectal samples of control subjects. CONCLUSIONS: This work represents one of the few studies to comprehensively examine the relationship between the vaginal, rectal, and endometrial microbiomes in the context of EC, suggesting a potential role for microbial imbalance in disease development. The findings underscore the importance of site-specific microbial analyses in gynecologic oncology and support further investigation into the microbiome as a possible biomarker for early detection and a target for preventive strategies.}, }
@article {pmid41975257, year = {2026}, author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z}, title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41975257}, issn = {1471-2105}, mesh = {*Software ; *Microbiota ; *Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Humans ; Metagenomics/methods ; *Microbial Interactions ; }, abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks. RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis. CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).}, }
@article {pmid41975274, year = {2026}, author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN}, title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655793}, pmid = {41975274}, issn = {1949-0984}, support = {R01 DK126691/DK/NIDDK NIH HHS/United States ; RC2 DK118619/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Metabolome ; Female ; Male ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Middle Aged ; *Liver Cirrhosis, Biliary/microbiology/metabolism ; *Cholangitis, Sclerosing/microbiology/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adult ; Metagenome ; Aged ; Metabolomics ; }, abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.}, }
@article {pmid41975427, year = {2026}, author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P}, title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41975427}, issn = {1746-6148}, support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; }, mesh = {Animals ; *Transcriptome ; Sheep/blood/microbiology ; Female ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; *Milk ; *Milk Substitutes ; Animal Feed/analysis ; }, abstract = {Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.}, }
@article {pmid41977149, year = {2026}, author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J}, title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977149}, issn = {1422-0067}, mesh = {*Malus/chemistry/microbiology/metabolism ; *Fermentation ; *Gastrointestinal Microbiome ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Fruit ; Bacteria/classification/genetics ; }, abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.}, }
@article {pmid41977414, year = {2026}, author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J}, title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977414}, issn = {1422-0067}, support = {2024YFF0907700//National Key R&amp;D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; }, mesh = {*Wood/microbiology/metabolism ; *Penicillium/metabolism/genetics/isolation &amp; purification ; *Microbiota ; Lignin/metabolism ; Biodegradation, Environmental ; }, abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.}, }
@article {pmid41979145, year = {2026}, author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA}, title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.}, journal = {Research report (Health Effects Institute)}, volume = {2026}, number = {237}, pages = {1-58}, pmid = {41979145}, issn = {1041-5505}, mesh = {Humans ; Female ; Infant ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; *Air Pollution/adverse effects/analysis ; *Environmental Exposure/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; California ; Particulate Matter/analysis/adverse effects ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; }, abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.<br><br>METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter &#x2264;2.5 &#xb5;m and &#x2264;10 &#xb5;m in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.<br><br>RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.<br><br>CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.}, }
@article {pmid41980294, year = {2026}, author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Glucose metabolism's impact on Blastocystis presence in the human gut.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106647}, doi = {10.1016/j.clnu.2026.106647}, pmid = {41980294}, issn = {1532-1983}, mesh = {Humans ; *Blastocystis/isolation &amp; purification ; *Gastrointestinal Microbiome/physiology ; Female ; *Glucose/metabolism ; Feces/microbiology/parasitology ; Metformin/therapeutic use/pharmacology ; Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; Blastocystis Infections/metabolism ; Middle Aged ; Adult ; }, abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.<br><br>METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.<br><br>RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.<br><br>CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.}, }
@article {pmid41980940, year = {2026}, author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z}, title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41980940}, issn = {2055-5008}, support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; }, mesh = {Animals ; *Ticks/microbiology ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Metagenome ; Sheep/microbiology ; Soil Microbiology ; Marmota/microbiology ; *Livestock/microbiology ; *Animals, Wild/microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Caves/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.}, }
@article {pmid41981035, year = {2026}, author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA}, title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41981035}, issn = {2045-2322}, support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; }, mesh = {*Permafrost/microbiology ; *Soil Microbiology ; Metagenome ; *Soil/chemistry ; Alaska ; *Bacteria/genetics/drug effects ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Sweden ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Although antimicrobial resistance is a contemporary public health concern, antimicrobial resistance genes (ARGs) have existed long before human use of antimicrobials, and recent attention has focused on whether permafrost thaw could release ARGs as the resistome shifts. We present a metagenomic analysis of permafrost samples from four sites in Alaska and Sweden, thawed under laboratory conditions. We used ABRicate, an alignment-based tool, and DeepARG, a deep learning tool, to identify ARGs, assessed their abundances under experimental thaw, measured taxonomic shifts, and examined metagenome-assembled genomes (MAGs) carrying ARGs. ARG abundance varied with depth, with some permafrost containing more ARGs than the seasonally thawed active layer. ARG abundance increased with soil carbon and decreased with pH across sites, suggesting site-specific influences. The majority of 164 high-quality MAGs contained ARGs, including 80 out of 105 species identified. This included bacteria from nine phyla, demonstrating widespread distribution across microbial taxa. Laboratory thaw experiments revealed that ARG abundances did not change significantly in two of the sites, but declined with thaw in the remaining two sites. Together, these findings demonstrate that ARGs are consistently present in permafrost microbiomes across multiple sites, but relative abundances generally do not increase during thaw. While ARGs that persist may pose potential risks, our results suggest that permafrost thaw may not substantially elevate environmental or public health risks.}, }
@article {pmid41981426, year = {2026}, author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L}, title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].}, journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery}, volume = {40}, number = {4}, pages = {548-556}, pmid = {41981426}, issn = {1002-1892}, mesh = {Humans ; Female ; Male ; *Prosthesis-Related Infections/microbiology ; *Gastrointestinal Microbiome ; *Osteoarthritis/microbiology/surgery ; Aged ; *Dysbiosis/microbiology ; Middle Aged ; Arthroplasty, Replacement, Hip/adverse effects ; *Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; Feces/microbiology ; Bacteria/isolation &amp; purification/classification ; }, abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.<br><br>METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7&#xb1;1) and (14&#xb1;1); for the AF group, preoperatively and on postoperative day (7&#xb1;1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).<br><br>RESULTS: Analysis of gut microbiota diversity showed that the preoperative &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7&#xb1;1), the &#x3b1;-diversity indices in the PJI group on postoperative day (7&#xb1;1) were lower, but the difference was not significant (P>0.05); by postoperative day (14&#xb1;1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the &#x3b1;-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.<br><br>CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.}, }
@article {pmid41981555, year = {2026}, author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C}, title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41981555}, issn = {1472-6831}, support = {P51 OD011132/OD/NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; P51 OD011132/CD/ODCDC CDC HHS/United States ; }, mesh = {Humans ; Longitudinal Studies ; *Microbiota ; *Periodontal Diseases/microbiology/virology/immunology/complications ; *HIV Infections/complications ; *Papillomavirus Infections/complications/immunology ; *Mouth/microbiology ; Human Papillomavirus Viruses ; Female ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is a major cause of oropharyngeal and other cancers, occurs more frequently among people with HIV (PWH). Despite antiretroviral therapy, HPV-related cancer incidence remains elevated in this group. Oral dysbiosis in PWH may impair mucosal immunity, promoting HPV persistence and inflammation. Periodontal disease, frequently observed in PWH, further contributes to microbial imbalance and immune dysregulation, increasing susceptibility to oral HPV infection. This study investigates the relationship among oral microbiome composition, periodontal disease and oral HPV infection behavior in PWH, considering immunologic and social determinants of health. METHODS: The characterizing oral microbiome and periodontal disease in oral HPV-positive individuals (COMP-HPV), an observational longitudinal study will enroll 500 PWH and follow them up for two years. Oral rinse for HPV testing and periodontal assessment will be collected every six months; saliva for inflammatory markers, oral rinse for microbiome and oral cytobrush for immunological profiling will be collected annually. Immune profiling will include high-dimensional flow cytometry and 10X RNA-sequencing to characterize innate and adaptive immune subsets, with emphasis on HLA-DR–positive populations, enabling evaluation of oral immune modulation during HPV infection. The study has four specific aims such as to examine associations between oral microbiome composition (16S and metagenomics) and oral HPV infection, including prevalence, incidence, persistence, and clearance; to assess the impact of periodontal disease on oral HPV infection and investigate whether the oral microbiome mediates this relationship; to determine how oral microbiome composition influences immunological responses in HPV-positive PWH and to evaluate the role of social determinants on oral microbiome composition and HPV infection. Data from this longitudinal study will be used to understand the natural history of oral HPV infection, the interplay with periodontal disease, microbial alterations, and immunological changes, providing evidence to guide interventions for reducing HPV-associated disease in PWH. TRIAL REGISTRATION NUMBER: Not applicable. DISCUSSION: The COMP-HPV study aims to contribute to the body of research designed to investigate mechanisms underlying oral HPV infection among PWH to improve immune responses to reduce HPV infection and relevant carcinoma.}, }
@article {pmid41984912, year = {2026}, author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , }, title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e86058}, pmid = {41984912}, issn = {1929-0748}, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Male ; Birth Cohort ; *Drug Resistance, Bacterial ; *Gastrointestinal Microbiome/drug effects ; Longitudinal Studies ; Prospective Studies ; Risk Factors ; South Africa ; Observational Studies as Topic ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.<br><br>OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.<br><br>METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.<br><br>RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.<br><br>CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.}, }
@article {pmid41985067, year = {2026}, author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR}, title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.}, journal = {Archives of insect biochemistry and physiology}, volume = {121}, number = {4}, pages = {e70159}, doi = {10.1002/arch.70159}, pmid = {41985067}, issn = {1520-6327}, support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science &amp; Technology, New Delhi, India (INSPIRE-JRF)/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; Metagenomics ; *Microbiota ; *Metamorphosis, Biological ; *Culicidae/microbiology/growth &amp; development ; Bacteria/classification/genetics ; }, abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.}, }
@article {pmid41985316, year = {2026}, author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P}, title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.}, journal = {Biomaterials advances}, volume = {185}, number = {}, pages = {214878}, doi = {10.1016/j.bioadv.2026.214878}, pmid = {41985316}, issn = {2772-9508}, mesh = {Animals ; *Inulin/chemistry/pharmacology ; *Diet, High-Fat/adverse effects ; *Bentonite/chemistry/pharmacology ; Rats ; Male ; *Inflammation/metabolism/drug therapy/chemically induced ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Lipid Metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.}, }
@article {pmid41986005, year = {2026}, author = {Ansari, A and Shete, O and Ghosh, TS}, title = {Artificial intelligence in microbial metagenomics.}, journal = {Progress in molecular biology and translational science}, volume = {221}, number = {}, pages = {255-276}, doi = {10.1016/bs.pmbts.2026.01.009}, pmid = {41986005}, issn = {1878-0814}, support = {//Non-US Government Research Support type/ ; }, mesh = {*Metagenomics ; *Artificial Intelligence ; Machine Learning ; Humans ; *Microbiota/genetics ; }, abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.}, }
@article {pmid41986664, year = {2026}, author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J}, title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41986664}, issn = {2399-3642}, mesh = {*Soil Microbiology ; *Microbiota/genetics ; Arctic Regions ; *Metagenomics ; *Metagenome ; Russia ; *Bacteria/genetics ; *Genes, Microbial ; }, abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.}, }
@article {pmid41987902, year = {2026}, author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S}, title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1729497}, pmid = {41987902}, issn = {2235-2988}, mesh = {Humans ; *Diarrhea/microbiology/prevention &amp; control/diagnosis ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Female ; *Probiotics/therapeutic use ; Pilot Projects ; Male ; Prognosis ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Prospective Studies ; DNA, Bacterial/genetics/chemistry ; Metagenome ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.<br><br>HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.<br><br>AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.<br><br>METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.<br><br>RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.<br><br>CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.}, }
@article {pmid41989380, year = {2026}, author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M}, title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659400}, pmid = {41989380}, issn = {1949-0984}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/metabolism ; Child ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Multiomics ; Diet ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; }, abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.}, }
@article {pmid41989870, year = {2026}, author = {Zhu, YC and Deng, Y and Zeng, JQ}, title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {73}, number = {2}, pages = {201-210}, doi = {10.1556/030.2026.02894}, pmid = {41989870}, issn = {1588-2640}, mesh = {Humans ; *Helicobacter Infections/microbiology/metabolism/complications ; Female ; *Helicobacter pylori/physiology ; *Intestine, Small/microbiology ; *Gastrointestinal Microbiome ; Male ; Multiomics ; Feces/microbiology ; *Metabolome ; Middle Aged ; Adult ; *Bacteria/classification/growth &amp; development/genetics/isolation &amp; purification/metabolism ; Aged ; }, abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.}, }
@article {pmid41990134, year = {2026}, author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J}, title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {5}, pages = {}, pmid = {41990134}, issn = {1574-6941}, support = {32471603//National Natural Science Foundation of China/ ; XZ202601ZY0248//Key Research and Development Program of Xizang Autonomous Region/ ; 2024-TG16//Central Financial Funds for Forestry and Grassland Reform and Development in 2024/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Rats ; *Hypoxia/microbiology ; Male ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolic Reprogramming ; Altitude ; Metagenomics ; }, abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.}, }
@article {pmid41990657, year = {2026}, author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D}, title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142056}, doi = {10.1016/j.jhazmat.2026.142056}, pmid = {41990657}, issn = {1873-3336}, mesh = {*Drug Resistance, Microbial/genetics ; Ecosystem ; Macau ; Sewage/virology ; Soil Microbiology ; Geologic Sediments/virology ; *Viruses/genetics ; *Virome ; }, abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.}, }
@article {pmid41991504, year = {2026}, author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S}, title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {4}, pages = {e70343}, pmid = {41991504}, issn = {1399-3038}, support = {//snfmi-remi/ ; //fai2r/ ; }, mesh = {Humans ; Female ; Haploinsufficiency ; Male ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Phenotype ; Child ; Liver/pathology ; Adolescent ; Feces/microbiology ; *Inflammatory Bowel Diseases/genetics/microbiology ; Liver Diseases/genetics ; Child, Preschool ; Ruminococcus ; *Intestines ; *Autoimmune Diseases/genetics/microbiology ; Eubacteriales ; }, abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.<br><br>METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.<br><br>RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.<br><br>CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.}, }
@article {pmid41991788, year = {2026}, author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T}, title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41991788}, issn = {1573-0972}, mesh = {*Nitrogen/metabolism ; *Rhizosphere ; Soil Microbiology ; *Microbiota ; *Cicer/microbiology/growth &amp; development ; *Solanum tuberosum/microbiology/growth &amp; development/metabolism ; *Mesorhizobium/physiology ; *Water/metabolism ; Biomass ; Droughts ; Tunisia ; Agriculture/methods ; Crop Production/methods ; Plant Roots/microbiology ; }, abstract = {Increasing water scarcity poses significant threats to crop production and agricultural sustainability. Water deficit and the environmental impacts of synthetic nitrogen fertilization necessitate the development of sustainable cropping systems that enhance resource use efficiency while mitigating climate and economic risks. This study investigates the effects of Mesorhizobium ciceri inoculation (CMG6 strain (SI-DP 40653)), varying water–nitrogen regimes, and a potato-chickpea intercropping system (IC) on plant performance, metabolic responses, rhizospheric microbial diversity. Field trials, located in northeastern Tunisia, showed that IC combined with efficient M. ciceri inoculation significantly outperformed sole cropping (SC) across all physiological parameters. Under standard conditions, this synergy bolstered chickpea biomass and photosynthetic capacity. Notably, under reduced nitrogen input, inoculated intercropping (IC) boosted chickpea shoot biomass by more than twofold compared with sole cropping (SC). Intercropping also improved drought resilience, reducing stress-induced metabolic decline by approximately 40% relative to monocropping systems. Secondary metabolite production was stimulated, with higher accumulation of polyphenols and tannins observed particularly under reduced nitrogen conditions in inoculated systems. Additionally, intercropping improved potato productivity under low-nitrogen conditions while maintaining stable yields under drought stress. Metagenomic analysis showed that water stress accounted for approximately 22% of microbial community variation. However, intercropping and inoculation reshaped rhizosphere communities by enhancing the abundance and diversity of beneficial bacterial groups, particularly Bacilli, and buffering drought-induced shifts. These results emphasized the synergistic benefits of IC and Rhizobium inoculation in improving crop productivity, stress resilience, and soil health while reducing reliance on synthetic inputs.}, }
@article {pmid41994961, year = {2026}, author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J}, title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.}, journal = {Biotechnology journal}, volume = {21}, number = {4}, pages = {e70228}, pmid = {41994961}, issn = {1860-7314}, support = {82203056//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Thalidomide/therapeutic use/pharmacology ; *Small Cell Lung Carcinoma/drug therapy/microbiology/metabolism ; *Lung Neoplasms/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Multiomics ; *Nausea/chemically induced/drug therapy/microbiology ; *Vomiting/chemically induced/drug therapy/microbiology ; Male ; Female ; Middle Aged ; Aged ; Metabolome/drug effects ; Metabolomics ; Antineoplastic Agents/adverse effects/therapeutic use ; }, abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.}, }
@article {pmid41995478, year = {2026}, author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS}, title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {64}, number = {2}, pages = {208-221}, pmid = {41995478}, issn = {1365-2036}, mesh = {Humans ; *Irritable Bowel Syndrome/metabolism/drug therapy/physiopathology/microbiology ; *Feces/chemistry ; *Fatty Acids, Volatile/metabolism ; Female ; Cross-Sectional Studies ; Male ; Adult ; Metabolomics ; Middle Aged ; Severity of Illness Index ; Gastrointestinal Transit/physiology ; Gastrointestinal Microbiome/physiology ; }, abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.<br><br>AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.<br><br>METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.<br><br>RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.<br><br>CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.}, }
@article {pmid41996042, year = {2026}, author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS}, title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {29}, number = {6}, pages = {877-887}, pmid = {41996042}, issn = {1618-1905}, mesh = {Adult ; Female ; Humans ; Middle Aged ; Young Adult ; Aging ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fibroblasts/metabolism ; *Metabolome ; Metabolomics ; *Microbiota ; Multiomics ; *Skin/microbiology/metabolism ; Skin Aging ; Skin Microbiome ; East Asian People ; }, abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.}, }
@article {pmid41996045, year = {2026}, author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P}, title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41996045}, issn = {1573-4978}, support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology/genetics ; *DNA, Bacterial/isolation &amp; purification/genetics ; RNA, Ribosomal, 16S/genetics ; DNA/isolation &amp; purification/genetics ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Metagenomics/methods ; }, abstract = {BACKGROUND: The symbiotic relationship between gut microbiota and their fish hosts has fuelled extensive research into microbial distribution besides their active role in host body metabolisms and paving the way for the sustainable aquaculture. This study aims to optimize and evaluate DNA extraction techniques for characterizing the gut microbiota of fish with diverse feeding habits: Hilsa (planktivorous), Catla (zooplankton feeder), Rohu (herbivorous), and Mrigal (illiophagus). METHODS AND RESULTS: Microbial genomic DNA was extracted using five traditional methods—PLICKS A, B, C, and CTAB (Methods D and E)—and three commercial kits (MN® Microbial, MN® Soil, and MN® Faecal), each with modifications. The efficacy of these methods was assessed based on DNA yield (traditional: 74–3070 ng/µL; commercial: 8.8–224 ng/µL), purity (traditional: A260/280: 1.38–1.92, A260/230: 1.03–2.21; commercial: A260/280: 1.30–3.25, A260/230: 0.5–2.0), and successful PCR amplification, a key step for downstream 16 S rRNA gene sequencing. Among traditional methods, PLICKS A (Catla), PLICKS C (Hilsa), CTAB (Mrigal and Catla), and PLICKS B (Catla, Rohu, Hilsa, Mrigal) delivered the highest DNA recovery (342–2080 ng/µL) and purity across different species. Similarly, among commercial kits, the MN® Microbial Modified Kit (Catla, Hilsa), MN® Soil Kit (Hilsa), MN® Soil Modified Kit (Catla, Rohu), MN® Faecal Kit (Catla), and MN® Modified Faecal Kit excelled, achieving optimal DNA recovery (108–224 ng/µL) and purity across various feeding habits. Overall, among traditional methods, PLICKS B proved to be the most effective, delivering high DNA yields (342–2080 ng/µL) with excellent purity (A260/280: 1.77–1.92; A260/230: 1.67–2.21) and enabling successful PCR amplification across fish species with diverse feeding habits. Similarly, among commercial kits, the MN Modified Faecal Kit achieved the highest DNA recovery (108–224 ng/µL) and purity (A260/280: 1.74–1.90; A260/230: 1.78–2.01), consistently supporting reliable amplification. CONCLUSIONS: These findings highlight effective DNA extraction methods tailored to fish with different feeding habits. Careful selection and optimization of extraction protocols are therefore essential for the accurate characterization of fish gut microbiota.}, }
@article {pmid41996860, year = {2026}, author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A}, title = {Relationship between pesticide exposure, gut microbiota, and hypertension.}, journal = {Environment international}, volume = {211}, number = {}, pages = {110250}, doi = {10.1016/j.envint.2026.110250}, pmid = {41996860}, issn = {1873-6750}, mesh = {Humans ; *Hypertension/epidemiology ; *Pesticides/blood/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Environmental Exposure/statistics &amp; numerical data ; China/epidemiology ; Adult ; Male ; Female ; }, abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.<br><br>METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.<br><br>RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC&#xa0;=&#xa0;0.897) for hypertension.<br><br>CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.}, }
@article {pmid41998050, year = {2026}, author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE}, title = {Metaproteomics uncovers the functional capacity of a soil microbiome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41998050}, issn = {2045-2322}, support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Proteomics/methods ; Bacteria/genetics/metabolism/classification ; Metagenome ; Archaea/genetics/metabolism/classification ; *Proteome ; Tandem Mass Spectrometry ; }, abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.}, }
@article {pmid41998770, year = {2026}, author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH}, title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {41998770}, issn = {1756-994X}, support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Female ; *Dermatitis, Atopic/immunology/etiology/microbiology/metabolism ; *Metabolome ; Pregnancy ; *Gastrointestinal Microbiome ; *Th2 Cells/immunology ; Case-Control Studies ; Infant ; Multiomics ; Male ; Prenatal Exposure Delayed Effects ; Adult ; Disease Susceptibility ; }, abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition. METHODS: We performed a longitudinal nested case–control study involving 128 well-characterized mother–offspring dyads from defined cases (offspring with atopic dermatitis (AD); n = 64) and controls (offspring without AD; n = 64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6 months of age for gut microbiome and metabolome analyses. RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation. CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome–immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring. TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).}, }
@article {pmid41998806, year = {2026}, author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z}, title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.}, journal = {Journal of medical primatology}, volume = {55}, number = {3}, pages = {e70074}, doi = {10.1111/jmp.70074}, pmid = {41998806}, issn = {1600-0684}, support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Diarrhea/veterinary/microbiology/immunology/drug therapy ; *Macaca mulatta/immunology/microbiology ; Longitudinal Studies ; *Monkey Diseases/immunology/microbiology ; *Gastrointestinal Microbiome ; Multiomics ; Anti-Bacterial Agents/therapeutic use ; Feces/microbiology ; Chronic Disease/veterinary ; Male ; }, abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.}, }
@article {pmid41999333, year = {2026}, author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG}, title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {17}, pages = {12853-12867}, doi = {10.1021/acs.est.6c02641}, pmid = {41999333}, issn = {1520-5851}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteriophages ; *Herbicide Resistance ; Herbicides ; }, abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.}, }
@article {pmid42000179, year = {2026}, author = {Iakovides, IC and Vasileiadis, S and Christou, A and Karaolia, P and Mina, T and Rocha, J and Duan, Y and Beretsou, VG and Gallois, N and Changey, F and Michael, C and Coelho, LP and Manaia, CM and Merlin, C and Fatta-Kassinos, D}, title = {Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125889}, doi = {10.1016/j.watres.2026.125889}, pmid = {42000179}, issn = {1879-2448}, mesh = {*Microbiota ; *Agricultural Irrigation ; Soil/chemistry ; *Wastewater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Bacteria/genetics ; Water Purification ; }, abstract = {Reclaimed water (RW) offers a sustainable solution for agricultural irrigation and freshwater conservation, but its microbial and chemical composition, shaped by treatment and storage processes, requires careful consideration for environmental and public health impacts. This study compared two RW types (conventional activated sludge with sand filtration and chlorination - CAS + SFC-RW - and membrane bioreactor - MBR-RW) with a tube well (TW) water control. The goal was to assess how storage influences the microbial composition, key antibiotic resistance and mobilome genes, and RW the impact on irrigated lysimeter soils during lettuce cultivation. Total bacteria were profiled using 16S rRNA gene sequencing and ddPCR, while antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were quantified by ddPCR and analysed by metagenomics. Initial RW samples had 1-1.5 orders of magnitude more 16S rRNA copies compared with the control, with significantly different bacterial and ARG/MGE profiles. Actinomycetota dominated CAS + SFC-RW, Bacteroidota the MBR-RW, and Pseudomonadota the TW water. Class 1 integrons and Tn916/Tn1545 were more abundant in CAS + SFC-RW compared with the MBR-RW. Storage reduced these differences toward convergence with the TW water profile, with putative pathogenic taxa, however, being more recalcitrant to change. RW irrigation altered soil bacterial composition, with MBR-RW having a greater impact as declared by the enhanced presence of Bacteroidota in the receiving soils. The RW influence was inversely related with vertical distance of the irrigation point, while the lettuce crop presence showed minimal/no impact. These results highlight the need for careful management of RW treatment and storage to ensure safe, resilient agricultural practices.}, }
@article {pmid42000463, year = {2026}, author = {Devika, NT and Jayaraman, K and Nadimuthu, S and Nathamuni, SP and Sreya, PS and Jangam, AK and Katneni, VK}, title = {Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101834}, doi = {10.1016/j.cbd.2026.101834}, pmid = {42000463}, issn = {1878-0407}, mesh = {Animals ; *Penaeidae/virology/microbiology ; *White spot syndrome virus 1/physiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.}, }
@article {pmid42000510, year = {2026}, author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S}, title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142094}, doi = {10.1016/j.jhazmat.2026.142094}, pmid = {42000510}, issn = {1873-3336}, mesh = {*Composting/methods ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Manure/microbiology ; *Humic Substances/analysis ; Animals ; Microbiota ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.}, }
@article {pmid42000556, year = {2026}, author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K}, title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.}, journal = {Marine environmental research}, volume = {218}, number = {}, pages = {108055}, doi = {10.1016/j.marenvres.2026.108055}, pmid = {42000556}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Environmental Monitoring/methods ; Norway ; Iceland ; Animals ; *Microbiota ; }, abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.}, }
@article {pmid42000726, year = {2026}, author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T}, title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42000726}, issn = {2041-1723}, mesh = {Humans ; *Bacteriophages/genetics/physiology ; Feces/microbiology/chemistry ; *Fatty Liver/microbiology/metabolism/virology ; *Gastrointestinal Microbiome/genetics/physiology ; Ruminococcus/virology/metabolism/genetics ; Metagenomics ; Faecalibacterium prausnitzii/metabolism/genetics/virology ; Bile Acids and Salts/metabolism ; Dysbiosis/microbiology ; *Bacteria/metabolism/genetics ; Metabolomics ; Female ; Male ; Case-Control Studies ; Eubacteriales ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.}, }
@article {pmid42001834, year = {2026}, author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A}, title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158119}, doi = {10.1016/j.phymed.2026.158119}, pmid = {42001834}, issn = {1618-095X}, mesh = {Animals ; *Catechin/analogs &amp; derivatives/pharmacology ; *Diarrhea/drug therapy/microbiology/veterinary ; Swine ; *Energy Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; Lymphocytes/drug effects/metabolism ; Escherichia coli ; Escherichia coli Infections ; }, abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.<br><br>OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.<br><br>METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and type&#x2161;innate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.<br><br>RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-&#x3b1;, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.<br><br>CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.}, }
@article {pmid42002296, year = {2026}, author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C}, title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70304}, doi = {10.1111/1462-2920.70304}, pmid = {42002296}, issn = {1462-2920}, support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth &amp; development/chemistry ; *Gastrointestinal Microbiome ; Metabolome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; }, abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.}, }
@article {pmid42002357, year = {2026}, author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z}, title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.}, journal = {Carbohydrate polymers}, volume = {382}, number = {}, pages = {125292}, doi = {10.1016/j.carbpol.2026.125292}, pmid = {42002357}, issn = {1879-1344}, mesh = {Animals ; *Curcuma/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Fructans/pharmacology/chemistry/therapeutic use/isolation &amp; purification ; Mice ; Dextran Sulfate ; Male ; *Colitis/chemically induced/drug therapy/metabolism ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Metabolic Networks and Pathways/drug effects ; Colon/drug effects/pathology ; Dysbiosis/drug therapy ; Disease Models, Animal ; }, abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.}, }
@article {pmid42002784, year = {2026}, author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C}, title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42002784}, issn = {2049-2618}, support = {2023YFD1301005//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Aflatoxin B1/toxicity ; *Curcumin/pharmacology/administration &amp; dosage ; *Rumen/microbiology/drug effects ; *Liver/drug effects/metabolism ; Sheep ; *Autophagy/drug effects ; *Pyroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Aflatoxin Poisoning ; }, abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.<br><br>RESULTS: In the experimental setup, 800&#xa0;mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500&#xa0;&#x3bc;g/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-&#x3ba;B-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.<br><br>CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.}, }
@article {pmid42002835, year = {2026}, author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E}, title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659397}, pmid = {42002835}, issn = {1949-0984}, mesh = {Humans ; *Adenine/analogs &amp; derivatives/adverse effects/therapeutic use ; *Piperidines/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Male ; Female ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects/metabolism ; Treatment Outcome ; *Pyrimidines/adverse effects/therapeutic use ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Diarrhea/chemically induced ; Aged ; *Pyrazoles/adverse effects/therapeutic use ; Metagenomics ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.}, }
@article {pmid42010118, year = {2026}, author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV}, title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.}, journal = {Nature medicine}, volume = {32}, number = {6}, pages = {2096-2106}, pmid = {42010118}, issn = {1546-170X}, support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i P&#xeb;rbashk&#xeb;t i BE-s&#xeb; p&#xeb;r K&#xeb;rkimet mbi S&#xeb;mundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/genetics ; Female ; Male ; *Genetic Predisposition to Disease ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Feces/microbiology ; *Glucosylceramidase/genetics ; Risk Factors ; Case-Control Studies ; *Microbiota/genetics ; Metagenomics ; Disease Progression ; }, abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.}, }
@article {pmid42010622, year = {2026}, author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M}, title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42010622}, issn = {1756-994X}, support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; }, mesh = {Humans ; Infant ; *Proctocolitis/microbiology/etiology ; *Food Hypersensitivity/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics/methods ; *Dietary Proteins/adverse effects ; Metagenome ; }, abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood. METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages. RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution. CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.}, }
@article {pmid42010710, year = {2026}, author = {Long, L and An, Y and Zhu, LT and Xu, XL and Lin, JJ and Xu, WJ and Chen, JY and Liu, FY and Liu, XY and Huang, Q}, title = {Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010710}, issn = {2049-2618}, support = {(42177362)//National Natural Science Foundation of China/ ; (2025J02030, 2025J01256)//Fujian Provincial Natural Science Foundation of China/ ; (NO. NBSDC-DB-21)//National Basic Science Data Center "Environment Health DataBase"/ ; }, mesh = {Child ; Humans ; Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; China ; *Dust/analysis ; Family Characteristics ; *Fungi/genetics/isolation &amp; purification/classification/pathogenicity ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.<br><br>RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39&#x2009;&#xd7;&#x2009;10[5] and 2.83&#x2009;&#xd7;&#x2009;10[6] DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF&#xa0;profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.<br><br>CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.}, }
@article {pmid42010711, year = {2026}, author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z}, title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010711}, issn = {2049-2618}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; }, mesh = {*Rhizosphere ; *Plant Roots/microbiology ; Streptomyces/genetics/metabolism/isolation &amp; purification ; *Metabolome ; Soil Microbiology ; Fusarium/isolation &amp; purification ; *Microbiota ; *Plants, Medicinal/microbiology ; *Angelica sinensis/microbiology/metabolism ; *Plant Diseases/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.<br><br>RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.<br><br>CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.}, }
@article {pmid42010713, year = {2026}, author = {Tang, J and Wang, L and Yang, Z and Song, Y and Wu, S and Liang, Q and Li, Z and Zhou, S and Xiong, H and Chen, D and Li, J and Li, F}, title = {Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010713}, issn = {2049-2618}, support = {32272874//National Natural Science Foundation of China/ ; 2021YFF1000601//National Key R&amp;D Program of China/ ; 2662025DKPY008//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Male ; Mice ; STAT5 Transcription Factor/metabolism ; *Gastrointestinal Microbiome/physiology ; Mice, Knockout ; *Spermatogenesis ; *gamma-Glutamyltransferase/genetics/deficiency/metabolism ; *Infertility, Male/microbiology/metabolism ; *Dysbiosis/microbiology ; STAT3 Transcription Factor/metabolism ; Fecal Microbiota Transplantation ; Testis/metabolism ; Signal Transduction ; *Glycine/analogs &amp; derivatives/metabolism ; Phenylacetates/metabolism ; Suppressor of Cytokine Signaling 3 Protein ; }, abstract = {BACKGROUND: Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.<br><br>RESULTS: This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1[-/-]) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1[-/-] mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1[-/-] mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1[-/-] mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1[-/-] mice (Ggt1[-/-]-FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&amp;Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites&#xa0;(TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates &#x3b2;2-adrenergic receptor (&#x3b2;2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.<br><br>CONCLUSION: Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via &#x3b2;2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced &#x3b2;2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B&#xa0;dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.}, }
@article {pmid42010766, year = {2026}, author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K}, title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2661415}, pmid = {42010766}, issn = {1949-0984}, mesh = {Humans ; *Obesity/metabolism/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; }, abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.}, }
@article {pmid42011762, year = {2026}, author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL}, title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.}, journal = {Zoological research}, volume = {47}, number = {2}, pages = {606-620}, pmid = {42011762}, issn = {2095-8137}, mesh = {Animals ; *Genetic Variation ; *Virome ; *Bacteriophages/genetics/classification ; *Mammals/virology ; *Animals, Zoo/virology ; Phylogeny ; *Viruses/genetics/classification ; }, abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.}, }
@article {pmid42012708, year = {2026}, author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P}, title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.}, journal = {European journal of nutrition}, volume = {65}, number = {4}, pages = {}, pmid = {42012708}, issn = {1436-6215}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Alcohol Drinking/adverse effects ; *Carcinogenesis ; *Colorectal Neoplasms/microbiology/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Risk Factors ; }, abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood. OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions. METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis. RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria. CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).}, }
@article {pmid42012901, year = {2026}, author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T}, title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {17}, pages = {13990-13997}, pmid = {42012901}, issn = {1520-5118}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sweetening Agents/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Thiazines/metabolism ; Intestinal Barrier Function ; Caco-2 Cells ; Butyrates/metabolism ; Child ; }, abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.}, }
@article {pmid42013836, year = {2026}, author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and ,  and ,  and Korten, I and Xavier, RJ}, title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {925-941.e6}, doi = {10.1016/j.chom.2026.03.019}, pmid = {42013836}, issn = {1934-6069}, mesh = {Humans ; *Microbiota/genetics/drug effects ; Infant ; Haemophilus influenzae/genetics/growth &amp; development/drug effects ; *Cystic Fibrosis/microbiology/therapy ; Metagenomics ; *Nose/microbiology ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Saline Solution, Hypertonic/pharmacology ; }, abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.}, }
@article {pmid42013844, year = {2026}, author = {Bargheet, A and Bø, GH and Hetland, MAK and Justine, M and Moyo, SJ and Löhr, IH and Blomberg, B and Langeland, N and Klingenberg, C and Pettersen, VK}, title = {Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102752}, pmid = {42013844}, issn = {2666-3791}, mesh = {Humans ; *Probiotics/pharmacology/administration &amp; dosage ; *Bifidobacterium/metabolism/drug effects/physiology ; Infant ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metabolome ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; Male ; Female ; Infant, Newborn ; }, abstract = {Early-life probiotics that strengthen gut resilience in infants are a promising strategy to combat the global emergency of antibiotic resistance. Still, their effects on antibiotic-resistant opportunistic pathogens, i.e., pathobionts, remain unclear. We evaluate the effects of probiotic supplementation in 152 full-term Tanzanian infants enrolled in the ProRIDE trial. Oral probiotics during the first 4 weeks of life increase gut colonization by Bifidobacterium species, while suppressing pathobionts, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Integrated metagenomics and metabolomics show that probiotics reduce resistome load and mobilome richness at 6 weeks, accompanied by concurrent shifts in the fecal metabolome. Specifically, the intervention increases lactate and pyruvate and reduces cross-feeding pathways that lead to propionate and butyrate, which partly explains the reduction in ESBL-E carriage. Our study documents putative pathways by which probiotic-driven Bifidobacterium colonization modulates the infant gut toward a lower level of antibiotic resistance.}, }
@article {pmid42013850, year = {2026}, author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB}, title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102761}, pmid = {42013850}, issn = {2666-3791}, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Saliva/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; *Mouth/microbiology ; Male ; Metagenome ; Middle Aged ; *Microbiota ; Dysbiosis/microbiology ; Aged ; }, abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.}, }
@article {pmid42014006, year = {2026}, author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W}, title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.}, journal = {International journal of biological macromolecules}, volume = {362}, number = {}, pages = {152109}, doi = {10.1016/j.ijbiomac.2026.152109}, pmid = {42014006}, issn = {1879-0003}, mesh = {Animals ; *Spleen/metabolism/drug effects/immunology ; *Polysaccharides/pharmacology ; *Cyclophosphamide/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Metabolomics/methods ; Cytokines/metabolism ; Immunosuppression Therapy ; Male ; *Immunologic Factors/pharmacology ; *Metabolome/drug effects ; Immunosuppressive Agents ; }, abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.}, }
@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.}, }
@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.}, }
@article {pmid42014993, year = {2026}, author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C}, title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42014993}, issn = {1471-2180}, mesh = {Animals ; Female ; Pregnancy ; Swine ; *Coronavirus Infections/veterinary/microbiology/virology ; Multiomics ; *Diarrhea/microbiology/veterinary/virology/metabolism ; *Swine Diseases/microbiology/virology/metabolism ; *Porcine epidemic diarrhea virus ; *Metabolome ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.}, }
@article {pmid42018438, year = {2026}, author = {Sun, X and Jiang, X and Zhang, L and Li, M}, title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117284}, doi = {10.1016/j.celrep.2026.117284}, pmid = {42018438}, issn = {2211-1247}, mesh = {Humans ; *Circadian Rhythm/physiology ; *Microbiota/genetics ; Female ; Adult ; Male ; *Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.}, }
@article {pmid42018637, year = {2026}, author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM}, title = {Defining metabolic niches for marine microbial heterotrophs.}, journal = {Science advances}, volume = {12}, number = {17}, pages = {eadz0537}, pmid = {42018637}, issn = {2375-2548}, mesh = {Ecosystem ; *Heterotrophic Processes ; Phytoplankton/metabolism ; Carbon Cycle ; *Microbiota ; *Seawater/microbiology ; Oceans and Seas ; *Aquatic Organisms/metabolism ; Biomass ; Metagenomics ; }, abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.}, }
@article {pmid42019232, year = {2026}, author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X}, title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.}, journal = {International journal of food microbiology}, volume = {456}, number = {}, pages = {111785}, doi = {10.1016/j.ijfoodmicro.2026.111785}, pmid = {42019232}, issn = {1879-3460}, mesh = {*Quorum Sensing ; *Homoserine/analogs &amp; derivatives/metabolism ; *Lactones/metabolism ; Bacterial Proteins/metabolism/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Fermentation ; *Food Storage ; *Microbiota ; Food Microbiology ; Carbon-Sulfur Lyases/metabolism/genetics ; }, abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.}, }
@article {pmid42019469, year = {2026}, author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH}, title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106914}, pmid = {42019469}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/growth &amp; development/physiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Signal Transduction ; *Taurine/metabolism/analogs &amp; derivatives ; p38 Mitogen-Activated Protein Kinases/metabolism/genetics ; *Avian Proteins/metabolism/genetics ; *Muscle Fibers, Skeletal/physiology ; Pectoralis Muscles/growth &amp; development/physiology ; Male ; *Muscle Development ; }, abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.}, }
@article {pmid42019770, year = {2026}, author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J}, title = {Atopic dermatitis: Multi-omics insights into microbiota-driven modulation of the gut-skin axis.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108504}, doi = {10.1016/j.micpath.2026.108504}, pmid = {42019770}, issn = {1096-1208}, mesh = {Humans ; *Dermatitis, Atopic/microbiology/therapy/genetics/immunology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; Fecal Microbiota Transplantation ; Animals ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Receptors, Aryl Hydrocarbon/metabolism ; Skin Microbiome ; }, abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.}, }
@article {pmid42020064, year = {2026}, author = {Peters, BA}, title = {Evidence grows for the gut-kidney axis, but questions still remain.}, journal = {Kidney international}, volume = {109}, number = {5}, pages = {832-834}, doi = {10.1016/j.kint.2026.02.015}, pmid = {42020064}, issn = {1523-1755}, mesh = {Humans ; *Kidney/physiology/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Kidney Diseases/microbiology ; }, abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.}, }
@article {pmid42020426, year = {2026}, author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ}, title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020426}, issn = {2041-1723}, support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Escherichia coli/genetics/metabolism/growth &amp; development/physiology ; *Oligosaccharides/metabolism ; *Bifidobacterium bifidum/genetics/physiology/metabolism/growth &amp; development ; *Symbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/physiology ; Trisaccharides/metabolism ; Infant ; Infant, Newborn ; Breast Feeding ; }, abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.}, }
@article {pmid42020464, year = {2026}, author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH}, title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42020464}, issn = {2045-2322}, support = {5850.0109317.18.9 and 21167-2//Petr&#xf3;leo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Atlantic Ocean ; *Microbiota/genetics ; *Ecosystem ; Metagenomics/methods ; *Seawater/microbiology ; *Bacteria/genetics/classification ; Metagenome ; Water Microbiology ; }, abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.}, }
@article {pmid42021075, year = {2026}, author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K}, title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.}, journal = {The journal of medical investigation : JMI}, volume = {73}, number = {1.2}, pages = {186-207}, doi = {10.2152/jmi.73.186}, pmid = {42021075}, issn = {1349-6867}, mesh = {Animals ; *Ampicillin/adverse effects ; *Diet, Western/adverse effects ; Female ; *Fatty Liver/etiology ; Mice, Inbred C57BL ; Mice ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Dysbiosis ; Male ; Feces/microbiology ; }, abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.}, }
@article {pmid42021724, year = {2026}, author = {Batra, N and Rout, PR and Dey, P}, title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.}, journal = {Food &amp; function}, volume = {17}, number = {9}, pages = {4245-4261}, doi = {10.1039/d5fo04976h}, pmid = {42021724}, issn = {2042-650X}, mesh = {*Probiotics/pharmacology ; Humans ; *Butyrates/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Lactiplantibacillus plantarum/physiology ; Anaerobiosis ; *Colon/microbiology/metabolism ; Amino Acids/metabolism ; }, abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.}, }
@article {pmid42022809, year = {2026}, author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH}, title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799859}, pmid = {42022809}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; Multiomics ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; *Infant, Premature ; Male ; Infant, Newborn ; Feces/microbiology ; Infant ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Biomarkers ; Metabolomics ; Dysbiosis/microbiology ; }, abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.}, }
@article {pmid42023591, year = {2026}, author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y}, title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662556}, pmid = {42023591}, issn = {1949-0984}, mesh = {Humans ; Animals ; *Energy Metabolism ; *Major Depressive Disorder/metabolism/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation ; Male ; Female ; Mice ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adult ; Middle Aged ; Multiomics ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.}, }
@article {pmid42023843, year = {2026}, author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.}, journal = {mBio}, volume = {17}, number = {5}, pages = {e0053426}, pmid = {42023843}, issn = {2150-7511}, support = {R01 AI158527/AI/NIAID NIH HHS/United States ; }, mesh = {Ethiopia/epidemiology ; Humans ; *Trachoma/microbiology/epidemiology ; Female ; *Phylogeny ; Male ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; Child, Preschool ; Infant ; Eye/microbiology ; Metagenomics ; Aged ; }, abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.}, }
@article {pmid42024170, year = {2026}, author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y}, title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.}, journal = {Clinical oral investigations}, volume = {30}, number = {5}, pages = {}, pmid = {42024170}, issn = {1436-3771}, support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; }, mesh = {Humans ; *Biofilms ; *Microbiota ; *Dental Caries/microbiology ; Adult ; Microscopy, Electron, Scanning ; Microscopy, Confocal ; Candida albicans ; Streptococcus mutans ; Female ; Male ; Saliva/microbiology ; }, abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.<br><br>MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.<br><br>RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.<br><br>CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.<br><br>CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.}, }
@article {pmid42026467, year = {2026}, author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F}, title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42026467}, issn = {1471-2180}, support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Male ; *Infertility, Male/microbiology/metabolism ; *Metabolome ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; Adult ; Metabolomics ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Tandem Mass Spectrometry ; Multiomics ; Chromatography, Liquid ; Semen Analysis ; }, abstract = {BACKGROUND: Primary idiopathic male infertility (PIMI) is a complex condition with unclear biological mechanisms. Increasing evidence indicates that gut microbiome-derived functional and metabolic alterations can influence host physiological processes, yet microbiome-associated functional changes in PIMI remain poorly characterized. METHODS: In this case–control study, fecal shotgun metagenomics and untargeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) metabolomics were performed in 19 men with PIMI and 12 fertile controls, alongside computer-assisted semen analysis. The study workflow integrated differential analyses, correlation analyses among key microbial species, metabolites, and clinical traits, and Random Forest modeling to derive a microbial-metabolic panel. RESULTS: Compared with fertile controls, infertile men exhibited selective functional remodeling of gut microbial pathways and fecal metabolic profiles, accompanied by reduced sperm concentration and progressive motility and increased round cell counts. Although overall microbial diversity was broadly comparable between groups, 23 differentially abundant species and 53 altered Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified by metagenomic profiling. Untargeted metabolomics annotated 4,434 metabolites and identified 780 differential metabolites, with enrichment of 29 KEGG pathways. Eight key microbial species and eight key metabolites mapped to sperm- and testis-related pathways showed coordinated correlations with semen parameters. An integrated Random Forest model incorporating microbial and metabolic features demonstrated robust discrimination between infertile and fertile men, with optimal performance achieved using six top-ranked features. CONCLUSIONS: PIMI is associated with selective gut microbial functional shifts and fecal metabolic disturbances that correlate with semen quality. Multi-omics integration highlights coordinated microbiome-metabolome alterations, providing insights into host-associated microbial functional dysregulation in male infertility.}, }
@article {pmid42026803, year = {2026}, author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R}, title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662690}, pmid = {42026803}, issn = {1949-0984}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/genetics/drug effects ; Biomarkers, Tumor/genetics ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Deep Learning ; }, abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.}, }
@article {pmid42028995, year = {2026}, author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y}, title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0026826}, pmid = {42028995}, issn = {1098-5336}, mesh = {*Medicago sativa/growth &amp; development/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacillus/physiology ; Soil/chemistry ; *Coal ; Gene Expression Regulation, Bacterial ; }, abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.<br><br>IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.}, }
@article {pmid42029028, year = {2026}, author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M}, title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0030826}, pmid = {42029028}, issn = {1098-5336}, support = {37/1027-1//Deutsche Forschungsgemeinschaft/ ; 503493769//Deutsche Forschungsgemeinschaft/ ; PE501078509-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; }, mesh = {Biodegradation, Environmental ; Mining ; *Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Peru ; Oxidation-Reduction ; Acids/metabolism ; }, abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.}, }
@article {pmid42029951, year = {2026}, author = {Kallistova, A and Savvichev, A and Toshchakov, S and Tutubalina, N and Rusanov, I and Petrova, K and Kadnikov, V and Beletsky, A and Zakharova, E and Ravin, N and Pimenov, N}, title = {Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42029951}, issn = {1432-0991}, support = {22-14-00038-C//Russian Science Foundation/ ; }, mesh = {*Lakes/microbiology/chemistry ; Altitude ; *Carbon/analysis/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Dissolved Organic Matter/analysis/metabolism ; *Microbiota ; Climate Change ; }, abstract = {It is evident that climate change is causing glaciers to melt at an accelerated rate. This has a noticeable impact on the hydrological regime of high-altitude lakes, as well as the activity of microbial communities. However, the impact of climate change on microbial processes, abundance and diversity of microbial communities in high-altitude lakes remains to be elucidated. The objective of the study was to evaluate the structure, activity and metabolic capacity of microbial communities inhabiting the high-altitude Caucasus lake. Analytical and radiotracer methods were used together with 16S rRNA profiling, and metagenome analyses. Elevated concentrations of dissolved organic carbon (DOC) were observed in both the water column of the lake (12.2–19.4 mg/l) and the pore water of the sediments (6.3–15.8 mg/l). The intensity of photosynthesis in water column was very low. The bulk of phototrophs concentrated on the sediment surface where we suggest they produce organic matter due to sufficient light penetration and warming of the overlying water. The elevated DOC concentrations facilitated the activity of diverse heterotrophic microorganisms, resulting in oxygen depletion and activation of anaerobic processes in sediments. In case of an increase in the average annual temperature of the region, it is possible to predict the transformation of the lake into a eutrophic meromictic reservoir with constantly anoxic water layers, where sulfate reduction and methanogenesis would assume a pivotal role.}, }
@article {pmid42030718, year = {2026}, author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L}, title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142145}, doi = {10.1016/j.jhazmat.2026.142145}, pmid = {42030718}, issn = {1873-3336}, mesh = {*Arsenic/analysis/metabolism ; *Estuaries ; *Water Pollutants, Chemical/analysis/metabolism ; Rivers/chemistry/microbiology ; Geologic Sediments/chemistry ; China ; Bacteria/metabolism/genetics ; Seasons ; Metagenome ; Microbiota ; }, abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.}, }
@article {pmid42032005, year = {2026}, author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG}, title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42032005}, issn = {2045-2322}, support = {N. 24-45-20005//RSF grant/ ; }, mesh = {Animals ; *Ixodes/virology ; Russia ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; *Virome/genetics ; Genetic Variation ; }, abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.}, }
@article {pmid42032279, year = {2026}, author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G}, title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1739-1753}, pmid = {42032279}, issn = {2058-5276}, support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics/classification ; *Metagenomics/methods ; Colorectal Neoplasms/microbiology ; Substrate Specificity ; Carbohydrate Metabolism ; Mucins/metabolism ; }, abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .}, }
@article {pmid42032281, year = {2026}, author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J}, title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1626-1638}, pmid = {42032281}, issn = {2058-5276}, support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Metagenomics/methods ; Algorithms ; Polymorphism, Single Nucleotide ; Streptococcus pneumoniae/genetics ; Plasmodium falciparum/genetics ; Feces/microbiology ; COVID-19/transmission ; Malaria, Falciparum/transmission ; Gastrointestinal Microbiome/genetics ; Metagenome ; Infant ; High-Throughput Nucleotide Sequencing ; }, abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.}, }
@article {pmid42032888, year = {2026}, author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z}, title = {Rhizosphere microbiome influences fruit quality in citrus.}, journal = {The New phytologist}, volume = {250}, number = {6}, pages = {3914-3931}, doi = {10.1111/nph.71159}, pmid = {42032888}, issn = {1469-8137}, support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; }, mesh = {*Rhizosphere ; *Microbiota/genetics ; *Fruit/microbiology ; *Citrus/microbiology ; Iron/metabolism ; Bacteria/genetics/metabolism ; Siderophores/metabolism ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.}, }
@article {pmid42032992, year = {2025}, author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M}, title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {12}, pages = {2312-2324}, pmid = {42032992}, issn = {1672-7347}, support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *RNA, Ribosomal, 16S/genetics ; Child ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.<br><br>METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. &#x3b1;-diversity, &#x3b2;-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.<br><br>RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). &#x3b1;-diversity analysis showed that in the overall population, the Shannon index (5.49&#xb1;1.11) and Chao1 index (1 843.04&#xb1;580.78) in the V3 to V4 region were higher than the Shannon index (4.98&#xb1;0.65) and Chao1 index (379.59&#xb1;47.27) in the V4 region (all P<0.001). &#x3b2;-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41&#xb1;1.62) was not significantly different from that of metagenomic sequencing (6.39&#xb1;0.42) (P=0.169), while the Chao1 index (1 889.92&#xb1;781.73) was lower than that of metagenomic sequencing (3 092.71&#xb1;505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89&#xb1;0.94 vs 6.39&#xb1;0.42, 362.41&#xb1;35.22 vs 3 092.71&#xb1;505.89, respectively, both P<0.01).<br><br>CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of &#x3b1;-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.}, }
@article {pmid42033969, year = {2026}, author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C}, title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108068}, doi = {10.1016/j.marenvres.2026.108068}, pmid = {42033969}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; China ; *Environmental Monitoring ; *Microbiota ; Bacteria ; }, abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.}, }
@article {pmid42033990, year = {2026}, author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W}, title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.}, journal = {Biomaterials}, volume = {333}, number = {}, pages = {124234}, doi = {10.1016/j.biomaterials.2026.124234}, pmid = {42033990}, issn = {1878-5905}, mesh = {*Biofilms/drug effects ; Molybdenum/chemistry ; *Oxygen/chemistry ; *Periodontitis/microbiology/drug therapy/therapy ; *Microbiota/drug effects ; Humans ; Indocyanine Green/chemistry/pharmacology ; Animals ; *Nanoparticles/chemistry ; Photochemotherapy ; Photosensitizing Agents/chemistry/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.}, }
@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 &amp; 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.}, }
@article {pmid42034426, year = {2026}, author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H}, title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107059}, doi = {10.1016/j.pestbp.2026.107059}, pmid = {42034426}, issn = {1095-9939}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Metagenome ; Interspersed Repetitive Sequences ; }, abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.}, }
@article {pmid42034850, year = {2026}, author = {Gupta, E and Sharma, S and Dash, PK and Parida, M}, title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42034850}, issn = {2045-2322}, mesh = {Animals ; *Aedes/virology ; India ; *Metagenomics/methods ; Larva/virology ; *Nanopore Sequencing/methods ; *Virome ; Phylogeny ; *Arboviruses/genetics ; }, abstract = {Several arboviruses including Dengue, Chikungunya, Zika, West Nile and Japanese encephalitis viruses are emerging and re-emerging in many parts of the world over last two decades. Thus, environmental surveillance of the mosquito borne viruses employing latest next generation sequencing technology could enhance our comprehension about an impending outbreak, thereby, providing opportunity for timely intervention. In this study, Aedes larvae were collected from different locations of Gwalior, Central India, cultured and grown to adult and were screened utilizing metagenomic workflow in Oxford Nanopore platform. The results produced sufficient and valuable insights through demonstration of divergence of these mosquitoes’ virome. Viral families associated with Myoviridae, Mimiviridae, Iridoviridae, Bunyaviridae, Flaviviridae, Mesonivirdae etc. were prevailing across the pools, varying in relative abundance. Viruses like Betabaculovirus, Mimivirus, Shamonda virus were reported in most pools in high abundance. Viral analysis leads to Phasi Charoen-like virus (PCLV), Nam Dinh virus (NDiV), Hubei mosquito virus (HMV), Wenzhou sobemo-like virus 4 (WSLV) findings across samples. This work reports the first successful metagenomic profiling of field-collected mosquitoes from Gwalior, Central India. Consequently, this technique might be employed to wide spectrum investigation of field mosquitoes, aiding in public health awareness about currently circulating viruses as a preparedness against future epidemic.}, }
@article {pmid42035799, year = {2026}, author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K}, title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.}, journal = {Journal of affective disorders}, volume = {408}, number = {}, pages = {121858}, doi = {10.1016/j.jad.2026.121858}, pmid = {42035799}, issn = {1573-2517}, mesh = {Humans ; *Major Depressive Disorder/microbiology/psychology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Young Adult ; Adult ; Metagenomics ; Machine Learning ; Case-Control Studies ; }, abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.<br><br>METHODS: Fecal samples were collected from 121 first-episode, drug-na&#xef;ve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.<br><br>RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.<br><br>CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.}, }
@article {pmid42035921, year = {2026}, author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X}, title = {Molecular traces of microbial cross-kingdom migration: from the gut ecosystem to the intervertebral disc microenvironment.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {26}, number = {10}, pages = {2005-2021}, doi = {10.1016/j.spinee.2026.04.027}, pmid = {42035921}, issn = {1878-1632}, mesh = {Humans ; *Intervertebral Disc Degeneration/microbiology ; Female ; Cross-Sectional Studies ; Male ; Prospective Studies ; *Gastrointestinal Microbiome/physiology ; *Intervertebral Disc/microbiology ; Middle Aged ; Lumbar Vertebrae ; Multiomics ; Adult ; }, abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.<br><br>PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multiomics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.<br><br>STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.<br><br>PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.<br><br>OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).<br><br>METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multiomics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.<br><br>RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter 3 nonchondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-&#x3b2; pathway for profibrotic remodeling.<br><br>CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.}, }
@article {pmid42036496, year = {2026}, author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U}, title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {42036496}, issn = {1432-0614}, mesh = {Animals ; *Coumarins/metabolism ; *Feces/microbiology ; Rats, Sprague-Dawley ; Rats ; Hydrolyzable Tannins/metabolism ; *Plant Extracts/metabolism ; Ellagic Acid/metabolism ; Metagenomics ; Fermentation ; Male ; *Gastrointestinal Microbiome ; *Bacteria/metabolism/genetics/classification ; *Sapindaceae/chemistry ; }, abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.}, }
@article {pmid42036837, year = {2026}, author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L}, title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70359}, pmid = {42036837}, issn = {1751-7915}, support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; }, mesh = {*Microbiota/genetics ; Phenotype ; Soil Microbiology ; Chitin/metabolism ; *Chitinases/genetics/metabolism ; *Bacteria/enzymology/genetics/classification ; }, abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.}, }
@article {pmid42037322, year = {2026}, author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP}, title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {9}, pages = {e71828}, pmid = {42037322}, issn = {1530-6860}, support = {APIDOM-BACTERIOB//CHU de La R&#xe9;union/ ; //Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (Inserm)/ ; //University of La R&#xe9;union/ ; }, mesh = {Humans ; *Periodontitis/microbiology/metabolism/complications/pathology ; Female ; Male ; *Intra-Abdominal Fat/metabolism/pathology/microbiology ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/microbiology/pathology/metabolism ; *Metabolic Diseases/microbiology/metabolism/pathology ; Porphyromonas gingivalis ; Dysbiosis/microbiology ; *Mouth/microbiology ; }, abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.}, }
@article {pmid42037384, year = {2026}, author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ}, title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0358725}, pmid = {42037384}, issn = {2165-0497}, support = {K08 AI159384/AI/NIAID NIH HHS/United States ; K08AI159384/NH/NIH HHS/United States ; }, mesh = {Humans ; *Severe Acute Malnutrition/microbiology ; South Sudan ; Recurrence ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Infant ; Child, Preschool ; }, abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.}, }
@article {pmid42037401, year = {2026}, author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q}, title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0248125}, pmid = {42037401}, issn = {1098-5336}, mesh = {*Polyphosphates/metabolism ; *Phosphates/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics ; Geologic Sediments/microbiology/virology ; China ; *Viruses/genetics/metabolism ; Phosphorus/metabolism ; Rivers/microbiology/virology ; }, abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.}, }
@article {pmid42039195, year = {2026}, author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H}, title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1749584}, pmid = {42039195}, issn = {1664-3224}, mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/virology ; *Virome ; *Mycobiome ; *Genitalia, Female/microbiology/virology ; Microbiota ; Papillomavirus Infections/microbiology/virology ; *Reproductive Health ; Vagina/microbiology/virology ; }, abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.<br><br>METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.<br><br>RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.<br><br>CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.}, }
@article {pmid42041249, year = {2026}, author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS}, title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0286825}, pmid = {42041249}, issn = {2150-7511}, support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; *Streptococcus agalactiae/genetics/growth &amp; development/physiology ; *Vagina/microbiology ; Humans ; *Streptococcal Infections/microbiology ; Pregnancy ; Epithelial Cells/microbiology ; Animals ; Bacterial Adhesion ; Microbiota ; Akkermansia ; Mice ; }, abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.}, }
@article {pmid42043232, year = {2026}, author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S}, title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.}, journal = {Viruses}, volume = {18}, number = {4}, pages = {}, pmid = {42043232}, issn = {1999-4915}, support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; }, mesh = {Animals ; China ; Phylogeny ; *Virome ; Haemaphysalis longicornis/virology ; *Ticks/virology ; Genome, Viral ; Dermacentor/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Metagenomics ; Genetic Variation ; Transcriptome ; }, abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.}, }
@article {pmid42044543, year = {2026}, author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y}, title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129734}, doi = {10.1016/j.jenvman.2026.129734}, pmid = {42044543}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; *Geologic Sediments/microbiology ; *Microbial Consortia ; *Thiazines/metabolism ; Kinetics ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; Bacteria/metabolism ; }, abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.}, }
@article {pmid42045813, year = {2026}, author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , }, title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42045813}, issn = {1471-2180}, mesh = {Humans ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/drug therapy ; Female ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects/genetics ; Mesalamine/therapeutic use ; Male ; Adrenal Cortex Hormones/therapeutic use ; Adult ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Middle Aged ; Crohn Disease/microbiology/drug therapy ; Colitis, Ulcerative/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; }, abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome. METHODS: Fecal samples from 16 Crohn’s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy. RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the “pyrazinamide resistant rpsA” gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan). CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).}, }
@article {pmid42046871, year = {2026}, author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q}, title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.}, journal = {Journal of Zhejiang University. Science. B}, volume = {27}, number = {4}, pages = {375-389}, pmid = {42046871}, issn = {1862-1783}, support = {2021YFA0805904//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; Humans ; Mice ; Germ-Free Life ; *Gastrointestinal Microbiome/genetics ; *Fecal Microbiota Transplantation/methods ; *Metagenomics ; *Metagenome ; Reproducibility of Results ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Male ; Mice, Inbred C57BL ; }, abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.}, }
@article {pmid42049031, year = {2026}, author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q}, title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102780}, pmid = {42049031}, issn = {2666-3791}, mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/microbiology ; *Biomarkers/metabolism ; Prognosis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Animals ; *Microbiota ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.}, }
@article {pmid42049592, year = {2026}, author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , }, title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {25}, number = {4}, pages = {655-663}, doi = {10.1016/j.jcf.2026.04.005}, pmid = {42049592}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/complications/physiopathology ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Sputum/microbiology ; Male ; Microbiota ; Female ; *Bacteria, Anaerobic/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; }, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.}, }
@article {pmid42050358, year = {2026}, author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y}, title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.}, journal = {Plant, cell &amp; environment}, volume = {49}, number = {8}, pages = {5703-5719}, pmid = {42050358}, issn = {1365-3040}, support = {2024CXPT072//Key R&amp;D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; }, mesh = {*Indoleacetic Acids/metabolism ; *Rhizosphere ; *Salt Tolerance/physiology ; *Triticum/microbiology/physiology/metabolism ; *Bacillus cereus/physiology ; Plant Roots/microbiology/metabolism ; *Microbiota/physiology ; *Plant Proteins/metabolism ; Biological Transport ; }, abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.}, }
@article {pmid42052831, year = {2026}, author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S}, title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {4}, pages = {48982}, doi = {10.31083/FBL48982}, pmid = {42052831}, issn = {2768-6698}, support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; }, mesh = {Humans ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; *Bacteria/genetics/classification ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.<br><br>METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.<br><br>RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 &#xb1; 0.12, suggesting promising discriminatory potential that warrants further validation.<br><br>CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.}, }
@article {pmid42054100, year = {2026}, author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE}, title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.}, journal = {Microbial genomics}, volume = {12}, number = {4}, pages = {}, pmid = {42054100}, issn = {2057-5858}, mesh = {Animals ; *Metagenomics/methods ; Chickens/microbiology ; *Food Microbiology ; Cattle ; Salmon/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Meat/microbiology ; United Kingdom ; Anti-Bacterial Agents/pharmacology ; Swine ; Sheep ; Microbiota/genetics ; Genes, Bacterial ; }, abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.}, }
@article {pmid42055201, year = {2026}, author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M}, title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {306}, number = {}, pages = {110551}, doi = {10.1016/j.cbpc.2026.110551}, pmid = {42055201}, issn = {1532-0456}, mesh = {Animals ; *Fluoxetine/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Zebrafish/physiology ; Female ; *Water Pollutants, Chemical/toxicity ; *Feeding Behavior/drug effects ; *Selective Serotonin Reuptake Inhibitors/toxicity ; Homeostasis/drug effects ; Intestinal Barrier Function/drug effects ; Intestines/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.}, }
@article {pmid42057074, year = {2026}, author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T}, title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {42057074}, issn = {1746-6148}, mesh = {Animals ; *Microbiota ; Swine ; *Mycoplasma hyopneumoniae/immunology ; *Pneumonia of Swine, Mycoplasmal/prevention &amp; control/microbiology ; *Bacterial Vaccines/administration &amp; dosage/immunology ; *Vaccination/veterinary/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Nanotechnology ; Female ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; }, abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.}, }
@article {pmid42057198, year = {2026}, author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J}, title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42057198}, issn = {1756-994X}, support = {2021-01637//Vetenskapsr&#xe5;det/ ; 967569//V&#xe4;sterbotten L&#xe4;ns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; 09150162410022/ZONMW_/ZonMw/Netherlands ; }, mesh = {Humans ; *COVID-19/epidemiology/microbiology ; *Life Style ; Infant ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; Pandemics ; Feces/microbiology ; Metagenome ; Male ; Female ; Longitudinal Studies ; Hygiene ; }, abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.<br><br>METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.<br><br>RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value&#x2009;=&#x2009;0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.<br><br>CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.}, }
@article {pmid42057740, year = {2026}, author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM}, title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {18}, pages = {14335-14347}, doi = {10.1021/acs.jafc.5c17636}, pmid = {42057740}, issn = {1520-5118}, mesh = {Rhizosphere ; *Soil Microbiology ; Zea mays/growth &amp; development/microbiology/drug effects ; *Microbiota/drug effects ; Soil/chemistry ; *Soil Pollutants/chemistry/pharmacology/toxicity ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/drug effects ; *Microplastics/chemistry/toxicity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.}, }
@article {pmid42059388, year = {2026}, author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA}, title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0360225}, pmid = {42059388}, issn = {2165-0497}, support = {AI157981/NH/NIH HHS/United States ; AI167538/NH/NIH HHS/United States ; DK128053/NH/NIH HHS/United States ; GM136554/NH/NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; //Baylor College of Medicine/ ; }, mesh = {Humans ; Female ; *Arthritis, Rheumatoid/microbiology/immunology ; *Vagina/microbiology/immunology ; Adult ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Cytokines ; *Bacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Young Adult ; Rheumatoid Factor ; C-Reactive Protein/analysis ; Anti-Citrullinated Protein Antibodies/analysis ; }, abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.}, }
@article {pmid42059394, year = {2026}, author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS}, title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0251025}, pmid = {42059394}, issn = {2165-0497}, support = {AP19VSCEAH00C014//U.S. Department of Agriculture/ ; //Texas A&amp;M University/ ; }, mesh = {Animals ; Cattle/microbiology ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Female ; *Gastrointestinal Microbiome/drug effects ; Weaning ; *Drug Resistance, Bacterial ; Texas ; Dairying ; *Microbiota/drug effects ; }, abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.}, }
@article {pmid42059571, year = {2026}, author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF}, title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0164025}, pmid = {42059571}, issn = {2379-5077}, support = {EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft/ ; 237291755//Deutsche Forschungsgemeinschaft/ ; FOR 5042 - 426660215//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *N-Acetylgalactosaminyltransferases/genetics/metabolism ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; Male ; Bacteria/genetics/drug effects/classification ; Streptomycin/pharmacology ; }, abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.<br><br>IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.}, }
@article {pmid42059572, year = {2026}, author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L}, title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0080025}, pmid = {42059572}, issn = {2379-5077}, support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; }, mesh = {*Deep Learning ; *Microbiota/genetics ; Multiomics ; *Computational Biology/methods ; *Bacteria/classification/genetics ; *Metagenomics/methods ; }, abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.}, }
@article {pmid42059625, year = {2026}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0362625}, pmid = {42059625}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; R01 DE03013, R01 DE022586, 2R01 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Capnocytophaga/genetics/classification/isolation &amp; purification/physiology ; *Mouth/microbiology ; Microbiota ; Phylogeny ; Dental Plaque/microbiology ; Genome, Bacterial ; Metagenomics ; Metagenome ; }, abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.<br><br>IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.}, }
@article {pmid42059663, year = {2026}, author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y}, title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {42059663}, issn = {1477-4054}, support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; }, mesh = {Humans ; *COVID-19/complications/microbiology/virology ; Multiomics ; *Pulmonary Fibrosis/microbiology/etiology/virology ; *SARS-CoV-2 ; Disease Progression ; Female ; *Microbiota ; Male ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Metagenomics ; }, abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.}, }
@article {pmid42061404, year = {2026}, author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC}, title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117301}, doi = {10.1016/j.celrep.2026.117301}, pmid = {42061404}, issn = {2211-1247}, mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; *Tissue Donors ; Female ; Metagenome ; Male ; }, abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.}, }
@article {pmid42062403, year = {2026}, author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR}, title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42062403}, issn = {2045-2322}, mesh = {Egypt ; *Wastewater/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/drug effects ; *Drinking Water/microbiology ; Hospitals ; *Metagenome ; Humans ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; }, abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.}, }
@article {pmid42062664, year = {2026}, author = {Kieliszek, M}, title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.}, journal = {Biological trace element research}, volume = {204}, number = {9}, pages = {6552-6563}, pmid = {42062664}, issn = {1559-0720}, mesh = {*Selenium/metabolism ; Humans ; Oxidation-Reduction ; *Gastrointestinal Microbiome/physiology ; *Signal Transduction ; Animals ; Selenoproteins/metabolism ; Antioxidants/metabolism ; }, abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.}, }
@article {pmid42063908, year = {2026}, author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D}, title = {Gut microbial profiles of COVID-19 patients in Uganda.}, journal = {African health sciences}, volume = {26}, number = {1}, pages = {1-15}, pmid = {42063908}, issn = {1729-0503}, mesh = {Humans ; Uganda/epidemiology ; *COVID-19/microbiology/epidemiology ; Feces/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; Adult ; *Gastrointestinal Microbiome/genetics ; SARS-CoV-2 ; Middle Aged ; Severity of Illness Index ; *Bacteria/isolation &amp; purification/classification/genetics ; Young Adult ; Adolescent ; }, abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.<br><br>METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.<br><br>RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.<br><br>CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42066496, year = {2026}, author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y}, title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101823}, doi = {10.1016/j.animal.2026.101823}, pmid = {42066496}, issn = {1751-732X}, mesh = {Animals ; *Feces/chemistry/microbiology ; Biomarkers/analysis ; Metabolomics ; Swine ; Multiomics ; *Stress, Psychological/microbiology/metabolism ; Metagenomics ; *Gastrointestinal Microbiome ; Metabolome ; *Sus scrofa/microbiology/physiology ; Female ; Male ; }, abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.}, }
@article {pmid42066541, year = {2026}, author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X}, title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117442}, doi = {10.1016/j.diagmicrobio.2026.117442}, pmid = {42066541}, issn = {1879-0070}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Retrospective Studies ; *Metagenomics/methods ; Male ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Middle Aged ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification/classification ; Adult ; Aged, 80 and over ; Metagenome ; }, abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.<br><br>METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.<br><br>RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.<br><br>CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.}, }
@article {pmid42067625, year = {2026}, author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K}, title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1495-1510}, pmid = {42067625}, issn = {2058-5276}, support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; *Deoxycholic Acid/analogs &amp; derivatives/metabolism/pharmacology/therapeutic use ; Disease Models, Animal ; *Enterococcus/metabolism ; *Gastrointestinal Microbiome ; *Intestinal Barrier Function/drug effects ; Metabolomics ; *Sepsis/microbiology/drug therapy/metabolism ; Case-Control Studies ; }, abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.}, }
@article {pmid42067917, year = {2026}, author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q}, title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42067917}, issn = {2049-2618}, support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Capsaicin/pharmacology ; Mice ; TRPV Cation Channels/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Aminolevulinic Acid/metabolism ; *Blood Glucose/drug effects ; Male ; Glycemic Control ; Specific Pathogen-Free Organisms ; Metagenomics ; Eubacteriales/metabolism ; Feces/microbiology ; Capsicum/chemistry ; Germ-Free Life ; Akkermansia ; Metabolomics ; }, abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.<br><br>RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.<br><br>CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.}, }
@article {pmid42068031, year = {2026}, author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y}, title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2665870}, pmid = {42068031}, issn = {1949-0984}, mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Biofilms/growth &amp; development ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Mice ; Mice, Knockout ; *Intestinal Mucosa/metabolism/microbiology ; *Faecalibacterium prausnitzii/physiology/growth &amp; development ; Humans ; Homeostasis ; Colitis/microbiology/chemically induced ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Disease Models, Animal ; Intestinal Barrier Function ; }, abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.}, }
@article {pmid42068877, year = {2026}, author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G}, title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {156}, number = {}, pages = {158256}, doi = {10.1016/j.phymed.2026.158256}, pmid = {42068877}, issn = {1618-095X}, mesh = {Animals ; *Apoptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Thyroid Gland/drug effects/metabolism ; Male ; Rats ; *Goiter/drug therapy/chemically induced/metabolism ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Propylthiouracil ; Thyroid Hormones/biosynthesis ; Disease Models, Animal ; }, abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.<br><br>METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.<br><br>RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.<br><br>CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.}, }
@article {pmid42069117, year = {2026}, author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA}, title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {402}, number = {}, pages = {128242}, doi = {10.1016/j.envpol.2026.128242}, pmid = {42069117}, issn = {1873-6424}, mesh = {Arctic Regions ; Humans ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Virulence/genetics ; *Environmental Monitoring ; Estuaries ; Sewage/microbiology ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Microbiota ; Metagenome ; Stress, Physiological/genetics ; Genes, Bacterial ; }, abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detected high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.}, }
@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 &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42069617}, issn = {1756-3305}, support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Animals ; *Toxoplasma/isolation &amp; 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.<br><br>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.<br><br>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.<br><br>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.}, }
@article {pmid42069941, year = {2026}, author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I}, title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42069941}, issn = {1432-0991}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; Animals ; Probiotics ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.}, }
@article {pmid42071059, year = {2026}, author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D}, title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42071059}, issn = {2045-2322}, support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; }, mesh = {Multiomics ; Animals ; Metabolomics/methods ; *Agriculture/methods ; Cattle ; Metagenomics/methods ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; Chromatography, Liquid ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Soil Microbiology ; }, abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.}, }
@article {pmid42071227, year = {2026}, author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z}, title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.}, journal = {Clinical and translational medicine}, volume = {16}, number = {5}, pages = {e70667}, pmid = {42071227}, issn = {2001-1326}, support = {2022YFA1304000//National Key R&amp;D Program of China/ ; 2024B1111150001//Guangdong S&amp;T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics ; *DNA Damage/drug effects ; Animals ; Humans ; Mice ; *Carcinogenesis ; *Lactates/adverse effects/metabolism ; Male ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Disease Models, Animal ; }, abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.}, }
@article {pmid42074337, year = {2026}, author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X}, title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {8}, pages = {}, pmid = {42074337}, issn = {1422-0067}, support = {2025YFE0121200//National Key R&amp;D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; }, mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth &amp; development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth &amp; development ; *Transcriptome ; *Microbiota ; *Hypocreales/physiology ; Soil Microbiology ; Gene Expression Profiling ; Trichoderma ; }, abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.}, }
@article {pmid42079638, year = {2026}, author = {Han, X and Zang, D and Lin, M and Yin, Y and Liu, D and Sun, Q and Chen, J}, title = {Dynamic changes in gut microbiota and metabolites in advanced lung cancer patients with immune-related adverse events.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1731931}, pmid = {42079638}, issn = {1664-3224}, mesh = {Humans ; *Lung Neoplasms/drug therapy/immunology/metabolism ; *Gastrointestinal Microbiome/drug effects/immunology ; Female ; Male ; *Metabolome ; *Immune Checkpoint Inhibitors/adverse effects ; Middle Aged ; Aged ; Metabolomics/methods ; Feces/microbiology ; *Drug-Related Side Effects and Adverse Reactions/metabolism/etiology ; }, abstract = {BACKGROUND: Immune-related adverse events (irAEs) represent an urgent clinical challenge. Although accumulating evidence suggests that irAEs are associated with the gut microbiota and its metabolites, our understanding of the dynamic alterations in the gut microbiota and related metabolic profiles throughout the onset and progression of irAEs remains limited.<br><br>METHODS: A total of 48 fecal samples were collected from 32 lung cancer patients treated with immune checkpoint inhibitors, including 16 patients who developed irAEs and 16 who did not. Fecal samples were collected at baseline and, in patients with irAEs, at the time of irAEs onset. Metagenomic sequencing and untargeted metabolomics analyses were performed to identify baseline differences in gut microbiota and metabolites, characterize longitudinal dynamic changes in gut microbiota and metabolite profiles in patients with irAEs, and construct a machine learning based random forest model to predict the occurrence of irAEs.<br><br>RESULTS: There were baseline differences in microbial communities and metabolites between the two groups. In the non-irAEs group, Phocaeicola coprocola was enriched and Micrococales decreased. At baseline, viomycin was positively correlated with irAEs, while metabolites such as calcitriol and L-isoleucine were negatively correlated with irAEs. The roles of valine, leucine and isoleucine metabolism and vitamin B6 metabolism pathways were downregulated in the irAEs group. Compared to baseline, there were significant changes in gut microbiota and metabolites during the onset of irAEs, and the abundance of Veillonella increased during irAEs onset. Dynamic monitoring of metabolic changes in irAEs revealed decreased levels of trypsin butylester, BQ 123, DL-o-tyrosine, and nicotinamide-beta-riboside during irAEs attacks. Lysine degradation, arachidonic acid metabolism, folate biosynthesis, nicotinate and nicotinamide metabolism, and C5-branched dibasic acid metabolism were downregulated during the progression of irAEs. A model for predicting the occurrence of irAEs based on differential microbiota and metabolites was constructed, and after robust validation, the model showed good performance and excellent discriminative power.<br><br>CONCLUSIONS: The occurrence and development of irAEs are associated with the composition of the gut microbiota and metabolites, as well as their dynamic changes over time. These findings highlight the potential of gut microbiota and metabolites as biomarkers for predicting the occurrence and progression of irAEs.}, }
@article {pmid42080548, year = {2026}, author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S}, title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0016326}, pmid = {42080548}, issn = {2379-5077}, support = {2021ZD0201900//Ministry of Science and Technology of the People's Republic of China/ ; 82071030//National Natural Science Foundation of China/ ; 82071029//National Natural Science Foundation of China/ ; 18DZ2260200//Science and Technology Commission of Shanghai Municipality/ ; }, mesh = {Animals ; *Hypoxia/complications/metabolism/microbiology ; Mice ; Male ; *Fatty Liver/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Disease Models, Animal ; Sleep Apnea, Obstructive/complications/metabolism ; Metabolomics ; }, abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.}, }
@article {pmid42081609, year = {2026}, author = {Wang, Y and Zhang, B and Shen, C and Cao, M and Wang, N and Chen, T and He, G and Sun, G and Li, C and Li, Y and Yin, X and Sun, Y and Li, C and Zhou, X}, title = {N-Carbamoylglutamate enhances bull spermatogenesis via Paraprevotella-mediated vitamin B6 biosynthesis in rumen microbiota.}, journal = {Reproduction (Cambridge, England)}, volume = {171}, number = {5}, pages = {}, doi = {10.1093/reprod/xaag049}, pmid = {42081609}, issn = {1741-7899}, support = {CARS-36//The China Agriculture Research System of MOF and MARA/ ; 20240303081NC//The key Research and Development Program of Jilin Province/ ; XZ202401ZY0053//The key Research and Development Project of Tibet Autonomous Region/ ; }, mesh = {Animals ; Male ; *Spermatogenesis/drug effects ; *Vitamin B 6/biosynthesis ; *Rumen/microbiology/drug effects ; Cattle ; *Glutamates/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Dietary Supplements ; }, abstract = {In brief: Emerging evidence suggests that gut microbial metabolites can influence male fertility, but how rumen microbiota regulate spermatogenesis in ruminants remains unclear. This study demonstrates that N-carbamoylglutamate promotes bull spermatogenesis through a rumen microbiota-vitamin B6 axis associated with Paraprevotella. Abstract: N-Carbamoylglutamate (NCG), a functional analog of the arginine precursor, shows strong potential in enhancing spermatogenesis in bulls. In this study, dietary NCG supplementation significantly increased sperm density and motility in XiangXi yellow bulls, the local beef cattle. Metagenomic and serum metabolomic analyses revealed that NCG altered the composition of rumen microbiota, notably increasing the abundance of Paraprevotella and elevating serum vitamin B6 levels (p < 0 .05), suggesting a possible microbiota-associated metabolic modulation underlying its reproductive benefits. To explore this mechanism, a busulfan-induced mouse model of impaired spermatogenesis was established. Mice received transplants of either rumen microbiota from NCG-treated bulls or the differential genus Paraprevotella. Both treatments alleviated reproductive damage and increased vitamin B6 levels in serum and testis. Mechanistic investigation indicated that Paraprevotella was associated with upregulated expression of 3-phosphoserine aminotransferase, a key enzyme involved in vitamin B6 biosynthesis. Subsequent vitamin B6 supplementation experiments showed increased testicular glutathione levels and reduced thiobarbituric acid-reactive substances level (expressed as MDA equivalents). These experiments supported a contributory role of vitamin B6 in promoting spermatogenesis, including increased sperm count and enhanced expression of spermatogenic cell markers. In summary, this study demonstrated that NCG enhanced spermatogenesis in bulls by reshaping the rumen microbiota, particularly through enrichment of Paraprevotella, which was associated with increased systemic vitamin B6 levels and contributed to reproductive improvement. These findings provide further insights into the application of NCG in improving fertility in ruminants.}, }
@article {pmid42083059, year = {2026}, author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B}, title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42083059}, issn = {2049-2618}, support = {284894//Fonds de recherche du Qu&#xe9;bec/ ; }, mesh = {Humans ; Metagenomics/methods ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/microbiology ; Male ; Female ; *Melanoma/drug therapy/immunology/microbiology ; Feces/microbiology ; Animals ; *Lung Neoplasms/drug therapy/immunology/microbiology ; Colitis/microbiology/chemically induced/immunology ; Middle Aged ; Mice ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Ruminococcus/isolation &amp; purification ; Eubacteriales ; }, abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.<br><br>RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade&#x2009;&#x2265;&#x2009;2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade&#x2009;&#x2265;&#x2009;2 irAE had a lower alpha diversity compared to those who did not develop grade&#x2009;&#x2265;&#x2009;2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade&#x2009;&#x2265;&#x2009;2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin&#xa0;immunofluorescence signal and increased TNF-&#x3b1; and IL-1&#x3b2; expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also&#xa0;maintained after treatment with P. bifermentans&#x2009;<&#x2009;3&#xa0;kDa filtered supernatant.<br><br>CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.}, }
@article {pmid42084497, year = {2026}, author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD}, title = {Characterizing microbiomes of African fermented foods in a global context.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42084497}, issn = {1465-2080}, mesh = {*Microbiota/genetics ; *Fermented Foods/microbiology ; Africa ; Metagenomics ; Metagenome ; *Bacteria/classification/genetics/isolation &amp; purification ; Fermentation ; *Food Microbiology ; Humans ; }, abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.}, }
@article {pmid42084683, year = {2026}, author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M}, title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {16}, pages = {7765-7777}, pmid = {42084683}, issn = {1614-7499}, mesh = {*Rivers/microbiology ; India ; Virulence Factors ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Anti-Bacterial Agents ; Water Microbiology ; Bacteria/genetics ; *Microbiota ; Drug Resistance, Bacterial ; }, abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.}, }
@article {pmid42084764, year = {2026}, author = {Joshi, G and Khannam, KS}, title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42084764}, issn = {1432-072X}, mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Ecosystem ; Aquatic Organisms ; Oceans and Seas ; }, abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.}, }
@article {pmid42085791, year = {2026}, author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D}, title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142255}, doi = {10.1016/j.jhazmat.2026.142255}, pmid = {42085791}, issn = {1873-3336}, mesh = {*Ciprofloxacin/pharmacology ; *Tetracycline/pharmacology ; *Sewage/microbiology ; Nitrification/drug effects ; *Anti-Bacterial Agents/pharmacology ; Denitrification/drug effects ; Bioreactors/microbiology ; *Microalgae/drug effects/metabolism ; *Microbiota/drug effects ; Bacteria/drug effects/metabolism/genetics ; Biological Oxygen Demand Analysis ; Aerobiosis ; *Water Pollutants, Chemical ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.}, }
@article {pmid42085931, year = {2026}, author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB}, title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.}, journal = {EBioMedicine}, volume = {127}, number = {}, pages = {106281}, pmid = {42085931}, issn = {2352-3964}, support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Male ; *Carotid Artery Diseases/etiology/complications/metabolism/microbiology ; Multiomics/methods ; *HIV Infections/complications ; *Gastrointestinal Microbiome ; Middle Aged ; Metagenomics/methods ; Biomarkers ; Aged ; Metabolomics/methods ; }, abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.<br><br>METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).<br><br>FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.<br><br>INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.<br><br>FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).}, }
@article {pmid42086631, year = {2026}, author = {Moon, K and Kang, I and Cho, JC}, title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42086631}, issn = {2052-4463}, support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; }, mesh = {*Fresh Water/virology ; *Aquaculture ; *Genome, Viral ; *Virome ; *Metagenome ; Republic of Korea ; Bacteriophages/genetics ; }, abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.}, }
@article {pmid42087721, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Luo, Z and Chen, J and Yang, Y and Ge, T and Marsden, KA and Liang, G and Chadwick, DR and Chen, X and Gregory, AS and Wu, L and Liang, Y and Jones, DL and Ma, Q}, title = {Microbial Community Traits and Necromass Dynamics Shape Soil Carbon Accumulation.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70906}, doi = {10.1111/gcb.70906}, pmid = {42087721}, issn = {1365-2486}, support = {U24A20575//National Natural Science Foundation of China/ ; 32573140//National Natural Science Foundation of China/ ; 32402680//National Natural Science Foundation of China/ ; 2024M752818//China Postdoctoral Science Foundation/ ; 2026SNJF084//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 2025SNJF025//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 202303AC100013//Yunnan Key Research and Development Program/ ; 05//Smart Fertilization Project/ ; BBS/E/RH/23NB0007//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; //Lawes Agricultural Trust/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; *Fertilizers/analysis ; *Microbiota ; *Carbon Sequestration ; }, abstract = {Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long-term response to fertilisation remains unclear. Using the 180-year Broadbalk Experiment (the world's longest-running fertilisation trial; Rothamsted, UK), combined with [14]C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource-limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no-fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy-intensive enzyme synthesis. This metabolic efficiency facilitated a dual-pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg[-1], while microbial assimilation and necromass accumulation concurrently increased mineral-associated organic carbon (MAOC) from 6.8 to 21.5 g kg[-1]. Conversely, inorganic fertilisation induced an oligotrophic 'mining' strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon-limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta-analysis of field experiments (0-120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time-dependent manner, reaching a 77% gain after 80 years (three-fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long-term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.}, }
@article {pmid42088021, year = {2026}, author = {Wang, A and Wang, Q and Zhang, T and Qi, G and Ren, W and Tian, W and Chen, J}, title = {Integrated multi-omics profiling reveals phenotype- and tissue-specific host-microbiota interactions in paired tumor and peritumoral tissues of advanced gastric cancer patients from Northwest China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1763765}, pmid = {42088021}, issn = {2235-2988}, mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; Multiomics ; China ; Female ; Male ; Gene Expression Profiling ; *Host Microbial Interactions/genetics ; Gastric Mucosa/microbiology/pathology ; Middle Aged ; Aged ; *Microbiota ; Phenotype ; Helicobacter pylori ; Transcriptome ; Metagenomics ; Helicobacter Infections ; Gene Expression Regulation, Neoplastic ; }, abstract = {BACKGROUND: Advanced gastric cancer (AGC) exhibits a high incidence in Northwest China, largely attributed to region-specific dietary patterns and environmental exposures. Its pathogenesis involves complex host-microbiota crosstalk, which has not yet been comprehensively elucidated through integrated multi-omics approaches. Herein, we employed trasncriptomic and shotgun metagenomic sequencing on paired tumoral and peritumoal mucosal tissues from 88 AGC patients in Northwest China. Our aim was to systematically characterize host gene expression profiles, the composition and functional potential of the gastric mucosal microbiota, and their intricate interrelationships.<br><br>RESULTS: Transcriptomic profiling clearly distinguished tumoral from peritumoral regions (PERMANOVA, R[2] = 0.24, P = 0.0001), with 8870 differentially expressed genes (DEGs) identified between the two tissue types. Tumor tissues harbored 8377 up-regulated DEG, which were enriched in extracellular matrix (ECM) organization, cell cycle regulation, signaling transduction, and inflammatory pathways (e.g., PI3K-Akt, IL-17 signaling). In contrast, peritumoral tissues showed 493 up-regulated DEGs primarily associated with metabolic processes. Host gene expression was significantly modulated by Lauren classification in tumoral mucosa (P = 0.025) and by Helicobacter pylori (Hp) infection in peritumoral tissues (P = 0.0424). Hp-infected tissues exhibited 65 up-regulated DEGs linked to transcriptional misregulation in cancer, inflammation, immune activation and mitochondrial pathways. Lauren subtypes displayed distinct transcriptomic signatures: intestinal-type AGC was enriched in metabolic processes, diffuse-type in immune and signal transduction pathways, and mixed-type in Ras/MAPK/ErbB and NF-&#x3ba;B signaling pathways. Correlation analysis between the 8870 DEGs and seven differentially abundant bacterial species (e.g., Serratia surfactantfaciens, Pseudomonas protegens, Prevotella jejuni, and Streptococcus infantis) revealed 13199 significant correlations. Among these, S. surfactantfaciens and P. protegens exhibited the strongest connectivity with host genes. Functionally, the correlated DEGs were involved in ECM structure, cell cycle progression, immune and inflammatory responses, cellular proliferation and differentiation, and metabolic processes.<br><br>CONCLUSIONS: Our findings demonstrated phenotype- and tissue-specific regulation of host gene expression in AGC and revealed extensive host-microbe interactions. This work fills a critical gap in multi-omics research on AGC in the Northwest Chinese population and suggests potential diagnostic and therapeutic targets for AGC.}, }
@article {pmid42091967, year = {2026}, author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K}, title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42091967}, issn = {2045-2322}, support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; }, mesh = {Animals ; *Anopheles/genetics/microbiology/classification ; *RNA, Ribosomal, 16S/genetics ; *Genetic Variation ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Gastrointestinal Microbiome/genetics ; *Electron Transport Complex IV/genetics ; Phylogeny ; India ; Bacteria/genetics/classification ; }, abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.}, }
@article {pmid42092044, year = {2026}, author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E}, title = {CCMRI: a classification and curated database of climate change-related microbiome studies.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42092044}, issn = {2045-2322}, support = {2772//Hellenic Foundation for Research and Innovation/ ; }, mesh = {*Microbiota/genetics ; *Climate Change ; Metagenomics/methods ; Biocuration ; Metagenome ; *Databases, Factual ; Data Curation ; }, abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.}, }
@article {pmid42092753, year = {2026}, author = {Palanisamy, M and Babalola, OO and Ramalingam, S}, title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {42092753}, issn = {2730-6844}, support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; }, mesh = {*Salvia officinalis/microbiology/genetics ; *Microbiota ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics ; Bacteria/genetics/classification ; Shotgun Sequencing ; *Metagenome ; }, abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.<br><br>DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.}, }
@article {pmid42093272, year = {2026}, author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q}, title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.}, journal = {Cancer biology &amp; medicine}, volume = {23}, number = {5}, pages = {737-754}, pmid = {42093272}, issn = {2095-3941}, support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; }, mesh = {Humans ; Animals ; Mice ; *Bifidobacterium animalis/metabolism ; Disease Progression ; *CD8-Positive T-Lymphocytes/immunology ; *YAP-Signaling Proteins/metabolism ; *Melanoma, Experimental/immunology/therapy ; Administration, Oral ; Gastrointestinal Microbiome ; Mannose/metabolism ; Male ; Mice, Inbred C57BL ; Probiotics ; }, abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.<br><br>METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.<br><br>RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.<br><br>CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.}, }
@article {pmid42096004, year = {2026}, author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X}, title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.}, journal = {Current medical science}, volume = {46}, number = {3}, pages = {791-801}, pmid = {42096004}, issn = {2523-899X}, mesh = {Humans ; Female ; Pregnancy ; Multiomics ; Adult ; *Abortion, Spontaneous/metabolism/microbiology/pathology/genetics ; *Decidua/metabolism/pathology ; *Inflammation/metabolism/pathology/genetics ; Gastrointestinal Microbiome/genetics ; Metabolomics ; Dysbiosis ; Cytokines/metabolism ; NF-kappa B/metabolism ; Signal Transduction ; *Maternal-Fetal Exchange ; }, abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.<br><br>METHODS: Women with SA (n&#x2009;=&#x2009;30) and those with normal early pregnancy (NP, n&#x2009;=&#x2009;28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.<br><br>RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1&#x3b2; and TNF-&#x3b1; (1.49-fold and&#xa0;1.51-fold, both&#xa0;P&#x2009;<&#x2009;0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-&#x3ba;B signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score&#x2009;>&#x2009;2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP&#x2009;>&#x2009;1.0, adjusted P&#x2009;<&#x2009;0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P&#x2009;<&#x2009;0.0001) in the decidual tissue of SA patients.<br><br>CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.}, }
@article {pmid42096157, year = {2026}, author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM}, title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3046}, number = {}, pages = {171-187}, pmid = {42096157}, issn = {1940-6029}, mesh = {*Clostridioides difficile/physiology ; Mucins/metabolism/chemistry ; *Gastrointestinal Microbiome ; Bacterial Adhesion ; Humans ; Bioreactors/microbiology ; Animals ; Intestinal Mucosa/microbiology ; *Plankton ; Hydrogels/chemistry ; Models, Biological ; }, abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.}, }
@article {pmid42096522, year = {2026}, author = {Zhao, D and Zhang, C and Li, M and Li, H and Su, S and Zhang, X}, title = {Characteristics of carbon-fixing microbial communities and pathways across different aquatic systems in the Tianjin Binhai region.}, journal = {Journal of applied microbiology}, volume = {137}, number = {5}, pages = {}, doi = {10.1093/jambio/lxag112}, pmid = {42096522}, issn = {1365-2672}, support = {25JCZDJC00400//Tianjin Natural Science Foundation/ ; 42102299//National Natural Science Foundation of China/ ; }, mesh = {*Carbon Cycle ; *Groundwater/microbiology ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; China ; *Rivers/microbiology ; *Water Microbiology ; *Microbiota ; Ecosystem ; Carbon/metabolism ; }, abstract = {AIMS: Microbial carbon fixation is central to carbon cycling and carbon sink functioning in coastal aquatic ecosystems. Although carbon fixation pathways have been increasingly investigated across diverse aquatic environments, comparative evidence remains limited for hydrologically connected yet hydrochemically contrasting coastal groundwater and surface water systems. This study aimed to compare carbon-fixation-associated microbial communities and major carbon fixation pathways across groundwater, river water, and reservoir water in the Tianjin coastal region.<br><br>METHODS AND RESULTS: We integrated metagenomic sequencing with hydrochemical analyses to characterize carbon-fixation-associated microbial communities and six representative carbon fixation pathways. Surface waters were dominated by bacteria and showed relatively stable community composition, whereas groundwater communities comprised both bacteria and archaea and displayed pronounced spatial heterogeneity. The Calvin-Benson-Bassham cycle was prevalent across all water types, and the reductive tricarboxylic acid (rTCA) cycle was also widely distributed. Groundwater showed higher contributions of the Wood-Ljungdahl pathway, the archaeal 3-hydroxypropionate/4-hydroxybutyrate and dicarboxylate/4-hydroxybutyrate cycles, together with the rTCA cycle, indicating coexisting carbon fixation strategies. Pathway abundance and module completeness further suggested differences in pathway integrity among water types. Total dissolved solids, HCO3&#x207b;, CO32&#x207b;, and dissolved organic carbon were key correlates of carbon fixation gene distribution.<br><br>CONCLUSIONS: Carbon-fixation-associated microbial communities, pathway distributions, and pathway integrity differed markedly between coastal groundwater and surface waters. Groundwater exhibited enhanced non-CBB cycle potentials and more diversified carbon fixation strategies, highlighting the importance of groundwater processes in evaluating carbon sequestration potential and carbon cycling in hydrochemically heterogeneous coastal aquatic systems.}, }
@article {pmid42097342, year = {2026}, author = {Yin, D and Chen, M and Chen, X and Feng, Y and Zhou, X and Guan, Y and Zhang, Y and Bai, S and Li, L and Ouyang, H and Cheng, J and Zhu, W}, title = {Integrative multi-omics reveals that Pueraria thomsonii Radix alleviates dyslipidemia by remodeling gut microbiota and regulating arachidonic acid metabolism.}, journal = {Journal of ethnopharmacology}, volume = {368}, number = {}, pages = {121816}, doi = {10.1016/j.jep.2026.121816}, pmid = {42097342}, issn = {1872-7573}, mesh = {Animals ; *Dyslipidemias/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Multiomics ; *Pueraria/chemistry ; *Arachidonic Acid/metabolism ; Diet, High-Fat ; Rats, Sprague-Dawley ; Rats ; Humans ; Liver/drug effects/pathology/metabolism ; Metabolomics ; *Drugs, Chinese Herbal/pharmacology ; *Plant Extracts/pharmacology ; Lipid Metabolism/drug effects ; }, abstract = {Pueraria thomsonii Radix (PTR, "Fen-ge") is a food-medicine herb widely used in China for metabolic complaints. Its putative lipid-modulating effects are supported by traditional practice, but the molecular basis remains incompletely understood.<br><br>AIM OF THE STUDY: To elucidate the active constituents and mechanisms by which PTR mitigates dyslipidemia.<br><br>MATERIALS AND METHODS: Chemical profiling and plasma exposure of PTR constituents were characterized by UPLC-Q-TOF-MS/MS. A high-fat-diet rat model was used to assess pharmacodynamic endpoints including serum lipid panel, hepatic histopathology, liver injury markers and inflammatory cytokines. Untargeted plasma metabolomics was performed in rats and patients; rat fecal 16S rRNA gene sequencing and hepatic transcriptomics complemented mechanism inference. Multivariate models were cross-validated and FDR-controlled; pathway and multi-omics correlation analyses integrated metabolite-microbe-gene relationships.<br><br>RESULTS: PTR significantly ameliorated dyslipidemia in high-fat diet-fed rats, as evidenced by improved serum lipid profiles, reduced ALT/AST levels, and alleviated hepatic steatosis and inflammation in histopathological examination. Integrated metabolomic analysis across rats and patients revealed that the restored metabolic pathways were primarily concentrated in arachidonic acid and unsaturated fatty acid metabolism. Gut microbiota analysis indicated that PTR remodeled microbial taxa correlated with arachidonic acid-related lipid metabolism. Meanwhile, hepatic transcriptomics data showed that differentially expressed genes were functionally enriched in biological processes such as lipid oxidation and were bioinformatically linked to the AMPK signaling pathway.<br><br>CONCLUSIONS: PTR may ameliorate dyslipidemia through coordinated modulation of the gut microbiota and arachidonic acid metabolic network. Based on integrated omics analysis, the hepatic AMPK signaling pathway may potentially be involved in this regulatory process; however, its direct mechanistic role requires further experimental validation. Future investigations employing targeted lipid-omics, protein phosphorylation assays, and microbiota-transfer experiments are warranted to elucidate the causal relationships.}, }
@article {pmid42098310, year = {2026}, author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C}, title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {42098310}, issn = {2399-3642}, support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Virome/genetics ; Humans ; *HIV Infections/virology/blood/drug therapy ; *Dysbiosis/virology ; Metagenomics ; *Respiratory System/virology ; }, abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.}, }
@article {pmid42098386, year = {2026}, author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y}, title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {42098386}, issn = {2399-3642}, support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Polyesters/metabolism ; *Lead/metabolism/toxicity ; Biodegradation, Environmental ; *Microbiota/drug effects/genetics ; Soil Microbiology ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/genetics/metabolism ; *Genes, Viral ; Rhizosphere ; }, abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.}, }
@article {pmid42098796, year = {2026}, author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V}, title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098796}, issn = {2049-2618}, support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Universit&#xe0; e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Vulva/microbiology ; *RNA, Messenger/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *RNA-Seq/methods ; Vagina/microbiology ; Transcriptome ; *Host Microbial Interactions/genetics ; }, abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.<br><br>RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.<br><br>CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.}, }
@article {pmid42098871, year = {2026}, author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI}, title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098871}, issn = {2049-2618}, support = {P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Campylobacter jejuni/immunology/genetics ; *Campylobacter Infections/prevention &amp; control/veterinary/immunology/microbiology ; Chickens/microbiology/immunology ; *Bacterial Vaccines/immunology/administration &amp; dosage/genetics ; *Poultry Diseases/prevention &amp; control/microbiology/immunology ; Protein Subunit Vaccines ; Adhesins, Bacterial/immunology/genetics ; Lactococcus lactis/genetics ; Bacterial Proteins/immunology/genetics ; *Gastrointestinal Microbiome ; Vaccines, Synthetic/immunology/administration &amp; dosage ; Bacterial Adhesion ; Bacterial Outer Membrane Proteins ; Carrier Proteins ; }, abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.<br><br>RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p&#x2009;<&#x2009;0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~&#x2009;1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~&#x2009;2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.<br><br>CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.}, }
@article {pmid42098876, year = {2026}, author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B}, title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098876}, issn = {2049-2618}, support = {2023YFD2000703//National Key R&amp;D Program of China/ ; 2023YFD2000701//National Key R&amp;D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism ; Cattle ; *Proanthocyanidins/pharmacology/metabolism ; Female ; *Oxidoreductases/metabolism ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; Molecular Docking Simulation ; Dietary Supplements ; Lactation ; }, abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.<br><br>RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150&#xa0;kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20&#xa0;g/kg dry matter) decreased daily CH4 emissions by&#x2009;~&#x2009;8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.<br><br>CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.}, }
@article {pmid42100652, year = {2026}, author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C}, title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799729}, pmid = {42100652}, issn = {2235-2988}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; Male ; *Metagenomics/methods ; Rats, Wistar ; Feces/microbiology/chemistry ; Disease Models, Animal ; Rats ; *Liver Failure/chemically induced/therapy ; Cytokines/metabolism ; *Liver Failure, Acute ; Ammonia/blood ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Galactosamine ; }, abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.<br><br>METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 &#x3bc;g/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1&#xd7;10&#x2078; CFU/day) and high (1&#xd7;10&#x2079; CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.<br><br>RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6&#xb1;6.8 to 512.4&#xb1;48.9 U/L), AST (78.3&#xb1;9.5 to 684.7&#xb1;62.1 U/L), and plasma ammonia (38.9&#xb1;5.2 to 128.6&#xb1;14.3 &#x3bc;mol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7&#xb1;41.6 U/L (low dose) and 248.9&#xb1;32.4 U/L (high dose). Ammonia levels decreased to 86.4&#xb1;9.7 &#x3bc;mol/L and 59.8&#xb1;7.6 &#x3bc;mol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8&#xb1;4.2 to 63.9&#xb1;6.4 mM), lower ammonia (8.9&#xb1;1.1 to 3.7&#xb1;0.5 mM), improved intestinal barrier integrity (TEER: 462&#xb1;38 to 721&#xb1;44 &#x3a9;&#xb7;cm&#xb2;), and reduced TNF-&#x3b1; (214.6&#xb1;22.8 to 74.9&#xb1;12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.}, }
@article {pmid42100978, year = {2026}, author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD}, title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {42100978}, issn = {0973-7138}, mesh = {Animals ; Female ; Rats ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Docosahexaenoic Acids/pharmacology/administration &amp; dosage ; *Malnutrition/metabolism/microbiology/genetics ; Developmental Origins of Health and Disease ; Xanthophylls/administration &amp; dosage/pharmacology ; Rats, Wistar ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; Metabolome ; Male ; Fetal Development/drug effects ; }, abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.}, }
@article {pmid42101034, year = {2026}, author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM}, title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70354}, pmid = {42101034}, issn = {1758-2229}, support = {NA19NOS4190106//Texas General Land Office/ ; }, mesh = {*Estuaries ; *Viruses/classification/genetics/isolation &amp; purification ; Salinity ; *Fresh Water/virology/microbiology ; *Temperature ; Bacteria/genetics/classification ; Microbiota ; Metagenomics ; *Virome ; }, abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.}, }
@article {pmid42101202, year = {2026}, author = {Yashar, M and Thigale, UY and Karakus, S}, title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.}, journal = {Current opinion in ophthalmology}, volume = {37}, number = {4}, pages = {299-307}, doi = {10.1097/ICU.0000000000001228}, pmid = {42101202}, issn = {1531-7021}, mesh = {Humans ; *Microbiota/physiology ; *Eye Infections, Bacterial/microbiology ; }, abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.<br><br>RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced &#x3b1;-diversity and shifts in dominant taxa. Genera such as Staphylococcus , Corynebacterium , and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.<br><br>SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.}, }
@article {pmid42102564, year = {2026}, author = {Long, Z and Zhang, B and Bing, H and Wu, Y}, title = {Identifying microbial candidates for assisted phytoremediation through long-term microbial succession and functional gene shifts across a 50-year chronosequence of vanadium-titanium magnetite tailings.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142304}, doi = {10.1016/j.jhazmat.2026.142304}, pmid = {42102564}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Vanadium/metabolism ; *Soil Microbiology ; *Titanium ; *Soil Pollutants/metabolism ; Mining ; *Bacteria/genetics/metabolism ; *Microbiota ; }, abstract = {Soil microorganisms are central to vegetation restoration in metalliferous wastes. However, within mine tailings restoration chronosequences, particularly those enriched with vanadium (V), the long-term successional dynamics of microbial communities, their functional potentials, and the functional partitioning between key microbial taxa and lower-abundance microbial lineages remain poorly understood. Here, we utilized metagenomic sequencing across a 50-year restoration chronosequence to investigate changes in the microbial community and functional genes related to plant growth-promotion (phosphorus, nitrogen, and iron acquisition) and V tolerance/bioreduction. The results demonstrated significant shifts in the microbial community after five years of restoration. At the phylum level, Actinobacteria, Acidobacteria, Pseudomonadota, and Gemmatimonadota were dominant. In early stages (< 15 years), nitrogen and phosphorus acquisition genes (e.g., nif, fix, phoD) were 1.3-2.5 times more prevalent than in later stages, whereas functional genes associated with V (e.g., napA, narG, nirS) increased 1.5- to 2-fold over time. Vanadium and nitrogen were the primary environmental factors regulating both community structure and the relative abundance of critical functional genes. Keystone taxa possessed more nitrogen and phosphorus acquisition genes (65% and 45%, respectively), while metagenome-assembled genomes (MAGs) were enriched in genes related to siderophore biosynthesis (71%) and denitrification (potential V bioreduction) (65%). Based on functional gene profiles, Bradyrhizobium, Allosphingosinicella, Baekduia, Sphingomicrobium, and Hylemonella were identified as promising microbial candidates for enhancing restoration in V-contaminated sites. This study enables the development of targeted microbial consortia to mitigate nutrient deficiency and V toxicity, directly informing the design of more efficient, stage-specific phytoremediation strategies in V-rich tailings.}, }
@article {pmid42102934, year = {2026}, author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J}, title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134810}, doi = {10.1016/j.biortech.2026.134810}, pmid = {42102934}, issn = {1873-2976}, mesh = {Food Loss and Waste ; Aerobiosis ; *Fungi/metabolism ; *Caproates/metabolism ; *Bacteria/metabolism ; *Microbial Consortia/physiology ; Bioreactors/microbiology ; }, abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.}, }
@article {pmid42103024, year = {2026}, author = {Zhang, T and Li, S and Wu, Y and Leung, J and Jiang, H and Xu, Z and Ng, SC and Kwok, T}, title = {Gut microbial signatures for aging-related sarcopenia and dietary links among community-dwelling old-old adults: A metagenomic study.}, journal = {Experimental gerontology}, volume = {220}, number = {}, pages = {113161}, doi = {10.1016/j.exger.2026.113161}, pmid = {42103024}, issn = {1873-6815}, mesh = {*Sarcopenia/microbiology/epidemiology ; Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Aging/physiology ; Aged, 80 and over ; *Diet ; Metagenomics ; Longitudinal Studies ; Independent Living ; }, abstract = {BACKGROUND AND OBJECTIVES: Sarcopenia, characterized by progressive loss of muscle mass, strength and function, poses a major aging-related health challenge. While a gut-muscle axis is implicated, microbiota-sarcopenia associations in the old-old (≥80 years) remain unexplored.<br><br>METHODS: This cross-sectional analysis included 315 community-dwelling adults aged &#x2265;80&#xa0;years from a longitudinal cohort at the 20-year follow-up timepoint, of whom 180 met the inclusion criteria. Gut microbiota was profiled by shotgun metagenomic sequencing alongside sarcopenia assessment. Microbial taxa associated with sarcopenia were identified using MaAsLin2, and dietary associations were assessed by partial Spearman correlation.<br><br>RESULTS: The prevalence of sarcopenia in this old-old cohort (mean age 86.8&#xa0;&#xb1;&#xa0;4.3&#xa0;years) was 51.7%. Sarcopenic individuals showed lower nutrition scores, reduced microbial richness and altered &#x3b2;-diversity (all P&#xa0;<&#xa0;0.05). Multivariable analysis identified six differentially abundant species associated with sarcopenia (FDR&#xa0;<&#xa0;0.10), including two positively associated (Ruthenibacterium lactatiformans and Catenibacillus scindens), and four negatively associated (Phascolarctobacterium faecium, Pyramidobacter piscolens, Lacrimispora saccharolytica and Limosilactobacillus mucosae). Random forest and LEfSe analysis validated R. lactatiformans and P. faecium as the most discriminative signatures for sarcopenia. After adjusting for obesity, these signatures remained significant (P&#xa0;<&#xa0;0.05). These alterations were linked to functional dysregulation, including increased purine degradation and reduced biotin biosynthesis potential. R. lactatiformans abundance negatively correlated with dietary maltose intake (P&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: In old-old adults, we identified distinct gut microbiota signatures associated with sarcopenia. R. lactatiformans and P. faecium emerged as candidate features. The dietary-microbiota correlations suggest potential nutrition strategies. These findings provide a basis for exploring microbiota-based approaches in advanced aging.}, }
@article {pmid42103726, year = {2026}, author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G}, title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42103726}, issn = {2041-1723}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; Reproducibility of Results ; *DNA Contamination ; *Metagenome/genetics ; Microbiota/genetics ; *Software ; Animals ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.}, }
@article {pmid42103925, year = {2026}, author = {Anil,  and Ramesh, KB and Gouda, MNR and Subramanian, S}, title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42103925}, issn = {2045-2322}, mesh = {Animals ; Larva/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract/microbiology ; }, abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.}, }
@article {pmid42103932, year = {2026}, author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B}, title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.}, journal = {EMBO molecular medicine}, volume = {18}, number = {6}, pages = {2404-2435}, pmid = {42103932}, issn = {1757-4684}, support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; }, mesh = {Animals ; *Oocytes/physiology/drug effects/metabolism/cytology ; Female ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome ; Mice ; Fecal Microbiota Transplantation ; Aging ; Metabolome ; Fertility ; }, abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.}, }
@article {pmid42104260, year = {2026}, author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R}, title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42104260}, issn = {1471-2180}, mesh = {*Hydrothermal Vents/microbiology ; *Antimicrobial Peptides/pharmacology/genetics/chemistry ; Arctic Regions ; *Microbiota ; Biofilms ; *Bacteria/genetics/classification/drug effects ; *Seawater/microbiology ; Archaea/genetics/classification/metabolism ; Metagenomics ; *Antimicrobial Cationic Peptides/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.<br><br>RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.<br><br>CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.}, }
@article {pmid42104558, year = {2026}, author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y}, title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.}, journal = {The New phytologist}, volume = {251}, number = {5}, pages = {2832-2851}, pmid = {42104558}, issn = {1469-8137}, support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, mesh = {*Symbiosis/genetics ; Multiomics ; *Root Nodules, Plant/microbiology ; *Microbiota/genetics ; Phylogeny ; Frankia/genetics ; Fabaceae/microbiology ; Transcriptome/genetics ; }, abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.}, }
@article {pmid42104576, year = {2026}, author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R}, title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70246}, doi = {10.1111/aji.70246}, pmid = {42104576}, issn = {1600-0897}, mesh = {Female ; Humans ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Dysbiosis ; }, abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.<br><br>METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.<br><br>RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.<br><br>CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).}, }
@article {pmid42104663, year = {2026}, author = {Yang, KL and Zhai, JN and Ye, JW and Zhang, XN and Wei, QC and Wang, H and Wang, HM and Chu, LL and Yang, J}, title = {Dysbiosis of Gut Archaea is Associated with Obesity and Could be Recovered after Bariatric Surgery.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {4}, pages = {437-446}, doi = {10.3967/bes2026.019}, pmid = {42104663}, issn = {2214-0190}, mesh = {Humans ; *Bariatric Surgery ; *Obesity/surgery/microbiology ; *Dysbiosis/microbiology ; *Archaea/physiology/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; }, abstract = {OBJECTIVE: Obesity is closely associated with an altered gut microbiota; however, the role of archaea in obesity remains unknown. We aimed to delineate the alterations in gut archaea in obese subjects and explore the changes in bariatric surgery-associated gut archaeal composition.<br><br>METHODS: Metagenomic sequencing data from 191 obese subjects and 184 lean controls were retrieved from three public cohorts. Of these, 23 obese patients who underwent bariatric surgery were followed up for 3 months.<br><br>RESULTS: The gut archaea of obese subjects showed significantly lower Shannon diversity index than those of lean controls. Principal component analysis of the gut archaea revealed distinct clusters in obese subjects and lean controls. A model using the 20 top archaeal genera discriminated obese from lean controls with an area under the receiver operating characteristic curve (AUC) of 0.79, 0.83, and 0.86 in three cohorts. Ecological analysis showed decreased trans-kingdom correlations between archaea and bacteria in obese subjects compared to those in lean controls, with partial restoration observed after bariatric surgery.<br><br>CONCLUSION: This is the first study to demonstrate that obesity is characterized by gut archaeal dysbiosis across multiple cohorts. Bariatric surgery-induced weight loss is associated with significant changes in the gut archaea.}, }
@article {pmid42106331, year = {2026}, author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P}, title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42106331}, issn = {2041-1723}, support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; }, mesh = {Humans ; Multiomics ; *Open Reading Frames/genetics ; Proteomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Micropeptides ; Proteome/genetics ; Metagenomics/methods ; Mass Spectrometry ; }, abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.}, }
@article {pmid42106335, year = {2026}, author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I}, title = {Population-scale characterization of the oral microbiome and associations with metabolic health.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42106335}, issn = {2041-1723}, mesh = {Humans ; *Microbiota/genetics ; Female ; *Mouth/microbiology ; Male ; Phenotype ; Metagenome ; Liver/metabolism/diagnostic imaging ; Adult ; Continuous Glucose Monitoring ; Middle Aged ; *Metabolic Diseases/microbiology/metabolism ; Adiposity ; Absorptiometry, Photon ; }, abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.}, }
@article {pmid42106361, year = {2026}, author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X}, title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42106361}, issn = {2055-5008}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&amp;D Programme/ ; }, mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Early Detection of Cancer/methods ; *Gastrointestinal Microbiome ; Metagenome ; Cohort Studies ; Computational Biology/methods ; Adenoma/diagnosis/microbiology ; }, abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.}, }
@article {pmid42106412, year = {2026}, author = {Guo, L and Holyoak, GR and DeSilva, U}, title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42106412}, issn = {2045-2322}, mesh = {Animals ; Female ; Horses/virology ; *Uterus/virology/microbiology ; *Virome/genetics ; Phylogeny ; Microbiota ; Genome, Viral ; Bacteriophages/genetics ; }, abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.}, }
@article {pmid42107405, year = {2026}, author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L}, title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142282}, doi = {10.1016/j.jhazmat.2026.142282}, pmid = {42107405}, issn = {1873-3336}, mesh = {*Plant Roots/metabolism ; *Aminosalicylic Acids/analysis/metabolism ; *Heptanoates/analysis/metabolism ; *Phenols/metabolism/toxicity ; *Rhizosphere ; Soil Microbiology ; *Soil Pollutants/metabolism/toxicity ; Microbiota/drug effects/physiology ; Biodegradation, Environmental ; Astragalus Plant/metabolism/microbiology ; *Plant Exudates/metabolism ; }, abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.}, }
@article {pmid42108251, year = {2026}, author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J}, title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42108251}, issn = {2045-2322}, support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; }, mesh = {Animals ; *Feces/virology ; *Metagenomics/methods ; *Virome/genetics ; *Felidae/virology ; Risk Assessment ; Animals, Wild/virology ; *Zoonoses/virology ; Phylogeny ; DNA Viruses/genetics ; *Viruses/genetics/classification ; }, abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.}, }
@article {pmid42108276, year = {2026}, author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK}, title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42108276}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; }, mesh = {*Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Oxygen/metabolism ; *Chemoautotrophic Growth ; Metagenomics ; Metabolomics ; *Microbiota ; }, abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.}, }
@article {pmid42108292, year = {2026}, author = {Guo, JX and Gao, YZ}, title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {91-103}, pmid = {42108292}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; *DNA, Bacterial/genetics ; Humans ; *Metagenomics/methods ; Genomics/methods ; Reference Standards ; }, abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.}, }
@article {pmid42108295, year = {2026}, author = {Peng, B and Chang, X}, title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {147-164}, pmid = {42108295}, issn = {1940-6029}, mesh = {Multiomics/methods ; Humans ; *Lung/metabolism/microbiology ; Metabolomics/methods ; *Gastrointestinal Microbiome ; Animals ; *Lung Diseases/metabolism/microbiology ; Dysbiosis ; Metagenomics/methods ; }, abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.}, }
@article {pmid42112348, year = {2026}, author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H}, title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782828}, pmid = {42112348}, issn = {1664-3224}, mesh = {*Dysbiosis/immunology/therapy ; *Microbiota ; *Lupus Erythematosus, Systemic/diagnosis/immunology/microbiology/therapy ; Humans ; Animals ; Molecular Mimicry ; Autoimmunity ; }, abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.}, }
@article {pmid42112819, year = {2026}, author = {Wei, X and Song, W and Li, S}, title = {Seasonal variations drive microbial community structure and nitrogen cycling in sediments of tributary pumping station forebays.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0304725}, pmid = {42112819}, issn = {2165-0497}, support = {B240201187//Fundamental Research Funds for the Central Universities/ ; 52100175//National Natural Science Foundation of China/ ; }, mesh = {Seasons ; *Nitrogen Cycle ; *Geologic Sediments/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology/chemistry ; *Microbiota/genetics ; Denitrification ; Metagenomics ; }, abstract = {Discharge from tributary pumping stations often impacts mainstream water quality, yet microbial communities and nitrogen metabolism in pumping station forebays remain poorly understood. Therefore, this study investigated the microbial community structure and nitrogen cycling mechanisms in sediments of tributary pumping station forebays within the Qinhuai River Basin using 16S rRNA and metagenomic sequencing. Results showed significant seasonal variations in the diversity and structure of sediment microbial communities, with higher diversity in spring than in winter. Genes associated with denitrification (e.g., narG, nirS, and nosZ) showed the highest abundance, suggesting that denitrification may be a key nitrogen transformation pathway. Co-occurrence network analysis revealed tighter associations between microbial taxa and nitrogen-cycling genes in spring, indicating more complex potential interactions during this season. The shift of network hubs across seasons suggested a seasonal succession of potential core functions related to nitrogen cycling. Redundancy analysis revealed that nitrate nitrogen (NO3[-]-N), water temperature (WT), and ammonium nitrogen (NH4[+]-N) were the factors most strongly associated with microbial community variation, with WT showing the strongest association with functional gene distribution. Partial least squares path modeling revealed that seasonal variation had a significant positive association with denitrification gene abundance and a significant negative association with genes related to assimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. These findings improve our understanding of microbially mediated nitrogen cycling in pumping station forebays and provide a scientific basis for water quality management in river networks influenced by pumping station drainage.IMPORTANCEThis study is important because it reveals that pumping stations, which are key infrastructure in managed river systems, are not just hydraulic structures but dynamic bioreactors where microbial communities actively transform nitrogen. By demonstrating seasonal variations in microbial diversity and revealing a high denitrification potential, the research provides a mechanistic understanding of how nitrogen pollution is naturally mitigated in these engineered environments. Crucially, it pinpoints temperature as a primary regulator of these microbial functions. These insights allow water managers to proactively optimize pumping operations and design interventions that harness microbial activity, ultimately protecting downstream water quality from nutrient pollution in a changing climate.}, }
@article {pmid42114574, year = {2026}, author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J}, title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134795}, doi = {10.1016/j.biortech.2026.134795}, pmid = {42114574}, issn = {1873-2976}, mesh = {Animals ; *Fatty Acids/biosynthesis ; *Calcium/pharmacology ; *Bacteria/metabolism ; *Fungi/metabolism ; *Egg Shell/chemistry ; *Microbiota ; Ethanol/metabolism ; Caproates/metabolism ; *Waste Products ; }, abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.}, }
@article {pmid42115187, year = {2026}, author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X}, title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.}, journal = {Translational psychiatry}, volume = {16}, number = {1}, pages = {}, pmid = {42115187}, issn = {2158-3188}, mesh = {Animals ; *Autophagy/physiology ; Rats ; *TOR Serine-Threonine Kinases/metabolism ; *Major Depressive Disorder/microbiology/metabolism ; Male ; *Dysbiosis/metabolism/complications ; *Gastrointestinal Microbiome/physiology ; *Lysine/metabolism/blood ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Prefrontal Cortex/metabolism ; Behavior, Animal ; Humans ; Adolescent ; Sirolimus/pharmacology ; Depression ; }, abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.}, }
@article {pmid42115271, year = {2026}, author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W}, title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42115271}, issn = {2045-2322}, support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; }, mesh = {Humans ; Multiomics ; *Anorexia/microbiology/metabolism ; *Gastrointestinal Microbiome ; Child, Preschool ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Infant ; Case-Control Studies ; Metagenomics/methods ; Feces/microbiology ; *Metabolome ; Bacteria/genetics/classification ; }, abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.}, }
@article {pmid42115921, year = {2026}, author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F}, title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42115921}, issn = {1471-2180}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; DNA, Bacterial/genetics ; Adult ; Metagenomics/methods ; Middle Aged ; Phylogeny ; Sequence Analysis, DNA ; Young Adult ; Aged ; }, abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.}, }
@article {pmid42116469, year = {2026}, author = {Liu, D and Li, J and Zhang, J and Zhang, C}, title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119201}, doi = {10.1016/j.foodres.2026.119201}, pmid = {42116469}, issn = {1873-7145}, mesh = {*Carbon Dioxide/chemistry ; *Taste ; Biogenic Amines/analysis/metabolism ; *Vegetables/microbiology/chemistry/metabolism ; *Microbiota ; *Food Microbiology ; Food Handling/methods ; *Atmosphere ; Sodium Chloride/analysis ; Amino Acids ; }, abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.}, }
@article {pmid42116470, year = {2026}, author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W}, title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119200}, doi = {10.1016/j.foodres.2026.119200}, pmid = {42116470}, issn = {1873-7145}, mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Oligosaccharides/pharmacology ; *Food Hypersensitivity/drug therapy/prevention &amp; control ; *Anti-Bacterial Agents/adverse effects ; *Indoles/metabolism ; Humans ; Dysbiosis/chemically induced ; *Receptors, Aryl Hydrocarbon/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice ; Prospective Studies ; Oxidative Stress/drug effects ; Female ; }, abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.<br><br>OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.<br><br>METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.<br><br>RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.<br><br>CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.}, }
@article {pmid42116511, year = {2026}, author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W}, title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119274}, doi = {10.1016/j.foodres.2026.119274}, pmid = {42116511}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota/physiology ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Metabolome ; *Wine/microbiology/analysis ; Taste ; Bacteria/metabolism/classification ; Metabolomics ; *Alcoholic Beverages/microbiology/analysis ; Amino Acids/analysis ; }, abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.}, }
@article {pmid42118429, year = {2026}, author = {Tekin, B and Gurbanov, R}, title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42118429}, issn = {1573-0972}, mesh = {*Aging/physiology ; Humans ; Biomarkers/analysis ; *Gastrointestinal Microbiome/physiology ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Host Microbial Interactions ; Metagenomics ; }, abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.}, }
@article {pmid42119030, year = {2026}, author = {Yu, J and Tang, SN and Lee, PKH}, title = {Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42119030}, issn = {1751-7370}, support = {//TAL Apparel Limited/ ; 9231297//City University of Hong Kong/ ; }, mesh = {*Bacteria/virology/genetics/classification ; *Wastewater/microbiology/virology ; *Virome ; Sewage/virology/microbiology ; Metagenomics ; Bioreactors/virology/microbiology ; Water Purification ; *Microbiota ; *Host Microbial Interactions ; Ecosystem ; }, abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1046 and 1386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.}, }
@article {pmid42119140, year = {2026}, author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH}, title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {20}, pages = {14712-14725}, doi = {10.1021/acs.est.5c13903}, pmid = {42119140}, issn = {1520-5851}, mesh = {*Rivers ; Seasons ; *Microbiota ; Temperature ; *Microplastics ; Hong Kong ; }, abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.}, }
@article {pmid42119385, year = {2026}, author = {Pan, L and Huang, Y and Chen, Y and Peng, T and Yang, J and Qiu, Y and Ji, M and Wu, X}, title = {Responses of soil microbes to antimony stress and coupled nutrient cycling in karst mining areas of Southwest China.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120248}, doi = {10.1016/j.ecoenv.2026.120248}, pmid = {42119385}, issn = {1090-2414}, mesh = {*Antimony/toxicity/analysis ; *Soil Microbiology ; China ; *Soil Pollutants/toxicity/analysis ; *Mining ; *Bacteria/drug effects/genetics/metabolism/classification ; Environmental Monitoring ; *Microbiota/drug effects ; }, abstract = {Persistent and poorly mobile heavy metals in soil present a widespread environmental challenge. Among these, antimony (Sb) is a contaminant of emerging concern whose transformation and migration in soil require further investigation to inform effective remediation strategies. Microbial processes are central to these dynamics, yet the mechanisms underlying Sb-microbe interactions remain poorly defined. In this study, we used integrated geochemical and metagenomic analyses to assess Sb contamination and microbial community responses systematically in an abandoned Sb mining area in Southwest China. The data reveal how microbial communities respond to low and moderate levels of Sb contamination. Contamination was highest in the mining area, followed by the smelting and tailings areas; the control area exhibited the lowest levels. Community structure analysis revealed significant enrichment of Thiobacillus, Geothrix, and Anaeromyxobacter in the mining area, while Nocardioides and Sphingomonas were more abundant in the smelting area. Bradyrhizobium dominated in the control area. These patterns reflect distinct microbial responses to the Sb contamination gradient. Critically, partial least squares path modeling revealed that Sb contamination did not directly affect microbial α-diversity. Instead, its influence was indirectly mediated through disruptions in sulfur cycling functions-a novel finding highlighting the indirect ecological impact of Sb. Sb, along with co-occurring copper, may drive adaptive microbial succession by interfering with sulfate respiration. This process enriches microbial groups with sulfur-cycling-related detoxification functions, resulting in simplified community structure and reduced diversity. Thus, the primary mechanism by which Sb alters microbial communities in karst soils is indirect, operating via perturbation of the sulfur cycle rather than direct toxicity. These findings offer a theoretical basis for developing targeted microbial remediation strategies and restoring ecological functions in Sb-contaminated environments by regulating key elemental cycles.}, }
@article {pmid42119567, year = {2026}, author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W}, title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102777}, pmid = {42119567}, issn = {2666-3791}, mesh = {Humans ; *Sjogren's Syndrome/microbiology/metabolism ; *Metabolome ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Bacteria/genetics/classification ; Feces/microbiology ; Male ; Metabolomics ; Metagenome ; Dysbiosis/microbiology ; Adult ; }, abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.}, }
@article {pmid42119966, year = {2026}, author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC}, title = {Metagenomic characterization of bacterial communities on beach macroplastics: Insights into antimicrobial resistance and virulence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128213}, doi = {10.1016/j.envpol.2026.128213}, pmid = {42119966}, issn = {1873-6424}, mesh = {*Bacteria/genetics/classification ; *Drug Resistance, Bacterial/genetics ; Virulence ; *Bathing Beaches ; Metagenomics ; India ; Drug Resistance, Microbial/genetics ; *Microbiota ; Seashore ; Metagenome ; }, abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1264-2046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.}, }
@article {pmid42120383, year = {2026}, author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW}, title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42120383}, issn = {2041-1723}, support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; }, mesh = {Animals ; *Carrageenan/metabolism ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; Rumen/microbiology ; Seaweed ; Glycoside Hydrolases/metabolism/genetics ; Phylogeny ; Bacteria/genetics/metabolism/classification ; Feces/microbiology ; }, abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.}, }
@article {pmid42120930, year = {2026}, author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X}, title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42120930}, issn = {2045-2322}, support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/complications ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome ; Female ; *Coronary Artery Disease/microbiology/metabolism/complications ; Middle Aged ; Metabolome ; Aged ; Case-Control Studies ; }, abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.}, }
@article {pmid42121077, year = {2026}, author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X}, title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.}, journal = {BMC neurology}, volume = {26}, number = {1}, pages = {}, pmid = {42121077}, issn = {1471-2377}, mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; *Epilepsy, Temporal Lobe/microbiology/epidemiology ; *RNA, Ribosomal, 16S/genetics ; Adult ; Case-Control Studies ; Comorbidity ; Middle Aged ; Feces/microbiology ; *Mental Disorders/microbiology/epidemiology ; }, abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.}, }
@article {pmid42121260, year = {2026}, author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E}, title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42121260}, issn = {2049-2618}, support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; }, mesh = {Animals ; *Cecum/microbiology ; Mice ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Diet, High-Fat ; *Body Weight ; Metagenome ; Age Factors ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Transcriptome ; Liver/metabolism ; Diet, Fat-Restricted ; Female ; Diet ; }, abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.<br><br>RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730&#xa0;days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering&#x2009;>&#x2009;300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC&#x2009;=&#x2009;0.84 for CD, 0.79 for HF) and chronological age (AUC&#x2009;=&#x2009;0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.<br><br>CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC&#x2009;=&#x2009;0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC&#x2009;=&#x2009;0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.}, }
@article {pmid42121284, year = {2026}, author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C}, title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42121284}, issn = {2049-2618}, support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; R01 DK108366/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Zimbabwe ; *HIV Infections/immunology/microbiology/drug therapy ; Female ; Male ; Adult ; Rural Population ; *Gastrointestinal Microbiome ; *Diet ; Urban Population ; Middle Aged ; Inflammation ; }, abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.<br><br>RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4&#x2009;+&#x2009;T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24&#xa0;weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.<br><br>CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.}, }
@article {pmid42123477, year = {2026}, author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M}, title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123477}, issn = {1422-0067}, mesh = {Humans ; *Mineral Waters/therapeutic use ; *Balneology/methods ; Dermatitis, Atopic/therapy ; Psoriasis/therapy ; Animals ; Skin/drug effects ; Skin Microbiome ; *Skin Diseases/therapy ; }, abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.}, }
@article {pmid42123517, year = {2026}, author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ}, title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123517}, issn = {1422-0067}, support = {10180//United States Department of Agriculture/ ; }, mesh = {Humans ; *Microbiota/drug effects ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/chemistry ; *Saliva/microbiology ; *Plant Extracts/pharmacology/chemistry ; Propylthiouracil/pharmacology ; *Photinia/chemistry ; *Mouthwashes/pharmacology/chemistry ; Female ; Male ; Adult ; *Fruit and Vegetable Juices ; Young Adult ; Taste/drug effects ; }, abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.}, }
@article {pmid42126224, year = {2026}, author = {Abuah, CY and Sipes, K and Buongiorno, J and Steen, AD and Bradley, JA and Giovannelli, D and Abramov, A and Peters, SL and Giannone, RJ and Hettich, RL and Liang, R and Boike, J and Vishnivetskaya, TA and Lloyd, KG}, title = {Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0045626}, pmid = {42126224}, issn = {2165-0497}, support = {DESC0020369//U.S. Department of Energy/ ; FG-2015-65399//Alfred P. Sloan Foundation/ ; OCE-2145434//National Science Foundation/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Permafrost/microbiology/chemistry ; Arctic Regions ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification/enzymology ; Soil Microbiology ; Metagenome ; Estuaries ; Biodegradation, Environmental ; Microbiota ; *Carbohydrate Metabolism ; Metagenomics ; Carbohydrates/chemistry ; Soil/chemistry ; Svalbard ; }, abstract = {The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches-metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics-we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass-remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.IMPORTANCEPermafrost thaw may be a critical climate feedback because microbial degradation of organic matter (OM) can release greenhouse gases. While fjords serve as major carbon burial sites, our results show that burial of terrestrial-derived OM in these sediments does not ensure protection from microbial degradation. Microbial communities in both active layer soils and fjord sediments harbor a broad arsenal of carbohydrate-active enzymes, with evidence of activity across diverse taxa. This functional continuity indicates that once terrestrial material is washed into fjords, it remains vulnerable to microbial breakdown despite different environmental conditions. Understanding these cross-system continuities in microbial function is essential for predicting the fate of OM in a rapidly warming Arctic and highlights the importance of including fjord sediments in global carbon cycle models.}, }
@article {pmid42127418, year = {2026}, author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC}, title = {Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42127418}, issn = {1751-7370}, support = {IN219624//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT)/ ; IN217821//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT)/ ; //Universidad Nacional Aut&#xf3;noma de Mexico/ ; //Calgary Foundation/ ; //Office of the Associate Dean Research of the University of Calgary's Cumming School of Medicine/ ; //Alberta Children's Hospital Research Institute/ ; //internal University of Calgary start-up funds/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Bacteria/classification/genetics/isolation &amp; purification ; Eukaryota/classification/genetics/isolation &amp; purification ; *Family Characteristics ; Feces/microbiology ; Longitudinal Studies ; Metagenomics ; Mexico ; RNA, Ribosomal, 18S/genetics ; Rural Population ; Sequence Analysis, DNA ; *Gastrointestinal Microbiome ; }, abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S ribosomal RNA gene sequencing, we characterized bacterial and eukaryotic gut microbiomes in an intensively sampled longitudinal cohort of 10 infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing a detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, and bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and birth mode also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.}, }
@article {pmid42127824, year = {2026}, author = {Bouzek, DC}, title = {What the nose knows of cystic fibrosis microbes and hypertonic saline.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {827-829}, doi = {10.1016/j.chom.2026.04.017}, pmid = {42127824}, issn = {1934-6069}, mesh = {*Nasopharynx/microbiology ; Humans ; *Cystic Fibrosis/drug therapy/microbiology ; Infant ; Case-Control Studies ; *Microbiota/drug effects/genetics ; Metagenomics ; *Saline Solution, Hypertonic/administration &amp; dosage ; Administration, Inhalation ; Nebulizers and Vaporizers ; Osmotic Pressure/drug effects ; }, abstract = {In this issue of Cell Host &amp; Microbe, Steinberg et al.[1] present a microbial gene atlas of nasopharyngeal swabs in infants with cystic fibrosis and healthy controls using shotgun metagenomic sequencing. The impacts of clinical interventions on respiratory microbial function can be identified and experimentally validated using the atlas.}, }
@article {pmid42127905, year = {2026}, author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y}, title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.}, journal = {Cell reports. Medicine}, volume = {7}, number = {6}, pages = {102797}, pmid = {42127905}, issn = {2666-3791}, mesh = {Humans ; Aged ; *Cognition/physiology ; *Diet, Plant-Based ; *Gastrointestinal Microbiome/physiology/genetics ; China ; Female ; Aged, 80 and over ; Male ; Multiomics ; Longitudinal Studies ; Rural Population ; Feces/microbiology ; Metagenomics ; East Asian People ; }, abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.}, }
@article {pmid42129189, year = {2026}, author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E}, title = {Network topology of the gut microbiome associates with metabolic health in obesity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42129189}, issn = {2041-1723}, mesh = {Humans ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology/genetics ; Feces/microbiology ; Cross-Sectional Studies ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Female ; Male ; Phenotype ; Dysbiosis/microbiology ; }, abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.}, }
@article {pmid42129938, year = {2026}, author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z}, title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42129938}, issn = {2049-2618}, support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology/physiology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Reproduction/physiology ; Multiomics ; Pregnancy ; Metagenomics/methods ; Metabolomics ; Litter Size ; *Gastrointestinal Microbiome ; Lactation ; }, abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.<br><br>RESULTS: No significant difference was observed in the ruminal microbial &#x3b1;-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.<br><br>CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.}, }
@article {pmid42130304, year = {2026}, author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z}, title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70324}, pmid = {42130304}, issn = {1462-2920}, support = {LP160101508//Australian Research Council/ ; }, mesh = {Animals ; *Anthozoa/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Coral Reefs ; Islands ; }, abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.}, }
@article {pmid42132952, year = {2026}, author = {Özel, &#x15e; and Lauritano, D}, title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42132952}, issn = {1573-4978}, mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Mouth Mucosa/microbiology ; Recurrence ; Dysbiosis/microbiology ; Case-Control Studies ; }, abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.}, }
@article {pmid42133155, year = {2026}, author = {Zhang, Q and He, G and Guo, Z and He, Y and Xiong, J and He, T and Lee, SL}, title = {Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils and a forest-derived fermentation-enriched microbial community.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42133155}, issn = {1573-0972}, support = {42367039, 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//National Key Research and Development Program of China/ ; Z2024417//Guizhou Provincial Science and Technology Department/ ; Liu Jin Xiang [2024] No. 44, 202406670023//Overseas Study Program for Young Key Teachers/ ; }, mesh = {*Zea mays/growth &amp; development/microbiology ; *Nitrogen/metabolism ; *Soil Microbiology ; *Metagenomics ; Fermentation ; *Metabolomics ; Forests ; *Soil/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fertilizers/analysis ; China ; *Microbiota/genetics ; Carbon/metabolism ; Agriculture ; Metagenome ; }, abstract = {Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.}, }
@article {pmid42133477, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Gut species Porphyromonas asaccharolytica and Bacteroides fragilis are associated with whole body fat percentage.}, journal = {Journal of applied microbiology}, volume = {137}, number = {6}, pages = {}, pmid = {42133477}, issn = {1365-2672}, support = {/NH/NIH HHS/United States ; 2016YFC1201805//National Key R&amp;D Program of China/ ; 2017YFC1001100//National Key R&amp;D Program of China/ ; 201604020007//Science and Technology Program of Guangzhou, China/ ; 81770878//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Bacteroides fragilis/genetics/physiology/isolation &amp; purification ; Male ; *Porphyromonas/genetics/physiology/isolation &amp; purification ; *Obesity/microbiology ; *Adipose Tissue/metabolism ; *Gastrointestinal Microbiome ; Cohort Studies ; Middle Aged ; Metagenomics ; }, abstract = {AIMS: Obesity is linked to various adverse health effects, with body fat percentage being a key indicator of these risks. While the gut microbiota (GM) plays important roles in obesity, the specific species involved remain poorly understood. We aimed to identify gut species that may influence obesity in a cohort of US men.<br><br>METHODS AND RESULTS: We conducted a comprehensive integrative analysis using metagenomics and whole-genome sequencing data in the US cohort. MaAsLin2 was used to identify associations between GM and whole body fat percentage (PFAT). Mendelian randomization (MR) was applied to investigate potential directional relationships between GM species and PFAT, as well as possible interactions between microbial species. Porphyromonas asaccharolytica (P. asaccharolytica) was negatively associated (&#x3b2; = -0.181, P =&#xa0;0.005) with PFAT, while Bacteroides fragilis (B. fragilis) was positively associated (&#x3b2; = 0.239, P =&#xa0;0.001); these associations were validated in an independent Chinese cohort. MR analysis suggested that P. asaccharolytica may influence PFAT in part through its potential effect on B. fragilis abundance.<br><br>CONCLUSION: Gut species P. asaccharolytica and B. fragilis are associated with host body fat percentage and may influence obesity individually or collaboratively. The observed associations provide evidence consistent with a potential directional relationship between these species and human adiposity.}, }
@article {pmid42134120, year = {2026}, author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S}, title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.}, journal = {Food chemistry}, volume = {518}, number = {}, pages = {149574}, doi = {10.1016/j.foodchem.2026.149574}, pmid = {42134120}, issn = {1873-7072}, mesh = {Animals ; Fermentation ; *Flavoring Agents/metabolism/analysis/chemistry ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Microbiota ; *Penaeidae/microbiology ; *Fermented Foods/microbiology/analysis ; Taste ; *Shellfish/microbiology/analysis ; Metagenomics ; Amino Acids/metabolism/analysis ; }, abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.}, }
@article {pmid42134135, year = {2026}, author = {Huang, Z and Wang, J and Yang, C and Lv, Z and Wang, R}, title = {Integrated transcriptomics and metagenomics analyze the dynamic correlations between cecal mucosal tissue and cecal microbiota in Liangshan Yanying chickens during early postnatal development.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {106904}, pmid = {42134135}, issn = {1525-3171}, mesh = {Animals ; *Chickens/growth &amp; development/microbiology/genetics ; *Cecum/microbiology ; Metagenomics ; *Gastrointestinal Microbiome ; *Transcriptome ; Gene Expression Profiling/veterinary ; *Intestinal Mucosa/microbiology ; China ; }, abstract = {Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380-4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n = 10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14-28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.}, }
@article {pmid42134588, year = {2026}, author = {Chauhan, A and Santhiya, D and Sharma, JG}, title = {Microbial consortium driven degradation of mixed microplastics: systematic review on enzymes and omics-based insights.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134885}, doi = {10.1016/j.biortech.2026.134885}, pmid = {42134588}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; *Enzymes/metabolism ; *Microbial Consortia ; *Microplastics/metabolism ; *Multiomics ; }, abstract = {Microplastics (MPs) are among the most persistent pollutants in the environment. Mixed polymer waste further complicates the remediation due to their toxic additives and heterogenous composition. Conventional remediation methods show limited efficiency, especially for mixed MPs. As a result, biological approaches, particularly microbial consortium mediated degradation is a promising alternative. It is gaining increasing attention due to their cooperative metabolism and ability to degrade multiple polymers simultaneously. This review summarizes recent advances in consortium-based degradation of mixed MPs. It compares existing studies and identifies key challenges in translating laboratory findings to real-world. This review further discusses enzymes involved in the degradation of major polymer constituting mixed MPs. In addition, the role of multi-omics approaches like metagenomics, meta-transcriptomics, metabolomics, and integrated systems biology is also highlighted to explain microbial-metabolite interaction, functional pathways, and degradation mechanisms. Further, this review proposed future research directions focusing on green and scalable technologies. These include green biosensors for real-time monitoring, agro based aerogels and biochar for microbial immobilization, and nano-bubble assisted systems to enhance degradation under economic real-world conditions.}, }
@article {pmid42134644, year = {2026}, author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X}, title = {Antibiotic-mediated gut microbiota depletion partially attenuates methamphetamine-induced reward and linoleic acid metabolic disturbance.}, journal = {Neuropharmacology}, volume = {296}, number = {}, pages = {111022}, doi = {10.1016/j.neuropharm.2026.111022}, pmid = {42134644}, issn = {1873-7064}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Methamphetamine/administration &amp; dosage/pharmacology ; *Reward ; *Linoleic Acid/metabolism ; *Anti-Bacterial Agents/pharmacology ; Multiomics ; Male ; Animals ; Mice ; Mice, Inbred C57BL ; *Central Nervous System Stimulants/administration &amp; dosage/pharmacology ; *Bacteria/drug effects/metabolism ; *Brain-Gut Axis/drug effects/physiology ; }, abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of its oxidative metabolism could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.}, }
@article {pmid42135633, year = {2026}, author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X}, title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42135633}, issn = {1471-2180}, support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; }, mesh = {*Phytophthora/physiology/pathogenicity ; *Soil Microbiology ; *Microbiota/genetics ; *Nicotiana/microbiology/parasitology ; *Plant Diseases/microbiology ; Rhizosphere ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.<br><br>RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p&#x2009;<&#x2009;0.05, |log2FC| &#x2265; 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+&#x2009;52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.<br><br>CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.}, }
@article {pmid42139081, year = {2026}, author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Dietary niches drive microbial community assembly, network reorganization, and symbiont evolution in freshwater fish gut microbiomes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42139081}, issn = {1751-7370}, support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; }, mesh = {Animals ; *Symbiosis ; Fresh Water ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; China ; *Diet ; *Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.}, }
@article {pmid42140024, year = {2026}, author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L}, title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.}, journal = {International journal of food microbiology}, volume = {457}, number = {}, pages = {111847}, doi = {10.1016/j.ijfoodmicro.2026.111847}, pmid = {42140024}, issn = {1879-3460}, mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Fungi/genetics/classification/isolation &amp; purification ; *Alcoholic Beverages/analysis/microbiology ; Hot Temperature ; Taste ; China ; *Volatile Organic Compounds/analysis ; Metagenomics ; Flavoring Agents/analysis ; }, abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.}, }
@article {pmid42140051, year = {2026}, author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M}, title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.}, journal = {Marine pollution bulletin}, volume = {230}, number = {}, pages = {119879}, doi = {10.1016/j.marpolbul.2026.119879}, pmid = {42140051}, issn = {1879-3363}, mesh = {Animals ; *Bass/metabolism ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; Multiomics ; *Dysbiosis/chemically induced ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.}, }
@article {pmid42140378, year = {2026}, author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA}, title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {590}, number = {}, pages = {121086}, doi = {10.1016/j.cca.2026.121086}, pmid = {42140378}, issn = {1873-3492}, mesh = {Humans ; Male ; *Prostatic Neoplasms/metabolism/therapy/diagnosis/blood ; *Biomarkers, Tumor/metabolism/blood ; *Gastrointestinal Microbiome ; *Prostate/metabolism ; }, abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.}, }
@article {pmid42140961, year = {2026}, author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM}, title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140961}, issn = {2041-1723}, support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, mesh = {*Introduced Species ; *Asteraceae/microbiology ; Species Specificity ; Microbiota ; Ecosystem ; Bacteria/genetics ; }, abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.}, }
@article {pmid42141123, year = {2026}, author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X}, title = {Decoding the human gut bacterial plasmids in colorectal cancer.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {42141123}, issn = {2399-3642}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics ; Metagenomics ; }, abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.}, }
@article {pmid42141277, year = {2026}, author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G}, title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.}, journal = {Nature food}, volume = {7}, number = {5}, pages = {428-440}, pmid = {42141277}, issn = {2662-1355}, mesh = {*Soil Microbiology ; *Microbiota ; *Ecosystem ; Agriculture ; Soil/chemistry ; Climate Change ; Global Warming ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.}, }
@article {pmid42141292, year = {2026}, author = {Ghori, R and Ramadoss, D and Ramsland, PA and Blanch, EW and Ammanabrolu, BS}, title = {Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {42141292}, issn = {1433-4909}, mesh = {India ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Metagenome ; }, abstract = {Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.}, }
@article {pmid42142571, year = {2026}, author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Seasonal shifts in the Belgrade airborne resistome and virulome: A metagenomic perspective.}, journal = {Environmental research}, volume = {303}, number = {Pt 2}, pages = {124700}, doi = {10.1016/j.envres.2026.124700}, pmid = {42142571}, issn = {1096-0953}, mesh = {*Seasons ; *Air Microbiology ; Serbia ; *Microbiota ; *Metagenome ; Metagenomics ; *Bacteria/genetics ; Environmental Monitoring ; }, abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.}, }
@article {pmid42143007, year = {2026}, author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW}, title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {26}, number = {5}, pages = {699-707}, doi = {10.1016/j.pan.2026.05.002}, pmid = {42143007}, issn = {1424-3911}, mesh = {Animals ; Humans ; *Autoimmune Pancreatitis/drug therapy/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/therapeutic use ; Middle Aged ; Mice ; Aged ; Adult ; Feces/microbiology ; Streptococcus anginosus ; Disease Models, Animal ; Case-Control Studies ; }, abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.<br><br>METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.<br><br>RESULTS: Significant differences in both &#x3b1;-diversity and &#x3b2;-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.<br><br>CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.}, }
@article {pmid42143215, year = {2026}, author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ}, title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42143215}, issn = {1471-2180}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {*Drinking Water/microbiology ; *Biofilms/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Microbiota/genetics ; Metagenomics ; Water Supply ; Seasons ; Water Microbiology ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.<br><br>RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.<br><br>CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.}, }
@article {pmid42143455, year = {2026}, author = {Jia, W and Li, J and Wang, K and Cheng, L and Jin, N and Yang, Q and Zhang, D and Xia, X and Xu, N and Wang, M and Meng, J and Zhu, Y and Ding, A}, title = {Convergent shifts in microbial communities: Petroleum hydrocarbon contamination suppresses matrix heterogeneity.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142349}, doi = {10.1016/j.jhazmat.2026.142349}, pmid = {42143455}, issn = {1873-3336}, mesh = {*Groundwater/microbiology/chemistry ; *Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; *Petroleum/analysis ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota/drug effects ; Bacteria/genetics/metabolism ; Petroleum Pollution ; }, abstract = {Accurate characterization of microbial communities in aquifers is essential for understanding groundwater ecosystem responses to petroleum hydrocarbon contamination. However, existing studies have focused primarily on groundwater, largely overlooking the coupled interactions between groundwater and aquifer sediments, which may bias aquifer-scale evaluations of microbial functional potential. In this study, contaminated groundwater and corresponding aquifer sediment samples were collected from a petroleum hydrocarbon impacted site, together with uncontaminated groundwater and sediment samples outside the contaminant plume as controls. Petroleum hydrocarbon concentrations and principal component analysis (PCA) revealed comparable contamination levels in groundwater and aquifer sediments. Integrating 16S rRNA gene sequencing analysis and metagenomic sequencing analysis, we found that microbial communities in contaminated groundwater exhibited broader niche breadth, higher niche overlap, and increased representation of low-molecular-weight carbon (LMW-C) metabolism, particularly pathways associated with ribose and amino sugar utilization. In contrast, aquifer sediment communities showed higher abundances of multidrug efflux pump genes and functional pathways involved in naphthalene and benzene degradation (PAH-C and MAH-C). Further correlation and community assembly analyses indicated that petroleum hydrocarbon contamination was the primary driver shaping microbial communities in both matrices, overriding intrinsic physicochemical differences. Meanwhile, sediment-specific properties, such as stronger sorption capacity for organic matter and differences in microbial lifestyles contributed to the observed divergence between groundwater and sediment communities. Overall, this study demonstrates that contamination induced selection dominates microbial community assembly in aquifers, and provides a mechanistic basis for improving the evaluation of natural attenuation potential and informing remediation strategies in contaminated aquifer systems.}, }
@article {pmid42143575, year = {2026}, author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J}, title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42143575}, issn = {1751-7370}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Plasmids/genetics ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Escherichia coli/genetics/drug effects ; Feces/microbiology/chemistry ; Metabolomics ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.}, }
@article {pmid42148043, year = {2026}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.}, journal = {Environmental health perspectives}, volume = {134}, number = {1}, pages = {75-90}, pmid = {42148043}, issn = {1552-9924}, mesh = {Adult ; Female ; Humans ; Middle Aged ; *Air Pollution, Indoor/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Lighting ; Uganda ; *Virome/drug effects ; }, abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.}, }
@article {pmid42148573, year = {2026}, author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC}, title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0411725}, pmid = {42148573}, issn = {2165-0497}, support = {AM22SCBPCA1133//Center for Produce Safety/ ; }, mesh = {*Pyrus/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; *Food Storage/methods ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Fruit/microbiology ; Metagenomics ; Food Preservation/methods ; Food Microbiology ; }, abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.}, }
@article {pmid42148581, year = {2026}, author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S}, title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0377525}, pmid = {42148581}, issn = {2165-0497}, support = {//Guizhou Province 2020 Science and Technology Support Plan Project/ ; }, mesh = {Fermentation ; Multiomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism/analysis ; Metagenomics ; China ; Microbiota ; Metagenome ; Metabolomics ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; }, abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.}, }
@article {pmid42148582, year = {2026}, author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L}, title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0346925}, pmid = {42148582}, issn = {2165-0497}, support = {2023AH051003//Scientific Research Project of Universities in Anhui Province/ ; SKLTOF20210113//Open Fund of State Key Laboratory of Tea Plant Biology and Utilization/ ; }, mesh = {*Bacillus/metabolism/genetics/physiology ; *Catechin/metabolism/biosynthesis ; *Camellia sinensis/microbiology/metabolism ; Rhizosphere ; Secondary Metabolism ; Plant Leaves/metabolism/microbiology/chemistry ; Soil Microbiology ; Microbiota ; }, abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.}, }
@article {pmid42148776, year = {2026}, author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y}, title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0029226}, pmid = {42148776}, issn = {2379-5077}, support = {82373960, 81974513//National Natural Science Foundation of China/ ; 2025ZZTS0793//Fundamental Research Funds for Central Universities of the Central South University/ ; 2023JJ30891, 2025JJ50675, 2026JJ50342//Natural Science Foundation of Hunan Province/ ; }, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Bile Acids and Salts/metabolism ; Male ; *Fatty Liver/metabolism/microbiology ; Liver/metabolism/pathology ; Receptors, Cytoplasmic and Nuclear/metabolism ; Disease Models, Animal ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Receptor, Farnesoid X-Activated ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; Cholesterol 7-alpha-Hydroxylase/metabolism ; }, abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.<br><br>IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.}, }
@article {pmid42149451, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {233-242}, pmid = {42149451}, issn = {1940-6029}, mesh = {*Laser Capture Microdissection/methods ; *Hair Follicle/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Scalp/microbiology ; Skin Microbiome ; }, abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.}, }
@article {pmid42149452, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {243-259}, pmid = {42149452}, issn = {1940-6029}, mesh = {Humans ; *Hair Follicle/microbiology ; Skin Microbiome ; In Situ Hybridization, Fluorescence/methods ; Azides/chemistry ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Metagenomics/methods ; Propidium/analogs &amp; derivatives/chemistry ; Real-Time Polymerase Chain Reaction/methods ; Shotgun Sequencing ; Microbial Viability ; }, abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.}, }
@article {pmid42150504, year = {2026}, author = {Pan, Z and Wang, W and Torabi, E and Zhang, M and Su, Z and Xu, X and Yin, Y and Xu, W and Duan, Y and Chen, J and Maróti, G and Huang, Q}, title = {Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142406}, doi = {10.1016/j.jhazmat.2026.142406}, pmid = {42150504}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; Metagenomics ; *Metals, Heavy/toxicity/analysis ; Oryza ; China ; Adaptation, Physiological ; Metagenome ; *Microbiota/drug effects ; Bacteria/genetics ; }, abstract = {The spatial heterogeneity of multi-metal contamination and its ecological consequences for soil microbial communities remain poorly characterized on a national scale, particularly within paddy ecosystems. This study investigated microbial ecological and genomic responses to heavy metal stress across 48 paddy soils from major rice-growing regions in China, categorized into low (LMS), moderate (MMS), and high (HMS) contamination levels. Our results indicate that multi-metal contamination triggered a significant restructuring of microbial communities, which was accompanied by increased alpha diversity and the enrichment of metal-tolerant taxa (e.g., Planctomycetes and Cyanobacteria). Conversely, microbial co-occurrence networks exhibited systematic simplification as contamination levels increased, characterized by reduced connectivity and a significant loss of keystone taxa. This suggests a transition from functionally redundant communities to modularized, survival-oriented network configurations. Metagenomic analysis revealed positive correlations between metal contamination and the abundance of nitrogen, phosphorus, and sulfur-cycling genes, while carbon-cycling genes remained relatively stable. Furthermore, genome-resolved metagenomics demonstrated widespread co-localization of metal resistance genes (MRGs) and nutrient cycling genes within metagenome-assembled genomes, particularly among key taxa (e.g., Burkholderiaceae, MBNT15). Collectively, these findings elucidate the mechanistic basis of microbial adaptation to multi-metal stress in paddy soils, providing critical insights for optimizing soil health management, developing targeted bioremediation strategies, and enhancing environmental risk assessment frameworks for contaminated agricultural ecosystems.}, }
@article {pmid42150526, year = {2026}, author = {Thompson, LR}, title = {Microbial ecology: Rise of the planet of the microbes.}, journal = {Current biology : CB}, volume = {36}, number = {10}, pages = {R432-R434}, doi = {10.1016/j.cub.2026.03.072}, pmid = {42150526}, issn = {1879-0445}, mesh = {*Microbiota ; *Ecosystem ; *Bacteria/genetics ; Ecology ; Metagenomics ; }, abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.}, }
@article {pmid42151282, year = {2026}, author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G}, title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42151282}, issn = {2045-2322}, support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Universit&#xe0; e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; }, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Shotgun Sequencing ; *Metagenome ; Nanopore Sequencing/methods ; Benchmarking ; Bacteria/genetics/classification ; }, abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.}, }
@article {pmid42151682, year = {2026}, author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS}, title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3000}, number = {}, pages = {251-275}, pmid = {42151682}, issn = {1940-6029}, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/genetics ; *Space Flight ; Weightlessness ; *Microbiota/physiology ; *Host Microbial Interactions ; }, abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.}, }
@article {pmid42153646, year = {2026}, author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV}, title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.}, journal = {mSphere}, volume = {11}, number = {6}, pages = {e0013926}, pmid = {42153646}, issn = {2379-5042}, support = {075-15-2025-475//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Humans ; *COVID-19/microbiology ; *Metagenome ; *Lung/microbiology ; *Gastrointestinal Microbiome/genetics ; SARS-CoV-2 ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Metagenomics/methods ; Plasmids/genetics ; Feces/microbiology ; Male ; Klebsiella pneumoniae/genetics ; Female ; Middle Aged ; Aged ; Candida/genetics/drug effects/isolation &amp; purification ; Pandemics ; }, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.}, }
@article {pmid42153961, year = {2026}, author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {44}, pages = {e17087}, pmid = {42153961}, issn = {2198-3844}, support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Metagenome/genetics ; Metagenomics/methods ; *Dysbiosis/microbiology ; }, abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.}, }
@article {pmid42154337, year = {2026}, author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP}, title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {42154337}, issn = {1559-1182}, mesh = {Humans ; *alpha-Synuclein/metabolism ; *Parkinson Disease/metabolism/microbiology/pathology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Protein Aggregates ; *Protein Aggregation, Pathological/metabolism/pathology ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.}, }
@article {pmid42154370, year = {2026}, author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG}, title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.}, journal = {Advances in therapy}, volume = {43}, number = {8}, pages = {3247-3280}, pmid = {42154370}, issn = {1865-8652}, mesh = {Humans ; *Eye Diseases/microbiology/therapy ; *Microbiota/physiology ; Probiotics/therapeutic use ; *Eye/microbiology ; Prebiotics ; }, abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.}, }
@article {pmid42156414, year = {2026}, author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and ,  and Guarner, F and Ehrlich, SD}, title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42156414}, issn = {2045-2322}, support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Feces/microbiology ; Female ; Adult ; Male ; Phenotype ; Middle Aged ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Inflammation/microbiology ; Recurrence ; Leukocyte L1 Antigen Complex/analysis ; Metagenomics ; Quality of Life ; }, abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.}, }
@article {pmid42156610, year = {2026}, author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z}, title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.}, journal = {International journal of clinical oncology}, volume = {31}, number = {7}, pages = {1175-1188}, pmid = {42156610}, issn = {1437-7772}, support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; }, mesh = {Humans ; *Stomach Neoplasms/microbiology/therapy/pathology ; *Dysbiosis/microbiology/complications ; Disease Progression ; *Gastrointestinal Microbiome/physiology ; Prognosis ; Animals ; }, abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.}, }
@article {pmid42156647, year = {2026}, author = {Ravikrishnan, A}, title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {1-23}, pmid = {42156647}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Computational Biology/methods ; Shotgun Sequencing ; Software ; Workflow ; Data Analysis ; }, abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.}, }
@article {pmid42156648, year = {2026}, author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A}, title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {25-32}, pmid = {42156648}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota/genetics ; Humans ; }, abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.}, }
@article {pmid42156650, year = {2026}, author = {Miliotis, G and Tumeo, A}, title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {47-73}, pmid = {42156650}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Wetlands ; *Wastewater/microbiology ; *Metagenome ; *Water Purification/methods ; *Microbiota/genetics ; Shotgun Sequencing ; Computational Biology/methods ; Bacteria/genetics ; }, abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.}, }
@article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics ; Bacteriophages/genetics ; *Virome ; Bacteria/genetics ; Ecology ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, }
@article {pmid42156658, year = {2026}, author = {Roma Pi, J and Heinken, A}, title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {233-260}, pmid = {42156658}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Humans ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; Systems Biology/methods ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Workflow ; }, abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.}, }
@article {pmid42156772, year = {2026}, author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and ,  and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E}, title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42156772}, issn = {2041-1723}, support = {T32 GM150407/GM/NIGMS NIH HHS/United States ; U19 AG057377/AG/NIA NIH HHS/United States ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, mesh = {Animals ; Dogs/microbiology ; *Aging/physiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Metagenomics ; Diet/veterinary ; Cohort Studies ; Humans ; Pets/microbiology ; }, abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.}, }
@article {pmid42157110, year = {2026}, author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F}, title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {}, pmid = {42157110}, issn = {1471-2229}, support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; }, mesh = {*Solanum lycopersicum/microbiology/growth &amp; development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Microbial Consortia ; Bacteria/genetics ; Fungi ; }, abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.<br><br>RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.<br><br>CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype &#xd7; microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.}, }
@article {pmid42158968, year = {2026}, author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W}, title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71946}, pmid = {42158968}, issn = {2045-7634}, support = {82200151//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/drug effects/immunology ; *Dysbiosis/immunology/microbiology ; Aged ; Middle Aged ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.<br><br>METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.<br><br>CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.}, }
@article {pmid42159601, year = {2026}, author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y}, title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42159601}, issn = {2057-5858}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/drug effects/isolation &amp; purification ; *Pneumonia, Mycoplasma/microbiology/metabolism ; Metagenomics/methods ; Metabolomics/methods ; Child, Preschool ; Female ; Prospective Studies ; Male ; Microbiota ; Child ; Bronchoalveolar Lavage Fluid/microbiology ; Community-Acquired Pneumonia ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Metabolome ; Machine Learning ; Severity of Illness Index ; }, abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.}, }
@article {pmid42159838, year = {2026}, author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA}, title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42159838}, issn = {1678-4405}, mesh = {Animals ; Brazil ; *Porcupines/virology ; *Virome ; *Feces/virology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; *Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.}, }
@article {pmid42160933, year = {2026}, author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M}, title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142454}, doi = {10.1016/j.jhazmat.2026.142454}, pmid = {42160933}, issn = {1873-3336}, mesh = {*Polybrominated Biphenyls/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Anaerobiosis ; Aerobiosis ; Bacteria/metabolism/genetics ; }, abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.}, }
@article {pmid42161089, year = {2026}, author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S}, title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.}, journal = {Placenta}, volume = {181}, number = {}, pages = {168-174}, doi = {10.1016/j.placenta.2026.05.010}, pmid = {42161089}, issn = {1532-3102}, mesh = {Female ; Humans ; Pregnancy ; *Placenta/virology ; *DNA, Viral/analysis ; *RNA, Viral/analysis ; Pre-Eclampsia/virology ; Adult ; *Virome ; Cesarean Section ; }, abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.<br><br>METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n&#x202f;=&#x202f;6), (2) delivered by emergency caesarean section (n&#x202f;=&#x202f;6), and (3) complicated by preeclampsia (n&#x202f;=&#x202f;5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.<br><br>RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.<br><br>CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.}, }
@article {pmid42161263, year = {2026}, author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {6}, pages = {1033-1049.e8}, pmid = {42161263}, issn = {1934-6069}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological/genetics ; DNA Methylation ; Fecal Microbiota Transplantation ; Infant ; *Bacteria/genetics/drug effects ; Metagenomics ; Probiotics ; Feces/microbiology ; Akkermansia ; }, abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.}, }
@article {pmid42162115, year = {2026}, author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, &#xc5;V and Walter, S and Simon, R}, title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42162115}, issn = {2045-2322}, mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; Female ; *Metagenomics/methods ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Adult ; Middle Aged ; Case-Control Studies ; }, abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.}, }
@article {pmid42162287, year = {2026}, author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T}, title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42162287}, issn = {1432-8798}, support = {ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; }, mesh = {*Luteoviridae/genetics/classification/isolation &amp; purification ; Genome, Viral ; Phylogeny ; *Edible Grain/virology ; France ; *Plant Diseases/virology ; *Virome ; *Hordeum/virology ; Open Reading Frames ; RNA, Viral/genetics ; Metagenomics ; }, abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.}, }
@article {pmid42162574, year = {2025}, author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E}, title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.}, journal = {Asian journal of anesthesiology}, volume = {63}, number = {1}, pages = {20-29}, doi = {10.6859/aja.202503_63(1).0003}, pmid = {42162574}, issn = {2468-824X}, mesh = {Animals ; *Sevoflurane/pharmacology ; Female ; Male ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; }, abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.<br><br>METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.<br><br>RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.}, }
@article {pmid42162897, year = {2026}, author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J}, title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.}, journal = {Veterinary journal (London, England : 1997)}, volume = {318}, number = {}, pages = {106706}, doi = {10.1016/j.tvjl.2026.106706}, pmid = {42162897}, issn = {1532-2971}, mesh = {Animals ; *Goats/immunology/genetics ; *Autophagy/genetics ; *Lipopolysaccharides/immunology/pharmacology ; *Gastrointestinal Microbiome/immunology ; Macrophages/immunology ; *Brucellosis/immunology/veterinary/microbiology ; *Goat Diseases/immunology/microbiology ; Immunity, Innate ; Leukocytes, Mononuclear/immunology ; }, abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.}, }
@article {pmid42163161, year = {2026}, author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM}, title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {}, pmid = {42163161}, issn = {1471-244X}, mesh = {Humans ; *Major Depressive Disorder/genetics/microbiology ; *DNA, Mitochondrial/genetics ; Genome-Wide Association Study ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Adult ; Polymorphism, Single Nucleotide ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; }, abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.<br><br>METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.<br><br>RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p&#x2009;<&#x2009;0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.<br><br>CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).}, }
@article {pmid42165805, year = {2026}, author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM}, title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42165805}, issn = {2057-5858}, mesh = {Humans ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; *Colon/microbiology/virology ; Bacteria/genetics/virology/classification ; Escherichia coli/virology/genetics ; Phage Therapy ; }, abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.}, }
@article {pmid42166340, year = {2026}, author = {Sato, M and Kanaly, RA and Mori, JF}, title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42166340}, issn = {1465-2080}, mesh = {*Sphingomonadaceae/genetics/metabolism/growth &amp; development/isolation &amp; purification ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Achromobacter denitrificans/genetics/metabolism/growth &amp; development ; Genome, Bacterial ; Biodegradation, Environmental ; *Transcriptome ; *Achromobacter/genetics/metabolism ; Soil Microbiology ; Gene Expression Profiling ; *Microbial Consortia ; }, abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.}, }
@article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; }, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, }
@article {pmid42167986, year = {2026}, author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S}, title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.}, journal = {Journal of the World federation of orthodontists}, volume = {15}, number = {4}, pages = {299-309}, doi = {10.1016/j.ejwf.2026.03.003}, pmid = {42167986}, issn = {2212-4438}, mesh = {Humans ; *Zinc Oxide ; *Dental Implants/microbiology ; *Microbiota/genetics ; *Orthodontic Anchorage Procedures/instrumentation ; Female ; *Mouth/microbiology ; Metagenomics ; Male ; *Nanoparticles ; *Coated Materials, Biocompatible ; Adult ; Gingival Crevicular Fluid/microbiology ; }, abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.<br><br>METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.<br><br>RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri&#x2011;implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).<br><br>CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri&#x2011;implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.}, }
@article {pmid42168845, year = {2026}, author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P}, title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42168845}, issn = {1471-2180}, support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/metabolism/blood ; Biomarkers/blood ; Multiomics ; Metabolomics/methods ; Female ; *Gastrointestinal Microbiome ; Male ; Feces/microbiology ; Aged ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Dysbiosis/microbiology ; Metagenomics/methods ; }, abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.}, }
@article {pmid42169289, year = {2026}, author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I}, title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119324}, doi = {10.1016/j.foodres.2026.119324}, pmid = {42169289}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Odorants/analysis ; Fermentation ; *Meat Products/microbiology/analysis ; *Metagenomics ; Animals ; *Pea Proteins/metabolism ; Gas Chromatography-Mass Spectrometry ; *Food Microbiology ; Volatile Organic Compounds/analysis ; Microbiota ; Bacteria/metabolism/classification ; Swine ; Taste ; Humans ; Fermented Foods/microbiology ; }, abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.}, }
@article {pmid42169351, year = {2026}, author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S}, title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119400}, doi = {10.1016/j.foodres.2026.119400}, pmid = {42169351}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; *Whey/microbiology ; Goats ; Fermentation ; *Food Microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Biogenic Amines/analysis ; Milk/microbiology ; }, abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.}, }
@article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0030526}, pmid = {42171373}, issn = {2379-5077}, support = {K08AI159619//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; *Dysbiosis/microbiology/genetics/immunology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacterial Toxins/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Machine Learning ; Computational Biology/methods ; }, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, }
@article {pmid42172850, year = {2026}, author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R}, title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130036}, doi = {10.1016/j.jenvman.2026.130036}, pmid = {42172850}, issn = {1095-8630}, mesh = {Tibet ; *Wastewater/microbiology ; RNA, Ribosomal, 16S ; *Waste Disposal, Fluid ; *Microbiota ; Bacteria ; Altitude ; Metagenomics ; }, abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.}, }
@article {pmid42172982, year = {2026}, author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C}, title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158288}, doi = {10.1016/j.phymed.2026.158288}, pmid = {42172982}, issn = {1618-095X}, mesh = {Animals ; Homeostasis/drug effects ; Male ; *Zonula Occludens-1 Protein/metabolism ; *Bile Acids and Salts/metabolism ; Liver/drug effects/metabolism ; Rats ; Rats, Sprague-Dawley ; *Quinazolines/pharmacology ; *Cholestasis/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Liver Diseases/drug therapy/metabolism ; }, abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.<br><br>OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.<br><br>METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and &#x3b1;-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.<br><br>RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.<br><br>CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.}, }
@article {pmid42173516, year = {2026}, author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A}, title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {331}, number = {1}, pages = {G38-G59}, doi = {10.1152/ajpgi.00056.2026}, pmid = {42173516}, issn = {1522-1547}, support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Tumor Escape/drug effects ; Male ; Mice ; *Bile Acids and Salts ; Dysbiosis/chemically induced ; STAT1 Transcription Factor/metabolism ; Wnt1 Protein/genetics/metabolism ; STAT3 Transcription Factor/metabolism ; Disease Progression ; B7-H1 Antigen/metabolism ; Humans ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Mice, Inbred C57BL ; Interferon-gamma/metabolism ; }, abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes tumorigenesis, we evaluated the effects of HFD + ABS ± ABx treatment on tumor immune evasion in mice. In HFD + ABS + ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1, and programmed cell death-ligand 1 (PD-L1) was observed, along with apoptosis suppression. Protein expressions of interferon-gamma (IFNγ) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD + ABS + ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFNγ stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1, and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD + ABS + ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFNγ-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.NEW &amp; NOTEWORTHY Coadministration of antibiotics with a high-fat diet and acid bile salts exacerbated dysbiosis, insulin resistance, and systemic inflammation, thereby promoting tumor progression via tumor immune evasion at the squamocolumnar junction (SCJ) in K19-Wnt1/C2mE mice. In the tumor, interferon-gamma-induced programmed death-ligand 1 through the activation of signal transducer and activator of transcription 1 (STAT1) and STAT3. Understanding the link between dysbiosis and tumor immunity might aid in the development of new immunotherapies for SCJ tumors.}, }
@article {pmid42173938, year = {2026}, author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE}, title = {Metagenomic survey of pathogen prevalence in the infant gut.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42173938}, issn = {2045-2322}, support = {101039583//ERC Starting Grant/ ; }, mesh = {Humans ; *Metagenomics/methods ; Female ; Prevalence ; Infant ; *Gastrointestinal Microbiome/genetics ; Breast Feeding ; Anti-Bacterial Agents/therapeutic use ; *Metagenome ; Infant, Newborn ; Male ; *Opportunistic Infections/microbiology/epidemiology ; *Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.}, }
@article {pmid42174021, year = {2026}, author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W}, title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42174021}, issn = {2045-2322}, mesh = {Humans ; *Mucins/metabolism ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Alcohol Drinking ; *Diet ; *Eating ; }, abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.}, }
@article {pmid42175741, year = {2026}, author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z}, title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70929}, doi = {10.1111/gcb.70929}, pmid = {42175741}, issn = {1365-2486}, support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; }, mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota/genetics ; *Seawater/microbiology ; Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.}, }
@article {pmid42176010, year = {2026}, author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E}, title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42176010}, issn = {1432-184X}, mesh = {Animals ; *Isopoda/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; *Hepatopancreas/microbiology ; Metagenome ; Metagenomics ; Lignin/metabolism ; Phylogeny ; Italy ; }, abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.}, }
@article {pmid42176229, year = {2026}, author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB}, title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42176229}, issn = {1751-7370}, support = {//National Science Foundation/ ; #2025250//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; #2025337//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; #2025262//Rules of Life-Microbiome Theory and Mechanisms 2 collaborative/ ; LS-ECIAMEE-00001638//Simons Foundation/ ; DEB 2236782//NSF CAREER award/ ; }, mesh = {*Carbon/metabolism ; *Bacteria/genetics/metabolism/classification ; *Microbiota/genetics ; rRNA Operon ; Genome Size ; Metagenomics ; Heterotrophic Processes ; }, abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.}, }
@article {pmid42176246, year = {2026}, author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M}, title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {18}, number = {7}, pages = {8902-8918}, pmid = {42176246}, issn = {1867-1314}, support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Probiotics/administration &amp; dosage ; *Hepatitis, Autoimmune/microbiology/drug therapy/metabolism ; Multiomics ; Mice ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Liver/metabolism/pathology ; Male ; Mice, Inbred C57BL ; Female ; }, abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.}, }
@article {pmid42176375, year = {2026}, author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D}, title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.}, journal = {Water research}, volume = {302}, number = {}, pages = {126129}, doi = {10.1016/j.watres.2026.126129}, pmid = {42176375}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Phosphorus/metabolism ; *Freezing ; *Microbiota ; Geologic Sediments ; }, abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.}, }
@article {pmid42176589, year = {2026}, author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q}, title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128552}, doi = {10.1016/j.micres.2026.128552}, pmid = {42176589}, issn = {1618-0623}, mesh = {*Phosphorus/metabolism ; Soil Microbiology ; *Trichoderma/physiology/metabolism ; Rhizosphere ; *Pseudomonas/metabolism/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pyrus/microbiology/growth &amp; development/metabolism ; Biomass ; Microbiota ; Metagenome ; Plant Roots/microbiology ; }, abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.}, }
@article {pmid42176766, year = {2026}, author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM}, title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.}, journal = {Neuroscience and biobehavioral reviews}, volume = {187}, number = {}, pages = {106775}, doi = {10.1016/j.neubiorev.2026.106775}, pmid = {42176766}, issn = {1873-7528}, mesh = {Humans ; *Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology ; *Oxidative Stress/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/immunology/metabolism ; *Neuroinflammatory Diseases/immunology/metabolism ; Probiotics ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.}, }
@article {pmid42176923, year = {2026}, author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y}, title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.}, journal = {International journal of biological macromolecules}, volume = {368}, number = {}, pages = {152668}, doi = {10.1016/j.ijbiomac.2026.152668}, pmid = {42176923}, issn = {1879-0003}, mesh = {Animals ; *Atractylodes/chemistry ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism/pathology ; *Carbon/metabolism ; *Fatty Liver/drug therapy/metabolism ; Disease Models, Animal ; }, abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat and methionine/choline-deficient diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/d) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.}, }
@article {pmid42177457, year = {2026}, author = {Zhang, H and Abbas, Z and Li, H and Zhu, Y and Hu, X and Si, D}, title = {Synergistic fungal-enzymatic fermentation of corn straw enhances nutritional value, microbial stability, and bio-feed quality.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42177457}, issn = {1471-2180}, support = {2024TSYCTD0016//Xinjiang Uygur Autonomous Region "Tianshan Talents" Cultivation Program/ ; }, mesh = {*Zea mays/microbiology/metabolism/chemistry ; *Fermentation ; *Animal Feed/microbiology/analysis ; Lignin/metabolism ; *Nutritive Value ; Cellulase/metabolism ; Laccase/metabolism ; *Fungi/metabolism/enzymology/genetics ; Bacillus subtilis/metabolism/enzymology ; Aspergillus niger/metabolism/enzymology ; Biomass ; Animals ; Pediococcus acidilactici/metabolism/enzymology ; Microbial Consortia ; Bacteria/genetics/metabolism ; Endo-1,4-beta Xylanases/metabolism ; }, abstract = {Valorizing mature, dry corn straw into nutritional animal feed is constrained by its recalcitrant lignocellulosic matrix, while conventional silage methods face stability and logistical limitations. Existing enzymatic and bacterial approaches often lack synergistic efficacy and fail to mitigate pathogen risk in dry biomass systems. We engineered a two-stage fungal-enzymatic fermentation strategy employing a consortium of Aspergillus niger LFB-AN14, Coriolopsis trogii LFB-F1, Bacillus subtilis LFB-BS7, and Pediococcus acidilactici A62, integrated with cellulase, xylanase, and laccase under optimized conditions (1% inoculation, 5:5:1:1 ratio, 37 °C, 21 days). Our results demonstrated that the bacterial-enzyme co-treatment (Group A3) significantly reduced fiber content, with neutral detergent fiber (NDF) and acid detergent fiber (ADF) decreasing by 22.6% and 29.1%, respectively, compared to the control (p < 0.001). Lignin degradation was enhanced, accompanied by a 4.5-fold increase in water-soluble carbohydrates (WSC). The metabolic profile revealed elevated lactic acid production (36.54 g/kg FM) and the suppression of undesirable byproducts such as propionic and butyric acids. Microbial community analysis revealed a dominant shift toward Pediococcus (> 50% abundance) and inhibition of pathogenic Enterobacter spp. Structural analyses (SEM, FTIR) confirmed extensive lignocellulose deconstruction, particularly through carbonyl and hydroxyl functional groups. Metagenomic analysis revealed upregulated Auxiliary Activity (AA) enzymes and cellulosome modules, elucidating the mechanistic basis for enhanced degradation. KEGG enrichment highlighted enhanced aromatic compound metabolism and yeast proliferation, reflecting superior metabolic efficiency. This integrated fungal-enzymatic approach establishes a safe, scalable, and metabolically efficient strategy for transforming agricultural residues into high-quality bio-feed, resolving key challenges in fiber digestibility, pathogen control, and storage stability for sustainable livestock production.}, }
@article {pmid42178569, year = {2026}, author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T}, title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42178569}, issn = {2049-2618}, support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Ammonia/metabolism ; *Carbon/metabolism ; Oxidation-Reduction ; *Microbiota ; *Archaea/metabolism/classification/genetics ; Carbon Cycle ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Seawater/microbiology ; Autotrophic Processes ; }, abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.<br><br>RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67&#xa0;mg CO2 per g dry weight in a year.<br><br>CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.}, }
@article {pmid42178714, year = {2026}, author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2676162}, pmid = {42178714}, issn = {1949-0984}, mesh = {Humans ; *Alzheimer Disease/microbiology/psychology/metabolism/physiopathology ; Aged ; Female ; Male ; *Cognition ; *Gastrointestinal Microbiome ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Metabolic Networks and Pathways ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Aged, 80 and over ; }, abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.}, }
@article {pmid42178721, year = {2026}, author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M}, title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2675078}, pmid = {42178721}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; Female ; Child ; *Immunoglobulin A, Secretory/immunology ; Immunosuppressive Agents/adverse effects/therapeutic use ; Male ; *Organ Transplantation/adverse effects ; *Bacteria/classification/genetics/isolation &amp; purification ; Transplant Recipients ; Tacrolimus/adverse effects/therapeutic use ; Adolescent ; Child, Preschool ; Feces/microbiology ; Immunosuppression Therapy/adverse effects ; Metagenomics ; Heart Transplantation ; }, abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.}, }
@article {pmid42184066, year = {2026}, author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A}, title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42184066}, issn = {1573-0972}, support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; }, mesh = {Animals ; *Polyphenols/pharmacology/chemistry/administration &amp; dosage ; Male ; *Tea/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Chitosan/chemistry ; Rats, Sprague-Dawley ; Rats ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; Proteomics ; Proteome ; Bacteria/classification/genetics/drug effects ; *Ferric Compounds/chemistry ; Metagenomics ; }, abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.}, }
@article {pmid42184159, year = {2026}, author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C}, title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42184159}, issn = {1574-6941}, support = {//Scientific Committee on Antarctic Research/ ; 542264307//German Research Foundation/ ; 569718716//German Research Foundation/ ; }, mesh = {Antarctic Regions ; *Phytoplankton/metabolism/genetics/classification ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Diatoms ; Seawater/microbiology ; Polysaccharides/metabolism ; *Microbiota ; }, abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.}, }
@article {pmid42185302, year = {2026}, author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R}, title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42185302}, issn = {2055-5008}, support = {2020/06077-9//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; }, mesh = {*Triticum/microbiology/growth &amp; development ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; *Disease Resistance ; Rhizosphere ; Plant Roots/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; }, abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.}, }
@article {pmid42185318, year = {2026}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR}, title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42185318}, issn = {2041-1723}, support = {R35GM137828//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; }, mesh = {*Skin Microbiome ; Humans ; Metagenome ; *Skin/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Anti-Infective Agents/pharmacology/metabolism ; *Microbiota ; Multigene Family ; Phylogeny ; }, abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.}, }
@article {pmid42185948, year = {2026}, author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P}, title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42185948}, issn = {1471-2164}, support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; }, mesh = {Animals ; *Hemiptera/microbiology/genetics/classification ; *Symbiosis ; Phylogeny ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Genetic Variation ; Microbiota ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.<br><br>RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.<br><br>CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.}, }
@article {pmid42186028, year = {2026}, author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y}, title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.}, journal = {Nutrition journal}, volume = {25}, number = {1}, pages = {}, pmid = {42186028}, issn = {1475-2891}, mesh = {Humans ; Cross-Sectional Studies ; Child ; Adolescent ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; *Diet, Western/adverse effects ; Child, Preschool ; Feces/microbiology ; Feeding Behavior ; *Problem Behavior ; }, abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.<br><br>METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10&#xa0;years) and 133 adolescents (11-17&#xa0;years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.<br><br>RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.<br><br>CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.}, }
@article {pmid42187250, year = {2026}, author = {Liu, X and Kwok, L-Y and Zhang, W}, title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0024426}, pmid = {42187250}, issn = {2165-0497}, support = {2024ZY0168//Central Guiding Local Science and Technology Development Fund Project/ ; NMGIRT2411//Program of Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; 2025QN03001//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/metabolism/etiology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Stroke/complications/microbiology/metabolism ; Male ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; Female ; Aged ; Feces/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Metabolomics ; }, abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.<br><br>IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.}, }
@article {pmid42189287, year = {2026}, author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M}, title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {75}, number = {8}, pages = {}, pmid = {42189287}, issn = {1432-0851}, support = {PE00000019//NextGenerationEU/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/immunology/genetics ; *Neoplasms/drug therapy/microbiology/immunology ; *Immunotherapy/methods ; *Biomarkers, Tumor ; Machine Learning ; Feces/microbiology ; Biomarkers ; }, abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.}, }
@article {pmid42190464, year = {2026}, author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A}, title = {Age, strain, and gut section shape the microbiome of commercial laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107152}, pmid = {42190464}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/genetics/physiology ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; *Bacteria/classification/isolation &amp; purification/genetics ; RNA, Bacterial/analysis ; Age Factors ; Species Specificity ; }, abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.}, }
@article {pmid42190825, year = {2026}, author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J}, title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124845}, doi = {10.1016/j.envres.2026.124845}, pmid = {42190825}, issn = {1096-0953}, mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis/chemistry ; *Geologic Sediments/chemistry/microbiology ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Molecular Weight ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Microbiota ; }, abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.}, }
@article {pmid42191017, year = {2026}, author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Barra Caracciolo, A and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V}, title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.}, journal = {New biotechnology}, volume = {94}, number = {}, pages = {121-135}, doi = {10.1016/j.nbt.2026.05.013}, pmid = {42191017}, issn = {1876-4347}, mesh = {*Metals, Heavy/isolation &amp; purification/metabolism ; *Soil Pollutants/metabolism/isolation &amp; purification ; Biodegradation, Environmental ; *Soil Microbiology ; *Microbiota ; *Rhizosphere ; Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - such as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.}, }
@article {pmid42196140, year = {2026}, author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL}, title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196140}, issn = {1422-0067}, support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth &amp; development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; }, abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.}, }
@article {pmid42196196, year = {2026}, author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L}, title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196196}, issn = {1422-0067}, support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; }, abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.}, }
@article {pmid42196214, year = {2026}, author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT}, title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196214}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; }, abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.}, }
@article {pmid42196222, year = {2026}, author = {Zhang, X and Cai, L and Bai, Y and Peng, F}, title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196222}, issn = {1422-0067}, support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&amp;D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; }, abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.}, }
@article {pmid42197004, year = {2026}, author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH}, title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197004}, issn = {2072-6643}, support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.<br><br>METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.<br><br>RESULTS: The results showed that the a-FMT group recovered &#x3b1; diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.<br><br>CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.}, }
@article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, }
@article {pmid42197087, year = {2026}, author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y}, title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197087}, issn = {2072-6643}, support = {2020YFC2002902//Beijing Sport University/ ; }, mesh = {Aged, 80 and over ; Female ; Humans ; Male ; *Exercise/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Malnutrition/microbiology/therapy ; Nursing Home Residents ; Nursing Homes ; Nutrition Assessment ; *Nutritional Status ; }, abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.<br><br>METHODS: A total of 129 nursing home residents (&#x2265;80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF &#x2265; 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.<br><br>RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.<br><br>CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.<br><br>CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).}, }
@article {pmid42198703, year = {2026}, author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S}, title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198703}, issn = {1999-4915}, support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; }, mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Tropical Climate ; Phylogeny ; *Virome ; }, abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.}, }
@article {pmid42199008, year = {2026}, author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S}, title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2677951}, pmid = {42199008}, issn = {1949-0984}, mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration &amp; dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.}, }
@article {pmid42199424, year = {2026}, author = {Zhao, L and Wang, Q and Chen, J and Wang, J}, title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1767902}, pmid = {42199424}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; }, abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.<br><br>METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.<br><br>RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.<br><br>CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.}, }
@article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, }
@article {pmid42201863, year = {2026}, author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI}, title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0340244}, pmid = {42201863}, issn = {1932-6203}, mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; }, abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.}, }
@article {pmid42202778, year = {2026}, author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M}, title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {6}, pages = {1135-1150.e6}, doi = {10.1016/j.chom.2026.05.001}, pmid = {42202778}, issn = {1934-6069}, support = {K99 CA283146/CA/NCI NIH HHS/United States ; R00 CA283146/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/surgery/metabolism ; Female ; *Feces/microbiology/chemistry ; *Adenoma/microbiology/surgery ; *Metabolome ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Aged ; Metagenomics ; Metagenome ; }, abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.}, }
@article {pmid42202790, year = {2026}, author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R}, title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.}, journal = {Cell reports. Medicine}, volume = {7}, number = {6}, pages = {102835}, pmid = {42202790}, issn = {2666-3791}, mesh = {*Diabetes Mellitus, Type 2/microbiology/epidemiology ; Humans ; Female ; Sweden/epidemiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Prospective Studies ; Male ; Incidence ; Eubacteriales ; }, abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.}, }
@article {pmid42203372, year = {2026}, author = {McCann, P and Megaw, J and Gobert, GN}, title = {Parasite-associated microbiomes: An unseen microenvironment.}, journal = {Advances in parasitology}, volume = {131}, number = {}, pages = {31-70}, doi = {10.1016/bs.apar.2026.03.001}, pmid = {42203372}, issn = {2163-6079}, mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; }, abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.}, }
@article {pmid42203770, year = {2026}, author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M}, title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42203770}, issn = {2041-1723}, support = {1026-00386B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; }, mesh = {Adult ; Female ; Humans ; Infant ; Bifidobacterium/metabolism/genetics ; Clostridium/metabolism/genetics/isolation &amp; purification ; *Dietary Fiber/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Metagenome ; Metagenomics ; *Milk, Human/metabolism/chemistry ; *Oligosaccharides/metabolism ; *Weaning ; }, abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.}, }
@article {pmid42203854, year = {2026}, author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I}, title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42203854}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.}, }
@article {pmid42204574, year = {2026}, author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N}, title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.}, journal = {Annals of neurology}, volume = {100}, number = {2}, pages = {334-340}, pmid = {42204574}, issn = {1531-8249}, support = {R01NS097723/GF/NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; R01 AG085320/AG/NIA NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; R01 NS097723/NS/NINDS NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; RF1AG075922/GF/NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease/virology/diagnosis/genetics ; Female ; Male ; Case-Control Studies ; *Metagenomics/methods ; *Prodromal Symptoms ; Middle Aged ; Aged ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026;100:334-340.}, }
@article {pmid42204631, year = {2026}, author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH}, title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.}, journal = {Parasites &amp; vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42204631}, issn = {1756-3305}, support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Pediculus/microbiology/genetics/classification ; China ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Humans ; *Lice Infestations/parasitology/epidemiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; Female ; }, abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.<br><br>METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples&#xa0;(n&#x2009;=&#x2009;46) was investigated by metagenomic shotgun sequencing&#xa0;and comparatively analysed at the&#xa0;phylum,&#xa0;genus, and&#xa0;species levels. In addition, the prevalence of potential pathogen DNA in head lice samples&#xa0;(n&#x2009;=&#x2009;204) was assessed&#xa0;using real-time PCR with stringent negative controls.<br><br>RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722&#xa0;genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level,&#xa0;DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial&#xa0;DNA&#xa0;from these taxa.<br><br>CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB&#xa0;microbiome in head lice. The high proportion of unannotated genes (>95%)&#xa0;underscores the limited representation of louse-associated microbial genomes in public databases and suggests &#xa0;substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may&#xa0;suggest prior&#xa0;exposure, mechanical carriage, or residual DNA from&#xa0;blood meals. These exploratory findings contribute new&#xa0;insights into the microbiota associated with human lice.}, }
@article {pmid42204882, year = {2026}, author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H}, title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70339}, doi = {10.1111/1462-2920.70339}, pmid = {42204882}, issn = {1462-2920}, support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; }, abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH}}_4^{+} $$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.}, }
@article {pmid42206340, year = {2026}, author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF}, title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0124}, pmid = {42206340}, issn = {1471-2970}, support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; }, abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206586, year = {2026}, author = {Yeo, S and Park, H}, title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681840}, pmid = {42206586}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation &amp; purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation &amp; purification/classification/genetics ; }, abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.}, }
@article {pmid42206864, year = {2026}, author = {Zhao, R and Biddle, JF}, title = {Community structure and methylation of microbes in an artificially forced sediment core.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0353325}, pmid = {42206864}, issn = {2165-0497}, support = {//W. M. Keck Foundation/ ; }, mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Archaea/genetics/classification/isolation &amp; purification/metabolism ; *DNA Methylation ; Metagenome ; *Microbiota/genetics ; Epigenesis, Genetic ; Phylogeny ; }, abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.}, }
@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 &amp; 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.}, }
@article {pmid42207344, year = {2026}, author = {Cagirgan, OY and Korkmaz, S and Diker, KS}, title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.}, journal = {Tropical animal health and production}, volume = {58}, number = {5}, pages = {}, pmid = {42207344}, issn = {1573-7438}, support = {VTF-190002//Bilimsel Ara&#x15f;t&#x131;rma Projeleri Birimi, Ayd&#x131;n Adnan Menderes &#xdc;niversitesi/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration &amp; dosage ; Amoxicillin/therapeutic use/administration &amp; dosage ; Necrosis/veterinary/microbiology ; Male ; }, abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.}, }
@article {pmid42208188, year = {2026}, author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S}, title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.}, journal = {Water research}, volume = {302}, number = {}, pages = {126138}, doi = {10.1016/j.watres.2026.126138}, pmid = {42208188}, issn = {1879-2448}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Wastewater/microbiology/chemistry ; Anaerobiosis ; Caffeine/metabolism ; Carbon Isotopes ; Bacteria/metabolism/genetics ; Naproxen/metabolism ; Demethylation ; Methane/metabolism ; Archaea/metabolism/genetics ; *Seawater/microbiology ; Oceans and Seas ; }, abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.}, }
@article {pmid42208547, year = {2026}, author = {Goldberg, H and Dyhrman, ST and DeMers, MA and Braakman, R and Hennon, GMM}, title = {Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70315}, doi = {10.1111/1462-2920.70315}, pmid = {42208547}, issn = {1462-2920}, support = {OCE-1937715//National Science Foundation/ ; OCE-2019589//National Science Foundation/ ; }, mesh = {*Hydrogen Peroxide/metabolism ; *Seawater/microbiology ; *Catalase/genetics/metabolism ; Ecosystem ; Oceans and Seas ; *Bacteria/genetics/metabolism/classification ; Bacterial Proteins/genetics/metabolism ; Metagenome ; *Microbiota ; Genome, Bacterial ; }, abstract = {Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying 'helper' microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes-including within the known 'helper' genus Alteromonas-and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on 'helpers'. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.}, }
@article {pmid42208810, year = {2026}, author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB}, title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106774}, doi = {10.1016/j.jinf.2026.106774}, pmid = {42208810}, issn = {1532-2742}, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Female ; Male ; *Carrier State/microbiology/epidemiology ; Aged, 80 and over ; *Bacteria, Anaerobic/drug effects ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Aged ; Nursing Home Residents ; Prevalence ; }, abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.<br><br>METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.<br><br>RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (&#x3b2;=1.36, P=0.010) and higher overall pathobiont relative abundance (&#x3b2;=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (&#x3b2;=1.60, P=0.007) and relative abundance (&#x3b2;=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.<br><br>CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.}, }
@article {pmid42209465, year = {2026}, author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L}, title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42209465}, issn = {2041-1723}, mesh = {*Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Carbon Dioxide/metabolism ; Genome, Viral ; *Polymorphism, Single Nucleotide ; Evolution, Molecular ; Anaerobiosis ; CRISPR-Cas Systems/genetics ; }, abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.}, }
@article {pmid42209510, year = {2026}, author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH}, title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42209510}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Albendazole/pharmacology ; *Anthelmintics/pharmacology ; *Bacteria/drug effects/classification/genetics ; *Gastrointestinal Microbiome/drug effects ; *Ivermectin/pharmacology ; *Macrolides/pharmacology ; *Metagenomics/methods ; *Trichuriasis/drug therapy/parasitology ; Trichuris/drug effects ; }, abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.}, }
@article {pmid42209868, year = {2026}, author = {Ajeh, IJ and Ikukpla'si, OSI}, title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42209868}, issn = {2589-0409}, mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; }, abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.}, }
@article {pmid42210528, year = {2026}, author = {Zhou, X and Zhang, M and Zhou, J and Han, J}, title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.}, journal = {Journal of the science of food and agriculture}, volume = {106}, number = {12}, pages = {7197-7208}, pmid = {42210528}, issn = {1097-0010}, support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; }, mesh = {Animals ; *NF-kappa B/metabolism/genetics ; *Xanthine Oxidase/metabolism/antagonists &amp; inhibitors/genetics ; *Toll-Like Receptor 4/genetics/metabolism ; Mice ; *Kidney/metabolism/drug effects ; *Hyperuricemia/metabolism/microbiology/genetics/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Male ; *Limosilactobacillus reuteri/physiology ; *Probiotics/administration &amp; dosage ; Uric Acid/metabolism/blood ; Humans ; Mice, Inbred C57BL ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Signal Transduction ; }, abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.<br><br>RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-&#x3ba;B signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).<br><br>CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42212684, year = {2026}, author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X}, title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672791}, pmid = {42212684}, issn = {1949-0984}, mesh = {Humans ; *Precision Medicine/methods ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; Multiomics ; Animals ; }, abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.}, }
@article {pmid42212786, year = {2026}, author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E}, title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0171425}, pmid = {42212786}, issn = {2379-5077}, support = {PUT 1371, PRG1414//Estonian Research Competency Council/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; MEiN/2023/DIR/3796//Ministerstwo Edukacji i Nauki/ ; PLG/2023/016234,PLG/2024/017180//Infrastruktura PL-Grid/ ; TT17//Estonian Center of Genomics/Roadmap II, funded by the Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; }, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.<br><br>IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.}, }
@article {pmid42212790, year = {2026}, author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T}, title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0014426}, pmid = {42212790}, issn = {2379-5077}, support = {PUT 1371, PRG1414//Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; 2025/56/C/NZ2/00481//NCN Sonatina/ ; 2020/38/E/NZ2/00598//NCN Sonata BIS/ ; MEiN/2023/DIR/3796//Minister of Science and Higher Education/ ; }, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Humans ; }, abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.}, }
@article {pmid42213267, year = {2026}, author = {Gulnihol, S and Abdukhamid, N and Rustam, T and Firdavs, U and Gholami, AA}, title = {Methodological concerns in the association between gut microbiota and sarcopenia: from cross‑sectional associations to statistical fragility.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {}, pmid = {42213267}, issn = {1720-8319}, mesh = {Humans ; *Sarcopenia/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aged ; Iran ; }, abstract = {This commentary critically appraises the cross‑sectional study by Nasrollahizadeh et al. on gut microbiota and sarcopenia in Iranian older adults. Key limitations include; after FDR correction for twelve bacterial genera, no significant differences remained between groups; Akkermansia lost significance in sensitivity analyses; Lactobacillus showed a confidence interval including 1.00; four primer pairs lacked validation with no MIQE‑compliant efficiency data; the cross‑sectional design precludes causal inference; and no sample size justification was reported. The study offers valuable hypothesis‑generating data, but evidence remains preliminary. Future longitudinal studies with metagenomic approaches are essential.}, }
@article {pmid42214368, year = {2026}, author = {Karmarkar, B and Dhotre, D}, title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0321425}, pmid = {42214368}, issn = {2165-0497}, mesh = {*Gliadin/metabolism ; *Celiac Disease/microbiology/metabolism ; Humans ; *Stenotrophomonas maltophilia/enzymology/genetics ; Caco-2 Cells ; *Gastrointestinal Microbiome ; *Prolyl Oligopeptidases/metabolism/genetics ; Intestinal Barrier Function ; Peptides/metabolism ; *Bacterial Proteins/metabolism/genetics ; }, abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.<br><br>IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.}, }
@article {pmid42214386, year = {2026}, author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG}, title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.}, journal = {mBio}, volume = {17}, number = {7}, pages = {e0071126}, pmid = {42214386}, issn = {2150-7511}, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects/administration &amp; dosage ; Infant ; *Metabolome/drug effects ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Female ; Male ; Longitudinal Studies ; Amoxicillin/therapeutic use/adverse effects ; Metagenomics ; }, abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.<br><br>IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.<br><br>CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.}, }
@article {pmid42214595, year = {2026}, author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X}, title = {Nanoplastics reshape nitrogen cycling in submerged macrophyte systems: A metagenomic perspective.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124885}, doi = {10.1016/j.envres.2026.124885}, pmid = {42214595}, issn = {1096-0953}, mesh = {*Nitrogen Cycle/drug effects ; Metagenomics ; Rhizosphere ; *Water Pollutants, Chemical/toxicity ; Nitrogen/metabolism ; *Magnoliopsida/metabolism/drug effects ; Bacteria/metabolism/genetics ; Microbiota/drug effects ; }, abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.}, }
@article {pmid42214685, year = {2026}, author = {Jiang, TA and Prioult, G and Quann, E}, title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.}, journal = {The Journal of nutrition}, volume = {156}, number = {7}, pages = {101621}, doi = {10.1016/j.tjnut.2026.101621}, pmid = {42214685}, issn = {1541-6100}, mesh = {*Polyphenols/metabolism/pharmacokinetics ; Humans ; *Synbiotics ; Biotransformation ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; }, abstract = {BACKGROUND: Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health but are constrained by poor bioavailability. Only 5%-10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract, while the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits due to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways.<br><br>OBJECTIVES: This review aimed to synthesize recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and to evaluate how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes, as well as the potential of targeted synbiotic strategies to enhance metabolite production.<br><br>METHODS: We conducted a narrative synthesis of recent literature examining microbial conversion pathways of dietary bioactives and their associated physiological effects, with a specific focus on interindividual variability in metabolite production and emerging evidence on synbiotic interventions combining probiotics with selected bioactive precursors.<br><br>RESULTS: Production of microbial metabolites varied markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes (metabotypes) that influenced clinical and nutritional responsiveness. Evidence showed that microbially derived metabolites were key mediators of systemic benefits. Studies evaluating targeted synbiotics demonstrated the capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging.<br><br>CONCLUSIONS: Metabolite-guided synbiotics represent a promising paradigm for precision nutrition by enhancing the consistency and efficacy of bioactive compound metabolism. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate the translation of microbiota-targeted interventions into practice.}, }
@article {pmid42215097, year = {2026}, author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L}, title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119428}, doi = {10.1016/j.foodres.2026.119428}, pmid = {42215097}, issn = {1873-7145}, mesh = {Multiomics ; *Microbiota/physiology ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis/metabolism ; China ; Metabolomics/methods ; *Food Microbiology ; *Taste ; *Flavoring Agents/metabolism ; Metagenomics ; Bacteria/metabolism/classification ; Temperature ; Fungi/metabolism/classification/genetics ; }, abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.}, }
@article {pmid42215200, year = {2026}, author = {Jones, RC and Visger, CJ and Lopez, CA}, title = {The microbiota of wild fermented cider from U.S. west coast apples.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105120}, doi = {10.1016/j.fm.2026.105120}, pmid = {42215200}, issn = {1095-9998}, mesh = {*Malus/microbiology ; Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Yeasts/isolation &amp; purification/classification/genetics/metabolism ; United States ; Food Microbiology ; Fruit/microbiology ; }, abstract = {Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.}, }
@article {pmid42215210, year = {2026}, author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L}, title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105130}, doi = {10.1016/j.fm.2026.105130}, pmid = {42215210}, issn = {1095-9998}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; }, abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.}, }
@article {pmid42217383, year = {2026}, author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W}, title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.}, journal = {Water research}, volume = {303}, number = {}, pages = {126182}, doi = {10.1016/j.watres.2026.126182}, pmid = {42217383}, issn = {1879-2448}, mesh = {*Sulfates/metabolism ; *Sulfur ; *Rivers ; *Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Plastics ; Mining ; Oxidation-Reduction ; }, abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.}, }
@article {pmid42217591, year = {2026}, author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H}, title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.}, journal = {Pharmacological research}, volume = {229}, number = {}, pages = {108273}, doi = {10.1016/j.phrs.2026.108273}, pmid = {42217591}, issn = {1096-1186}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy ; Metabolomics ; Precision Medicine ; }, abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.}, }
@article {pmid42218119, year = {2026}, author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL}, title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42218119}, issn = {2041-1723}, support = {R21 CA290426/CA/NCI NIH HHS/United States ; R21CA290426//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {*Melanoma/therapy/immunology/microbiology ; *Fecal Microbiota Transplantation/methods ; Humans ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; *Microbiota/genetics ; *Immune Checkpoint Inhibitors/therapeutic use ; }, abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.}, }
@article {pmid42218218, year = {2026}, author = {Zhu, G and Yang, G}, title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42218218}, issn = {2055-5008}, support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; }, mesh = {Humans ; *Multiple Sclerosis/diagnosis/microbiology ; *Machine Learning ; Female ; Feces/microbiology ; Male ; *Gastrointestinal Microbiome ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; ROC Curve ; Metagenome ; Predictive Learning Models ; }, abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.}, }
@article {pmid42218533, year = {2026}, author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY}, title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42218533}, issn = {1756-994X}, support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bevacizumab/therapeutic use ; *Colorectal Neoplasms/pathology/drug therapy/microbiology ; Fluorouracil/therapeutic use ; Leucovorin/therapeutic use ; *Liver Neoplasms/secondary/drug therapy ; *Microbiota ; Neoadjuvant Therapy ; Organoplatinum Compounds/therapeutic use ; Treatment Outcome ; Tumor Microenvironment/drug effects ; }, abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.<br><br>METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n&#x2009;=&#x2009;60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n&#x2009;=&#x2009;20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.<br><br>RESULTS: Durable disease control (PFS&#x2009;&#x2265;&#x2009;24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.<br><br>CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).}, }
@article {pmid42218921, year = {2026}, author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X}, title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.}, journal = {Molecular phylogenetics and evolution}, volume = {223}, number = {}, pages = {108650}, doi = {10.1016/j.ympev.2026.108650}, pmid = {42218921}, issn = {1095-9513}, mesh = {Animals ; *Symbiosis/genetics ; Phylogeny ; *Nematoda/microbiology/genetics ; *Microbiota/genetics ; Gene Transfer, Horizontal ; *Coxiellaceae/genetics/classification ; Wolbachia/genetics/classification ; Genome, Bacterial ; Sequence Analysis, DNA ; Metagenome ; Genomics ; Evolution, Molecular ; *Bacteroidetes/genetics/classification ; }, abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.<br><br>METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.<br><br>PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.<br><br>CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.}, }
@article {pmid42219044, year = {2026}, author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A}, title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.}, journal = {Journal of microbiological methods}, volume = {246}, number = {}, pages = {107565}, doi = {10.1016/j.mimet.2026.107565}, pmid = {42219044}, issn = {1872-8359}, mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Pasteurellaceae/genetics/isolation &amp; purification/classification ; Chickens/microbiology ; DNA Primers/genetics ; Cecum/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Poultry Diseases/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Pasteurellaceae Infections/veterinary/microbiology/diagnosis ; }, abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.}, }
@article {pmid42219690, year = {2026}, author = {Zhu, P and Yuan, X and Wang, X and Shi, Y}, title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70343}, doi = {10.1111/1462-2920.70343}, pmid = {42219690}, issn = {1462-2920}, support = {SDAIT0107//Shandong Modern Agricultural Technology &amp; Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; }, mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention &amp; control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; }, abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.}, }
@article {pmid42219901, year = {2026}, author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B}, title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {6}, pages = {}, doi = {10.1093/jac/dkag190}, pmid = {42219901}, issn = {1460-2091}, support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ionophores/pharmacology/administration &amp; dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; }, abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.<br><br>OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.<br><br>METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.<br><br>RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.<br><br>CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.}, }
@article {pmid42222492, year = {2026}, author = {Tran, TTT and Nguyen, OTK and Hoang, PH and Nguyen, NP and To, HTM and Nguyen, HQ}, title = {Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21262}, pmid = {42222492}, issn = {2167-8359}, mesh = {*Feces/microbiology/chemistry ; Vietnam ; *Coffee/metabolism/microbiology ; *Metabolomics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Fermentation ; Humans ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism ; Animals ; }, abstract = {BACKGROUND: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets.<br><br>METHODS: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups.<br><br>RESULTS: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter, and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6-hydroxyangolensic acid methyl ester, 4-aminobenzoic acid and caffeine were more abundant in civets on a coffee-cherry diet, meanwhile the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs, and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.}, }
@article {pmid42222901, year = {2026}, author = {Dong, Y and Hu, D and Yang, R and Xin, T and Guan, Y and Zhu, X and Ding, Y and Cui, S and Wang, R and Wang, X and Niu, Y and Kong, X}, title = {Early-Life Obesity Leaves a Metabolic Memory That Accelerates Aging-Related Decline Through the Gut Microbiota-GABA Axis.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {11}, pages = {e70513}, doi = {10.1002/mnfr.70513}, pmid = {42222901}, issn = {1613-4133}, support = {2024YFF1106004//National Key Research and Development Program/ ; PL2025H095//Natural Science Foundation of Heilongjiang Province/ ; }, mesh = {Animals ; *gamma-Aminobutyric Acid/metabolism/pharmacology ; *Aging/metabolism/physiology ; *Obesity/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat/adverse effects ; Male ; Oxidative Stress ; Rats ; Lipid Metabolism ; }, abstract = {Childhood obesity is a critical public health concern. Whether diet-induced transient obesity during development negatively impacts later-life health remains unclear, and mechanisms are poorly understood. This study investigates whether these effects persist into aging and employs integrated omics to explore underlying mechanisms. Using a high-fat diet (HFD) to induce transient developmental obesity in post-weaning rats and larval Drosophila, we examined the long-term effects on aging metabolic health in both species. Transient developmental obesity in rats was linked to accelerated aging, weight loss, worsened metabolism, colonic inflammation, and oxidative stress. Metabolomics revealed persistent gamma aminobutyric acid (GABA) dysregulation associated with intestinal ammonia levels, and gut metagenomics showed a reduction in Lactobacillales, correlating with adverse health outcomes. In Drosophila, exogenous GABA extended HF-diet lifespan. It reduced trehalose, triglycerides (TG), and oxidative stress; concurrently, it restored intestinal Lactobacillus and activated the phosphotransferase system (PTS), thereby improving metabolic homeostasis and redox status. Transient developmental obesity is associated with reduced gut Lactobacillus abundance, which may contribute to decreased GABA levels and subsequent disruption of glucose (GLU) metabolism, potentially involving the PTS pathway. These interconnected alterations may ultimately lead to systemic dysregulation of GLU and lipid metabolism and redox homeostasis in later life, compromising overall health and longevity.}, }
@article {pmid42223530, year = {2026}, author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC}, title = {Predator avoidance promotes interbacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42223530}, issn = {1751-7370}, support = {P20GM103432//Institutional Development Award (IDeA)/ ; R01GM149795/GM/NIGMS NIH HHS/United States ; P20 GM103432/GM/NIGMS NIH HHS/United States ; R35GM140886/GM/NIGMS NIH HHS/United States ; R35 GM140886/GM/NIGMS NIH HHS/United States ; }, mesh = {*Symbiosis ; *Soil Microbiology ; *Myxococcales/physiology/genetics/classification/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; *Microbial Consortia ; Metagenomics ; Escherichia coli/physiology ; Gene Transfer, Horizontal ; Metagenome ; }, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to nonsymbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable interbacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid42227741, year = {2026}, author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD}, title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0018826}, pmid = {42227741}, issn = {2379-5077}, support = {U54AG089323/NH/NIH HHS/United States ; P30AI045008/NH/NIH HHS/United States ; U19AI174998/NH/NIH HHS/United States ; }, mesh = {Humans ; *Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Feces/virology ; DNA, Viral/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Saliva/virology ; Bacteriophages/genetics ; }, abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.}, }
@article {pmid42228562, year = {2026}, author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N}, title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117478}, doi = {10.1016/j.celrep.2026.117478}, pmid = {42228562}, issn = {2211-1247}, mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Proteolysis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Inflammatory Bowel Diseases/microbiology ; Peptide Hydrolases/metabolism ; Proteomics ; Colitis, Ulcerative/microbiology ; Feces/microbiology ; Pouchitis/microbiology ; }, abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.}, }
@article {pmid42229136, year = {2026}, author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E}, title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142560}, doi = {10.1016/j.jhazmat.2026.142560}, pmid = {42229136}, issn = {1873-3336}, mesh = {RNA, Ribosomal, 16S/genetics ; *Lactuca/drug effects/growth &amp; development ; Germination/drug effects ; *Soil Microbiology ; *Pesticides/toxicity ; Biological Assay ; Chlorpyrifos/toxicity ; *Soil Pollutants/toxicity ; Agriculture ; *Microbiota/drug effects ; }, abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.}, }
@article {pmid42229568, year = {2026}, author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G}, title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124851}, doi = {10.1016/j.envres.2026.124851}, pmid = {42229568}, issn = {1096-0953}, mesh = {*Wetlands ; *Soil Microbiology ; *Soil/chemistry ; *Rain ; *Carbon/metabolism/analysis ; *Microbiota ; Carbon Cycle ; Metagenomics ; *Carbon Sequestration ; }, abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (±40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.}, }
@article {pmid42229598, year = {2026}, author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135043}, doi = {10.1016/j.biortech.2026.135043}, pmid = {42229598}, issn = {1873-2976}, mesh = {*Lignin/metabolism ; *Methane/biosynthesis/metabolism ; Electron Transport ; *Microbial Consortia/physiology ; *Metabolic Networks and Pathways ; Hydrogen-Ion Concentration ; Animals ; Cattle ; Manure/microbiology ; }, abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.}, }
@article {pmid42231385, year = {2026}, author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N}, title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.}, journal = {Nutrition journal}, volume = {25}, number = {1}, pages = {}, pmid = {42231385}, issn = {1475-2891}, support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; }, mesh = {Humans ; Male ; *Altitude ; *Body Composition/drug effects ; *Curcumin/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Muscle, Skeletal/drug effects ; Young Adult ; Adult ; Acclimatization ; Electric Impedance ; }, abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.<br><br>METHODS: A total of 102 male Han participants was randomized to curcumin (812&#xa0;mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.<br><br>RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P&#x2009;=&#x2009;0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P&#x2009;<&#x2009;0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P&#x2009;<&#x2009;0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P&#x2009;<&#x2009;0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.<br><br>CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.<br><br>TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.}, }
@article {pmid42231497, year = {2026}, author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I}, title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42231497}, issn = {2049-2618}, mesh = {*Sulfates/metabolism ; *Ferrosoferric Oxide/metabolism/pharmacology ; Methane/metabolism/biosynthesis ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen Sulfide/metabolism ; Metagenomics/methods ; *Microbiota ; *Bacteria, Anaerobic/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Microbial Interactions ; }, abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.<br><br>RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.<br><br>CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.}, }
@article {pmid42231528, year = {2026}, author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA}, title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679516}, pmid = {42231528}, issn = {1949-0984}, mesh = {Animals ; *Prebiotics/administration &amp; dosage ; *Obesity/metabolism/microbiology/physiopathology/complications ; *Osteoarthritis, Knee/metabolism/microbiology/physiopathology ; Rats ; Multiomics ; Humans ; *Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; }, abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.}, }
@article {pmid42233252, year = {2026}, author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR}, title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42233252}, issn = {1758-0463}, support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; }, mesh = {Biocuration ; Humans ; *Autoimmune Diseases/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity/immunology ; *Antigens, Bacterial/immunology ; Animals ; *Databases, Protein ; }, abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.}, }
@article {pmid42233644, year = {2026}, author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M}, title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.}, journal = {mSystems}, volume = {11}, number = {6}, pages = {e0149825}, pmid = {42233644}, issn = {2379-5077}, support = {//March of Dimes Prematurity Research Center at UCSF/ ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; *Vagina/microbiology ; *Lactobacillus crispatus/genetics ; *Uterine Cervical Dysplasia/microbiology ; Databases, Genetic ; Metagenomics/methods ; Genome, Bacterial ; }, abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.}, }
@article {pmid42233654, year = {2026}, author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H}, title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0318325}, pmid = {42233654}, issn = {2165-0497}, support = {2024AB034//Science and Technology Bureau of Xinjiang Production and Construction Corps/ ; CZ004311//Science Fund for Distinguished Young Scholars of Xinjiang Autonomous Region/ ; 202358//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; }, mesh = {Animals ; *Camelus/microbiology/growth &amp; development ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Age Factors ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; }, abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.<br><br>IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.}, }
@article {pmid42234268, year = {2026}, author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M}, title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42234268}, issn = {1573-4978}, mesh = {Humans ; Myokines/metabolism ; *Exercise/physiology ; *Muscle, Skeletal/metabolism/physiology ; Signal Transduction ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism/physiology ; *Brain-Gut Axis/physiology ; Animals ; }, abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.}, }
@article {pmid42235155, year = {2026}, author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY}, title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107186}, pmid = {42235155}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/growth &amp; development ; *Archaea/genetics/physiology/classification ; *Gastrointestinal Microbiome ; *Metagenome ; *Genome, Archaeal ; Phylogeny ; }, abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.}, }
@article {pmid42235160, year = {2026}, author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X}, title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107187}, pmid = {42235160}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/physiology/blood ; *Cytokines/blood ; Female ; Cecum/microbiology ; *Gastrointestinal Microbiome ; *Nesting Behavior/physiology ; Bacteria/classification/isolation &amp; purification ; *Metabolome ; }, abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.}, }
@article {pmid42236101, year = {2026}, author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A}, title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e111607}, pmid = {42236101}, issn = {2044-6055}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Anticonvulsants/therapeutic use ; *Brain/physiopathology ; Diet, Ketogenic ; *Drug Resistant Epilepsy/therapy/microbiology ; *Epilepsy/therapy ; *Gastrointestinal Microbiome/physiology ; Italy ; Longitudinal Studies ; Prospective Studies ; Quality of Life ; Vagus Nerve Stimulation ; }, abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.<br><br>METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-na&#xef;ve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.<br><br>ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.}, }
@article {pmid42237409, year = {2026}, author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X}, title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42237409}, issn = {2049-2618}, support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; }, mesh = {*Stenotrophomonas maltophilia/genetics/physiology/metabolism ; *Skin Microbiome ; Multiomics ; Humans ; Metabolomics ; *Skin Aging/physiology ; *Skin/microbiology/metabolism ; Acinetobacter/metabolism ; Oxidative Stress ; Glutathione/metabolism ; Melanins/metabolism ; Metagenomics ; Metabolic Networks and Pathways ; Fibroblasts/metabolism ; Phenotype ; }, abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.<br><br>RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.<br><br>CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.}, }
@article {pmid42237424, year = {2026}, author = {Yang, L and Chen, J}, title = {mPower: a real data-based power analysis tool for microbiome study design.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42237424}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; Humans ; *Metagenomics/methods ; Computer Simulation ; Research Design ; *Bacteria/classification/genetics ; Cross-Sectional Studies ; Case-Control Studies ; }, abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/ . Video Abstract.}, }
@article {pmid42237904, year = {2026}, author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH}, title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {23}, pages = {16514-16525}, doi = {10.1021/acs.est.6c01505}, pmid = {42237904}, issn = {1520-5851}, mesh = {*Microbiota ; Halogenation ; Hospitals ; Disinfection ; *Virome ; Drug Resistance, Microbial/genetics ; }, abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.}, }
@article {pmid42237982, year = {2026}, author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC}, title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e37}, pmid = {42237982}, issn = {2048-6790}, mesh = {Animals ; Female ; Pregnancy ; *Dietary Fiber/administration &amp; dosage/pharmacology ; *Cecum/microbiology ; Rats, Sprague-Dawley ; *Prebiotics/administration &amp; dosage ; Male ; *Fatty Liver/prevention &amp; control ; *Maternal Nutritional Physiological Phenomena ; Fatty Acids, Volatile/metabolism ; Rats ; *Gastrointestinal Microbiome/drug effects ; Lactation ; Weaning ; *Obesity ; Liver/metabolism ; }, abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.}, }
@article {pmid42239539, year = {2026}, author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L}, title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765801}, pmid = {42239539}, issn = {2235-2988}, mesh = {Humans ; Female ; Metagenomics ; Infant ; *Infectious Disease Transmission, Vertical ; *Microbiota/genetics ; *Genomic Structural Variation ; *Bacteria/genetics/classification ; Infant, Newborn ; Metagenome ; Mothers ; Longitudinal Studies ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.<br><br>METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.<br><br>RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.<br><br>DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.}, }
@article {pmid42241759, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R}, title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107151}, pmid = {42241759}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/genetics ; Male ; Diet/veterinary ; Cecum/microbiology/metabolism ; *Dietary Fiber/administration &amp; dosage/metabolism ; *Transcriptome/drug effects ; Animal Feed/analysis ; Dietary Supplements/analysis ; *Metagenome/drug effects ; Random Allocation ; *Gastrointestinal Microbiome/drug effects ; *Poultry Diseases/microbiology ; Dose-Response Relationship, Drug ; Clostridium Infections/veterinary/microbiology ; Clostridium perfringens/physiology ; }, abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.}, }
@article {pmid42241861, year = {2026}, author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L}, title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130128}, doi = {10.1016/j.jenvman.2026.130128}, pmid = {42241861}, issn = {1095-8630}, mesh = {Animals ; *Aquaculture ; *Nitrogen/metabolism ; Anti-Bacterial Agents ; *Probiotics ; Metagenomics ; China ; Microbiota ; Penaeidae ; }, abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.}, }
@article {pmid42241983, year = {2026}, author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M}, title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {459}, number = {}, pages = {111881}, doi = {10.1016/j.ijfoodmicro.2026.111881}, pmid = {42241983}, issn = {1879-3460}, mesh = {*Cheese/microbiology/analysis ; Taste ; *Food Microbiology ; *Microbiota ; Humans ; Bacteria/classification/isolation &amp; purification/genetics ; Volatile Organic Compounds/analysis ; Fungi/isolation &amp; purification/genetics/classification ; Odorants/analysis ; Metagenomics ; }, abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.}, }
@article {pmid42242027, year = {2026}, author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M}, title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128569}, doi = {10.1016/j.micres.2026.128569}, pmid = {42242027}, issn = {1618-0623}, mesh = {Animals ; Male ; Mice ; *Bifidobacterium longum/physiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; *Fatty Liver/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function ; Liver/metabolism/pathology ; *Metabolic Diseases ; *Metabolome ; Metagenomics ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration &amp; dosage ; }, abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.}, }
@article {pmid42242076, year = {2026}, author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG}, title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142602}, doi = {10.1016/j.jhazmat.2026.142602}, pmid = {42242076}, issn = {1873-3336}, mesh = {*Dust/analysis ; Humans ; *Bacteria/genetics/drug effects ; *Fungi/genetics ; *Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.}, }
@article {pmid42242448, year = {2026}, author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F}, title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.}, journal = {Virologica Sinica}, volume = {41}, number = {3}, pages = {523-531}, pmid = {42242448}, issn = {1995-820X}, mesh = {Animals ; Pakistan/epidemiology ; Humans ; Antibodies, Viral/blood ; *Tick-Borne Diseases/virology/epidemiology/veterinary ; Rats/virology ; *Livestock/virology ; Phylogeny ; *Ticks/virology ; Metagenomics ; *Viruses/genetics/classification/isolation &amp; purification ; Virome ; *Communicable Diseases, Emerging/virology/veterinary/epidemiology ; }, abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), Brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.}, }
@article {pmid42243631, year = {2026}, author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW}, title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {33}, number = {8}, pages = {1446-1456}, pmid = {42243631}, issn = {1527-974X}, support = {//UTHealth Houston Seed/ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; U19 AI144297/AI/NIAID NIH HHS/United States ; //Alkek Foundation Seed/ ; //S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; //Baylor College of Medicine/ ; }, mesh = {*Dashboard Systems ; *Wastewater/virology ; *Genomics ; Humans ; *Virome ; User-Computer Interface ; }, abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.<br><br>MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.<br><br>RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.<br><br>DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.<br><br>CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.}, }
@article {pmid42243719, year = {2026}, author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS}, title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {}, pmid = {42243719}, issn = {1471-2229}, support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; }, mesh = {*Energy Metabolism/genetics ; Rhizosphere ; *Microbiota/genetics ; Soil Microbiology ; Computer Simulation ; }, abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.<br><br>RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.<br><br>CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).}, }
@article {pmid42246191, year = {2026}, author = {Das, D and Dixit, R and Pandey, M}, title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.}, journal = {Journal of gastroenterology and hepatology}, volume = {41}, number = {7}, pages = {2062-2072}, doi = {10.1111/jgh.70462}, pmid = {42246191}, issn = {1440-1746}, mesh = {Humans ; *Gallbladder Neoplasms/etiology/metabolism/microbiology ; Multiomics ; *Metabolomics ; *Carcinogenesis/metabolism/genetics ; Dysbiosis/complications ; *Microbiota ; Animals ; Proteomics ; Helicobacter ; Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.<br><br>METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.<br><br>RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7&#x3b1;-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.<br><br>CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.}, }
@article {pmid42247440, year = {2026}, author = {Levade, I and Delisle, B and Fournier, &#xc9; and Therrien, C}, title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350663}, pmid = {42247440}, issn = {1932-6203}, mesh = {Animals ; Quebec ; *Metagenomics/methods ; Phylogeny ; *Culicidae/virology ; *Virome/genetics ; Genome, Viral ; Mosquito-Borne Diseases ; *Mosquito Vectors/virology ; *RNA, Viral/genetics ; Arboviruses/genetics/classification ; }, abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.}, }
@article {pmid42248870, year = {2026}, author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F}, title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42248870}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, mesh = {Genome, Viral/genetics ; *Evolution, Molecular ; *Giant Viruses/genetics/classification ; Ecosystem ; Lakes/virology ; Metagenomics ; Metagenome ; *Fresh Water/virology ; Animals ; Phylogeny ; Gene Transfer, Horizontal ; Zooplankton/virology ; Virome/genetics ; }, abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.}, }
@article {pmid42249286, year = {2026}, author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z}, title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42249286}, issn = {1471-2180}, support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; }, mesh = {Animals ; *Hydrogen Sulfide/pharmacology/administration &amp; dosage/blood ; *Ischemia/microbiology/drug therapy ; Mice, Inbred C57BL ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Hindlimb/blood supply ; *Diabetes Mellitus, Experimental/complications/microbiology ; Muscle, Skeletal/drug effects/pathology/blood supply ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Disease Models, Animal ; Feces/microbiology ; Blood Glucose ; }, abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.<br><br>METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.<br><br>RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM&#x2009;+&#x2009;HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM&#x2009;+&#x2009;HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.<br><br>CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H&#x2082;S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.}, }
@article {pmid42249511, year = {2026}, author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H}, title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42249511}, issn = {2049-2618}, support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Aging/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Adaptive Immunity ; *Vitamin B 6/blood/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology/microbiology ; Immunity, Mucosal ; Ileum/immunology/microbiology ; }, abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.<br><br>RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced na&#xef;ve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of na&#xef;ve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.<br><br>CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.}, }
@article {pmid42249581, year = {2026}, author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W}, title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70397}, pmid = {42249581}, issn = {1751-7915}, support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; }, mesh = {*Escherichia coli/genetics ; *Polymorphism, Single Nucleotide ; *Colorectal Neoplasms/microbiology ; Humans ; Genome, Bacterial ; Genetic Markers ; Gastrointestinal Microbiome ; Case-Control Studies ; Chromosome Mapping ; Multilocus Sequence Typing ; }, abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.}, }
@article {pmid42249721, year = {2026}, author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W}, title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {11}, pages = {e70422}, doi = {10.1111/mec.70422}, pmid = {42249721}, issn = {1365-294X}, support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; Temperature ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota/genetics ; Seasons ; *Ecosystem ; Metagenomics ; }, abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.}, }
@article {pmid42250135, year = {2026}, author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M}, title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42250135}, issn = {1573-0972}, mesh = {*Agriculture/methods ; Soil Microbiology ; Climate Change ; Crops, Agricultural/microbiology/growth &amp; development ; Microbiota ; Stress, Physiological ; Ecosystem ; Biotechnology ; Mycorrhizae ; }, abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.}, }
@article {pmid42251226, year = {2026}, author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR}, title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.}, journal = {Journal of natural medicines}, volume = {80}, number = {4}, pages = {1301-1338}, pmid = {42251226}, issn = {1861-0293}, support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; }, mesh = {Humans ; *Biological Products/chemistry/metabolism/pharmacology ; *Microbiota ; Biosynthetic Pathways ; }, abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.}, }
@article {pmid42251689, year = {2026}, author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X}, title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.}, journal = {Inflammatory bowel diseases}, volume = {32}, number = {8}, pages = {1532-1546}, doi = {10.1093/ibd/izag090}, pmid = {42251689}, issn = {1536-4844}, support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; }, mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Virulence/genetics ; Female ; Male ; Case-Control Studies ; Adult ; *Virulence Factors/genetics ; Metagenome ; }, abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.<br><br>METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.<br><br>RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P&#x2009;=&#x2009;.040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P&#x2009;<&#x2009;.05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.<br><br>CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.}, }
@article {pmid42252423, year = {2026}, author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ}, title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42252423}, issn = {1471-2180}, support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Qu&#xed;mica Valaner-MGI Mexico/ ; }, mesh = {Fermentation ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Alcoholic Beverages/microbiology ; Microbiota ; *Microbial Consortia ; Metagenomics/methods ; }, abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.}, }
@article {pmid42252802, year = {2026}, author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M}, title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {3}, pages = {e70324}, pmid = {42252802}, issn = {2190-6009}, support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; }, mesh = {Humans ; *Cachexia/etiology ; *Bacteriophages/genetics ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; *Neoplasms/complications ; Metagenomics/methods ; Metagenome ; Feces/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.<br><br>METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67&#x2009;&#xb1;&#x2009;8&#x2009;years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.<br><br>RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4&#x2009;kg/m2), WL (mean -6.5 vs. -0.2&#x2009;kg), survival (median 5 vs. 13&#x2009;months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p&#x2009;<&#x2009;0.001) but not for other clinical covariables (e.g., cancer type) (all p&#x2009;>&#x2009;0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p&#x2009;<&#x2009;0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p&#x2009;>&#x2009;0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial &#x3b2;-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p&#x2009;<&#x2009;0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p&#x2009;<&#x2009;0.05; 2025: Myoviridae, Siphoridae, p&#x2009;<&#x2009;0.05) but also single-stranded (2022: Inoviridae, Microviridae, p&#x2009;<&#x2009;0.05; 2025: Inoviridae; p&#x2009;<&#x2009;0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).<br><br>CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.<br><br>TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).}, }
@article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, mesh = {Animals ; Humans ; *Dysbiosis/complications/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/immunology/microbiology/therapy ; Intestinal Barrier Function ; Precision Medicine/methods ; *Probiotics/therapeutic use ; Diet Therapy ; Fatty Acids, Volatile/biosynthesis ; Plant Preparations/therapeutic use ; Antimicrobial Peptides/physiology ; Immunomodulation ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, }
@article {pmid42260652, year = {2026}, author = {Le Moigne, A and Andrei, A&#x15e; and Pernthaler, J}, title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42260652}, issn = {2049-2618}, mesh = {*Bacteria/genetics/classification/metabolism ; Stochastic Processes ; Metagenomics/methods ; *Lakes/microbiology ; Genome, Bacterial ; *Microbiota/genetics ; Cellobiose/metabolism ; Ecosystem ; }, abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.<br><br>RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.<br><br>CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.}, }
@article {pmid42262077, year = {2026}, author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y}, title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.}, journal = {Microbiology spectrum}, volume = {14}, number = {7}, pages = {e0113225}, pmid = {42262077}, issn = {2165-0497}, mesh = {Animals ; Female ; Swine/blood/microbiology ; Pregnancy ; Multiomics ; *Reproduction/physiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Feces/microbiology ; Litter Size ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Serum/chemistry ; }, abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.<br><br>IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.}, }
@article {pmid42262118, year = {2026}, author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P}, title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0050126}, pmid = {42262118}, issn = {2379-5077}, mesh = {Animals ; Cattle ; Third Generation Cephalosporins ; *Feces/microbiology ; *Escherichia coli/drug effects ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cephalosporins/pharmacology ; Escherichia coli Infections/microbiology/veterinary ; }, abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.}, }
@article {pmid42262136, year = {2026}, author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G}, title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0028426}, pmid = {42262136}, issn = {2379-5077}, support = {ZIA BC 011152/NH/NIH HHS/United States ; MFAG-2024 ID 31114//AIRC/ ; ZIA BC010793/ImNIH/Intramural NIH HHS/United States ; ID 2721017//Fondazione Regionale Ricerca Biomedica/ ; ZIA BC011152/ImNIH/Intramural NIH HHS/United States ; ZIA BC 011153/NH/NIH HHS/United States ; ZIA BC 010793/NH/NIH HHS/United States ; ZIA BC011153/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Bacteria/genetics/classification ; }, abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.<br><br>IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.}, }
@article {pmid42262316, year = {2026}, author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J}, title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.}, journal = {Chemical research in toxicology}, volume = {39}, number = {7}, pages = {1302-1310}, doi = {10.1021/acs.chemrestox.5c00556}, pmid = {42262316}, issn = {1520-5010}, mesh = {Animals ; *Polyesters/chemistry/toxicity/pharmacology ; *Microplastics/chemistry/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polylactic Acid-Polyglycolic Acid Copolymer/chemistry/toxicity ; Male ; Liver/metabolism/drug effects ; }, abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.}, }
@article {pmid42263665, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.}, journal = {Blood advances}, volume = {10}, number = {16}, pages = {5505-5517}, pmid = {42263665}, issn = {2473-9537}, support = {K08 HL167161/HL/NHLBI NIH HHS/United States ; P30 CA015704/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Diet, Plant-Based ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Male ; Transplantation, Autologous ; *Microbiota ; Adult ; Aged ; }, abstract = {Plant-based whole food diets may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary end points were feasibility and tolerability, defined by successful enrollment and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary end points included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a potential influence of the dietary strategy on microbial metabolite production during the peritransplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial was registered at ClinicalTrials.gov as NCT06559709.}, }
@article {pmid42264042, year = {2026}, author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H}, title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135134}, doi = {10.1016/j.biortech.2026.135134}, pmid = {42264042}, issn = {1873-2976}, mesh = {*Metagenomics ; *Geologic Sediments/microbiology ; *Sewage/microbiology/chemistry ; *Carbon/metabolism ; Biological Oxygen Demand Analysis ; *Organic Chemicals/metabolism ; *Bacteria/metabolism/genetics ; *Cities ; Extracellular Polymeric Substance Matrix ; *Microbiota/genetics ; Biodegradation, Environmental ; }, abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.}, }
@article {pmid42264152, year = {2026}, author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TT}, title = {Enteral iron dose effect on iron storage, intestinal barrier, and gut microbiome in preterm infants: a randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {124}, number = {2}, pages = {101389}, pmid = {42264152}, issn = {1938-3207}, support = {K23 HL150300/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant, Newborn ; Male ; Dietary Supplements ; Double-Blind Method ; Enteral Nutrition ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Infant, Premature ; Intestinal Barrier Function/drug effects ; *Intestines/drug effects/microbiology ; *Iron/administration &amp; dosage/metabolism ; *Iron, Dietary/administration &amp; dosage ; }, abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.<br><br>OBJECTIVES: This study aimed to compare the effects of 2 enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.<br><br>METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/d, or a higher dose of 6 mg/kg/d of total enteral iron. The primary outcome was the fecal microbiome after 2 wk on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 wk postmenstrual age were also evaluated.<br><br>RESULTS: Among 151 randomly assigned infants who received study iron (77 low dose; 74 high dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In the subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/d had higher posttreatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/d. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.<br><br>CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/d is associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/d dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants. This trial was registered at clinicaltrials.gov as NCT04497012.}, }
@article {pmid42264245, year = {2026}, author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J}, title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.}, journal = {International journal of biological macromolecules}, volume = {371}, number = {}, pages = {152899}, doi = {10.1016/j.ijbiomac.2026.152899}, pmid = {42264245}, issn = {1879-0003}, mesh = {Animals ; *Lilium/chemistry ; Mice ; *Mannans/chemistry/pharmacology ; Intestinal Barrier Function/drug effects ; *Polysaccharides/chemistry/pharmacology ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; *Plant Roots/chemistry ; Colitis/chemically induced/drug therapy ; }, abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.}, }
@article {pmid42265587, year = {2026}, author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S}, title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42265587}, issn = {1471-2180}, support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Rumen/microbiology ; Fermentation ; *Pichia/classification/metabolism/genetics/isolation &amp; purification/physiology ; Cattle ; Animal Feed/microbiology/analysis ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.}, }
@article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {811-826}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, mesh = {Animals ; *beta-Thalassemia/genetics/complications/veterinary/microbiology ; *Macaca fascicularis ; *Gastrointestinal Microbiome/physiology ; Mutation ; *Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics ; *beta-Globins/genetics/metabolism ; Male ; }, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, }
@article {pmid42267859, year = {2026}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70307}, pmid = {42267859}, issn = {2045-8827}, support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; }, mesh = {*Rhizosphere ; *Metagenomics ; Soil Microbiology ; *Allium/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fertilizers/analysis ; Soil/chemistry ; }, abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.}, }
@article {pmid42268876, year = {2026}, author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR}, title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351562}, pmid = {42268876}, issn = {1932-6203}, mesh = {Humans ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/immunology ; Aged ; Healthy Volunteers ; Metagenomics ; Case-Control Studies ; Bacteria/genetics/isolation &amp; purification/classification ; COVID-19 ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.<br><br>METHODS: BAL specimens from healthy control volunteers (n&#x2009;=&#x2009;20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n&#x2009;=&#x2009;52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).<br><br>RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p&#x2009;<&#x2009;0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p&#x2009;=&#x2009;0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q&#x2009;<&#x2009;0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.<br><br>CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.}, }
@article {pmid42270094, year = {2026}, author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B}, title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {33}, number = {}, pages = {10732748261460118}, pmid = {42270094}, issn = {1526-2359}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation &amp; purification/genetics ; Aged ; Fungi/isolation &amp; purification ; }, abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.}, }
@article {pmid42270219, year = {2026}, author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y}, title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119489}, doi = {10.1016/j.foodres.2026.119489}, pmid = {42270219}, issn = {1873-7145}, mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; }, abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.}, }
@article {pmid42270261, year = {2026}, author = {Vandana,  and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP}, title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119548}, doi = {10.1016/j.foodres.2026.119548}, pmid = {42270261}, issn = {1873-7145}, mesh = {Animals ; *Polyphenols/pharmacology ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Fruit/chemistry ; *Cognitive Dysfunction/chemically induced/prevention &amp; control/drug therapy ; *Arsenic/toxicity ; Male ; *Rubus/chemistry ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; Disease Models, Animal ; }, abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.}, }
@article {pmid42270613, year = {2026}, author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J}, title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42270613}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rivers/microbiology ; *Nitrogen Cycle ; *Bacteria/metabolism/genetics/drug effects/classification ; *Nitrates/metabolism ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Denitrification ; *Drug Resistance, Microbial/genetics ; Metagenome ; Gene Transfer, Horizontal ; Nitrogen/metabolism ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.}, }
@article {pmid42270686, year = {2026}, author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ}, title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42270686}, issn = {2045-2322}, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; Metagenome ; *Sequence Analysis, DNA/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; DNA, Bacterial/genetics ; *Bacteria/genetics/classification ; }, abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.}, }
@article {pmid42271238, year = {2026}, author = {Bi, JG and Wang, YH and Li, PK and Liu, Q and Zheng, X}, title = {Metagenomic insights into regional gut microbiota variation of invasive Spodoptera frugiperda across the Gaoligong Mountains.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42271238}, issn = {1471-2180}, support = {202102AA310055//the Supported by the Major Science and Technique Programs of Yunnan Province/ ; YNWRQNBJ2020101//the Young Top Talents of the High-level Talents Training Support Program in Yunnan Province/ ; 202305AM340031//the Lower Nu River, Mountain Agroecosystem, Observation and Research Station of Yunnan Province/ ; 2026J1054//the Yunnan Provincial Department of Education Science Research Fund Project/ ; }, mesh = {Animals ; *Spodoptera/microbiology ; China ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Introduced Species ; Larva/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: The invasive pest Spodoptera frugiperda poses a potential threat to the ecological security of western Yunnan, using the Gaoligong Mountains as an important cross-border corridor and overwintering site. However, the potential role of gut microbiota in the local adaptation of S. frugiperda during its invasion remains poorly understood.<br><br>METHODS: Adult populations were monitored using sex pheromone traps, and metagenomic sequencing was performed on larval gut microbiota from different regions of the Gaoligong Mountains. The gut microbial composition and functional potential were analyzed, with specific focus on the microbial traits potentially associated with host adaptation and invasion.<br><br>RESULTS: S. frugiperda populations persisted year-round in the Gaoligong Mountains, with adult activity peaking from January to May. Microbial diversity was highest in southern samples. Enterococcus, typically dominant in S. frugiperda, displayed low abundance in the central and northern regions. In contrast, Providencia emerged as the dominant genus specifically at the Pianma site (PM, along the China-Myanmar border), where the gut microbiota exhibited higher abundance of site-specific functional genes compared to other regions. These genes encoded proteins including type 1 subunit membrane proteins and outer membrane-targeting proteins. Additionally, the PM samples showed a higher relative abundance of genes K07345, K07347, and K15125. Functional annotation highlighted a strong potential for vancomycin degradation and an enrichment of diverse antimicrobial resistance-associated genes, with adeL being the most abundant.<br><br>CONCLUSIONS: These findings suggest that the PM area may represent an important gateway or a priority monitoring site for the transboundary invasion of S. frugiperda, underscoring the urgency of strengthening local management of invasive pests.}, }
@article {pmid42271362, year = {2026}, author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D}, title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42271362}, issn = {1479-5876}, support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Metagenomics ; *Fungi/genetics ; Cohort Studies ; *Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.<br><br>METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.<br><br>RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.<br><br>CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.}, }
@article {pmid42271421, year = {2026}, author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED}, title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.}, journal = {Nutrition journal}, volume = {25}, number = {1}, pages = {}, pmid = {42271421}, issn = {1475-2891}, mesh = {Humans ; Female ; Male ; *Blood Pressure/physiology ; Australia ; Adult ; Cross-Sectional Studies ; *Metabolome ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Diet ; Cross-Over Studies ; Nuts ; Hypertension ; Feces/microbiology ; Biomarkers/blood/urine ; }, abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.<br><br>METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[&#xae;] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.<br><br>RESULT: Thirty-four Australian adults (mean age: 38.4&#x2009;&#xb1;&#x2009;18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.<br><br>CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.<br><br>TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).}, }
@article {pmid42271572, year = {2026}, author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E}, title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42271572}, issn = {1574-6941}, support = {//CNRS/ ; ANR-24-CE01-6539-01//French National Research Agency/ ; }, mesh = {*Groundwater/microbiology/chemistry ; *Caves/microbiology/chemistry ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; South Africa ; *Geologic Sediments/microbiology ; Metagenome ; Oxidation-Reduction ; }, abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.}, }
@article {pmid42272754, year = {2026}, author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C}, title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779298}, pmid = {42272754}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Metabolomics ; *Constipation/microbiology/immunology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; *Rhinitis, Allergic/microbiology/immunology/metabolism/complications ; Child ; Female ; Feces/microbiology ; Male ; Amino Acids/metabolism ; Multiomics ; Bacteria/classification/genetics ; Metabolome ; }, abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.<br><br>METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.<br><br>RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P&#xa0;=&#xa0;0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and &#x3b3;-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC&#xa0;=&#xa0;0.946).<br><br>CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.}, }
@article {pmid42275884, year = {2026}, author = {Zhao, J and Zuo, M and Cao, L and Li, Q and Zhang, R and Wu, H and Yuan, J and Lv, C and Yu, Y and Lu, J}, title = {The neutral and acidic polysaccharides from Ginseng are metabolized by specific gut microbial taxa and confer immunomodulatory effects.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {158}, number = {}, pages = {158400}, doi = {10.1016/j.phymed.2026.158400}, pmid = {42275884}, issn = {1618-095X}, mesh = {*Panax/chemistry ; *Polysaccharides/pharmacology/metabolism/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Immunologic Factors/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Fermentation ; }, abstract = {BACKGROUND: Ginseng (Panax ginseng C. A. Mey.) exerts immunomodulatory effects partly mediated by its polysaccharides and interactions with gut microbiota. However, due to the structural complexity of ginseng polysaccharides, knowledge of their oral fate and direct microbiota interactions remains limited.<br><br>PURPOSE: This study aims to elucidate the oral fate of neutral and acidic polysaccharides in ginseng, analyze core gut microbiota genera and their immunomodulatory effects mechanisms.<br><br>METHODS: Structural analysis was conducted on neutral and acidic polysaccharides from ginseng. Thereafter, in vitro digestion and fermentation were performed, with metagenomic and metatranscriptomic profiling. The results were validated in conventional and pseudo&#x2011;germ-free immunosuppressed mouse models, and the immunomodulatory mechanisms of the core gut microbiota were investigated.<br><br>RESULTS: The in vivo and in vitro findings indicated that neutral and acidic polysaccharides exhibit different digestive properties and gut microbiota degradation patterns, differ in short-chain fatty acid production tendencies, bind to GPR-41/43 receptors, upregulate MAPK-p38 phosphorylation, and promote proliferation of intestinal immune cells.<br><br>CONCLUSION: This work systematically elucidated the digestive characteristics of ginseng polysaccharides and laid the groundwork for future studies on the specificity and structure-function relationships of plant-derived polysaccharides.}, }
@article {pmid42276012, year = {2026}, author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T}, title = {IgG4-related disease has a specific intestinal microbiota signature.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106326}, pmid = {42276012}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.<br><br>METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).<br><br>FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.<br><br>INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.<br><br>FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.}, }
@article {pmid42277260, year = {2026}, author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C}, title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.}, journal = {Nature genetics}, volume = {58}, number = {7}, pages = {1595-1609}, pmid = {42277260}, issn = {1546-1718}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenome/genetics ; Genome-Wide Association Study ; Bacteria/genetics/classification ; Host-Pathogen Interactions/genetics ; }, abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.}, }
@article {pmid42278252, year = {2026}, author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B}, title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278252}, issn = {1422-0067}, support = {101079425//Centre of Biotechnologie of Sfax/ ; }, mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.}, }
@article {pmid42278256, year = {2026}, author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M}, title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278256}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital &amp; Research Centre/ ; }, mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota ; *Homeostasis ; *Breast/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.}, }
@article {pmid42278324, year = {2026}, author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y}, title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278324}, issn = {1422-0067}, support = {24-14-00059//Russian Science Foundation/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; Mice ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Chromosome Aberrations/radiation effects/drug effects ; RNA, Ribosomal, 16S/genetics ; *Radiotherapy/adverse effects ; Radiation-Protective Agents/pharmacology ; Male ; Lactobacillus ; *Minerals/pharmacology ; *Dysbiosis/etiology ; }, abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.}, }
@article {pmid42278475, year = {2026}, author = {Ermakov, VS and Falah, K and Nigam, SK}, title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278475}, issn = {1422-0067}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.}, }
@article {pmid42278495, year = {2026}, author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E}, title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278495}, issn = {1422-0067}, support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; }, abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.}, }
@article {pmid42278559, year = {2026}, author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH}, title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278559}, issn = {1422-0067}, support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; }, mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; }, abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.}, }
@article {pmid42278576, year = {2026}, author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T}, title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278576}, issn = {1422-0067}, mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; }, abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.}, }
@article {pmid42280335, year = {2026}, author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E}, title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280335}, issn = {2072-6643}, support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; }, mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration &amp; dosage/isolation &amp; purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; }, abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.<br><br>METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.<br><br>RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.}, }
@article {pmid42280338, year = {2026}, author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ}, title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280338}, issn = {2072-6643}, support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; }, mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.<br><br>METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.<br><br>RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.<br><br>CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.}, }
@article {pmid42281243, year = {2026}, author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE}, title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685381}, pmid = {42281243}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; }, abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.}, }
@article {pmid42284942, year = {2026}, author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.}, journal = {Water research}, volume = {303}, number = {}, pages = {126258}, doi = {10.1016/j.watres.2026.126258}, pmid = {42284942}, issn = {1879-2448}, mesh = {*Microbiota ; Risk Assessment ; Biodegradation, Environmental ; Multiomics ; Sulfur/metabolism ; }, abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.}, }
@article {pmid42285959, year = {2026}, author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X}, title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.}, journal = {Translational psychiatry}, volume = {16}, number = {1}, pages = {}, pmid = {42285959}, issn = {2158-3188}, mesh = {Humans ; Female ; Male ; Prospective Studies ; Aged ; *Gastrointestinal Microbiome/physiology ; *Cardiac Surgical Procedures/adverse effects ; Multiomics ; *Postoperative Complications/metabolism/microbiology ; Middle Aged ; *Amino Acids, Branched-Chain/metabolism ; Feces/microbiology ; *Delirium/metabolism/microbiology ; Preoperative Period ; Metabolomics ; }, abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.}, }
@article {pmid42286003, year = {2026}, author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M}, title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42286003}, issn = {2041-1723}, support = {101007799//Innovative Medicines Initiative (IMI)/ ; }, mesh = {Humans ; *Clostridioides difficile/drug effects/genetics/physiology ; Adult ; Female ; Vancomycin/administration &amp; dosage/pharmacology/therapeutic use ; Male ; Middle Aged ; Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Adolescent ; Young Adult ; *Clostridium Infections/microbiology/drug therapy ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.}, }
@article {pmid42286394, year = {2026}, author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W}, title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.}, journal = {Virus genes}, volume = {62}, number = {4}, pages = {533-541}, pmid = {42286394}, issn = {1572-994X}, support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Aedes/virology ; Phylogeny ; China ; Metagenomics/methods ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Virome/genetics ; Genome, Viral ; *Parvoviridae/genetics/classification ; }, abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.}, }
@article {pmid42286497, year = {2026}, author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H}, title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {42286497}, issn = {2730-6844}, support = {U54AG089334//National Institute for Health and Care Research/ ; U54 AG089334/AG/NIA NIH HHS/United States ; JPMJCR20H1//JST CREST/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; 20K10436//JSPS KAKENHI/ ; }, mesh = {*Microbiota ; Tokyo ; Shotgun Sequencing ; *Metagenomics ; Humans ; *Railroads ; *Metagenome ; }, abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.<br><br>DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 &#xd7; 150 bp paired-end reads.}, }
@article {pmid42286668, year = {2026}, author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA}, title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42286668}, issn = {2049-2618}, mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Vitamin B 12/metabolism/biosynthesis ; Cattle ; *Rumen/microbiology ; Microbiota ; Archaea/metabolism/genetics ; Female ; Fermentation ; Dietary Supplements ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/classification/genetics/metabolism ; Rhodophyta ; }, abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.<br><br>RESULTS: ASP supplementation reduced CH&#x2084; yield by 54% (g CH&#x2084;/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH&#x2084; were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are&#xa0;critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION&#xa0;: ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.}, }
@article {pmid42286862, year = {2026}, author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M}, title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679497}, pmid = {42286862}, issn = {1949-0984}, mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; }, abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.}, }
@article {pmid42287197, year = {2026}, author = {De Visscher, J and Tytgat, B and Hodgson, DA and Wilmotte, A and Willems, A and Verleyen, E and Vyverman, W}, title = {Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {7}, pages = {}, pmid = {42287197}, issn = {1574-6941}, support = {SD/BA/03A//Belgian Science Policy Office/ ; //EU Horizon 2020 InterAct project MiBiPol/ ; SD/CA/01A//Belspo project HOLANT/ ; //Research Foundation Flanders/ ; }, mesh = {*Lakes/microbiology ; Antarctic Regions ; Arctic Regions ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; *Bacteria/genetics/classification ; }, abstract = {Benthic microbial mat communities are key drivers of ecosystem functioning in polar lakes and ponds, forming the base of aquatic food webs and contributing substantially to nutrient cycling. Although Arctic, sub-Antarctic, and Antarctic microbial mats differ in community composition, their functional genetic potential remains poorly understood. We applied shotgun metagenomic sequencing to study 17 microbial mat communities from Arctic and (sub-)Antarctic lakes differing in salinity, catchment vegetation, and climatic conditions. Stress response genes, especially cold stress, and phosphorus cycling and metabolism genes were highly abundant in all lakes. A large proportion of functional genes was shared between regions, with core functions dominated by transport mechanisms and energy production. However, clear differences in particular gene abundances were observed. Several East-Antarctic lakes and inland ponds in the Transantarctic Mountains showed a dominance of oxygenic photosynthesis and Calvin cycle genes for carbon fixation, likely reflecting the dominance of Cyanobacteriota. In Arctic and sub-Antarctic lakes with catchment vegetation and higher arthropod abundances, lignin and chitin degradation genes were more important. Our study shows that, despite distinct biogeographic patterns in community composition, the functional genetic potential of polar lake microbial mats mainly reflects climatic and local environmental conditions, emphasizing specific adaptations to extreme polar environments.}, }
@article {pmid42287910, year = {2026}, author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K}, title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142686}, doi = {10.1016/j.jhazmat.2026.142686}, pmid = {42287910}, issn = {1873-3336}, mesh = {*Ice Cover/microbiology ; *Microbiota/genetics ; Tibet ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.}, }
@article {pmid42288625, year = {2026}, author = {Shin, DW and Oh, S and Hong, YJ and Park, KU}, title = {Direct microbiota profiling of apheresis-associated products for microbiological insights in cell therapy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42288625}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Cell- and Tissue-Based Therapy/methods ; *Leukapheresis ; Saliva/microbiology ; *Blood Component Removal ; Female ; High-Throughput Nucleotide Sequencing ; }, abstract = {Cellular therapies require rigorous prevention of bacterial contamination during cell collection, manufacturing, and infusion. We characterized 16 S rRNA profiles in blood-derived specimens obtained during leukapheresis. Leukapheresis donors provided five specimen types: buffy coats (BCs), whole-blood plasma (WBP), apheresis plasma stored at room temperature for 24 h (AP24) and 72 h (AP72), and saliva. Species-level identification was performed using next-generation sequencing-based 16 S rRNA analysis and a database-weighted method. In total, 40 samples from eight donors were analyzed. Plasma specimens (WBP, AP24, and AP72) exhibited higher alpha diversity than saliva (Shannon index, p < 0.05). Beta diversity analysis identified three distinct clusters corresponding to BC, plasma specimens, and saliva (permutational multivariate analysis of variance, p = 0.001). Streptococcus oralis subsp. tigurinus was predominant across all specimens types, Bifidobacterium kashiwanohense predominated in blood-derived specimens, and Enhydrobacter aerosaccus was observed exclusively in plasma specimens. Skin swab culture performed before and after venipuncture site disinfection exhibited no bacterial growth post-disinfection, suggesting that skin-derived carryover is unlikely to fully explain the detected microbial DNA signals. This study provides microbial DNA profiles of various blood-derived specimens obtained during leukapheresis. These findings provide preliminary reference information that may assist interpretation of molecular microbial signals in cellular therapy manufacturing.}, }
@article {pmid42290500, year = {2026}, author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F}, title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.}, journal = {Future microbiology}, volume = {21}, number = {8}, pages = {777-794}, pmid = {42290500}, issn = {1746-0921}, mesh = {*Synbiotics/administration &amp; dosage ; Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Liver/metabolism/microbiology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; Animals ; *Liver Diseases/therapy/microbiology ; Proteomics ; Metabolomics ; }, abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.}, }
@article {pmid42291297, year = {2026}, author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X}, title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809022}, pmid = {42291297}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; }, abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.<br><br>METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).<br><br>RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p&#xa0;<&#xa0;0.01). Candida albicans (p&#xa0;=&#xa0;0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p&#xa0;=&#xa0;0.038) and Prevotella pallens (p&#xa0;=&#xa0;0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p&#xa0;<&#xa0;0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.<br><br>CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.}, }
@article {pmid42293411, year = {2025}, author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z}, title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719445}, pmid = {42293411}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; }, abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.}, }
@article {pmid42295167, year = {2026}, author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P}, title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.}, journal = {Infection and immunity}, volume = {94}, number = {7}, pages = {e0054225}, pmid = {42295167}, issn = {1098-5522}, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; *Metagenomics/methods ; Vaginosis, Bacterial/microbiology ; Pregnancy Outcome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.}, }
@article {pmid42295179, year = {2026}, author = {Guitart-Matas, J and Ramayo-Caldas, Y and González-Rodríguez, O and Giler-Baquerizo, N and Migura-Garcia, L and Ballester, M}, title = {Implementation of a high-throughput microfluidic platform for antimicrobial resistance surveillance in swine production systems.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42295179}, issn = {2057-5858}, mesh = {Animals ; Swine/microbiology ; Metagenomics/methods ; Feces/microbiology ; *Microfluidics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Shotgun Sequencing ; }, abstract = {Antimicrobial resistance poses a serious threat to public health worldwide and demands interventions with a One Health perspective. A key challenge is determining the collection of antimicrobial resistance genes of a specific environment, also known as the resistome. Surveillance and monitoring of the resistome are essential for tracking the emergence and dissemination of resistance mechanisms. In this study, we took advantage of shotgun metagenomics and metatranscriptomics sequencing data of piglets treated with different post-weaning diarrhoea treatments to generate an antimicrobial resistance gene catalogue of the pig gut microbiome during pre-weaning and post-weaning stages. The selected catalogue, comprising a total of 102 genes and representing the majority of antibiotic classes, has been implemented in the microfluidic Biomark[™] X9 System and validated using total DNA and RNA extracted from piglets' faecal samples. Additionally, this platform has been verified by demonstrating a strong and statistically significant correlation with resistome quantification data from both metagenomic and metatranscriptomic sequencing. Overall, the microfluidic qPCR platform implemented here demonstrated enhanced detection of low-abundance targets, successfully identifying genes and transcripts that remained below the stochastic detection threshold of shotgun sequencing. This approach enables high-throughput monitoring and surveillance of antimicrobial resistance, providing a critical tool to support the reduction of antimicrobial use in farms.}, }
@article {pmid42298353, year = {2026}, author = {Strokach, A and Zakharevich, N and Aginova, V and Grigoryevskaya, Z and Petukhova, I and Bagirova, N and Romanov, M and Dyachkova, M and Morozov, M and Veselovsky, V and Kanaeva, V and Kalinin, D and Larin, A and Shitikov, E and Klimina, K}, title = {Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681788}, pmid = {42298353}, issn = {1949-0984}, mesh = {Humans ; *Immunotherapy ; *Melanoma/therapy/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome ; Female ; Cohort Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Russia ; Metagenomics ; Metagenome ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; Treatment Outcome ; Adult ; }, abstract = {Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.}, }
@article {pmid42298774, year = {2026}, author = {Chen, X and Ding, S and Tang, H and Yang, Q and Yuan, L and Zhang, A and Li, Y and Wang, Q and Yan, X and Wang, Z and Wang, M and Zheng, Z}, title = {Monochromatic light reprograms transcription, metabolism, and rhizosphere microbial communities in Salvia miltiorrhiza.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2686334}, pmid = {42298774}, issn = {1559-2324}, mesh = {*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics ; *Rhizosphere ; *Light ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Transcription, Genetic/radiation effects ; }, abstract = {Salvia miltiorrhiza is a valuable medicinal plant with diverse pharmacological applications and high market demand. Light quality is a critical environmental factor regulating plant growth, secondary metabolism, and interactions with rhizosphere microorganisms. However, the effects of short-term, pure monochromatic light exposure on S. miltiorrhiza remain largely unexplored. In this study, we employed integrated transcriptomic, metabolomic, and rhizosphere metagenomic analyzes to investigate the responses of S. miltiorrhiza under different monochromatic light conditions: ultraviolet (UV), blue (B), red (R), and far-red (FR), with white light (WL) as the control. GO enrichment analysis indicated that all monochromatic light treatments activated defense responses, while specific pathways related to light stimulus, wounding, and reactive oxygen species were uniquely enriched under B, R, and FR light. Metabolomic analysis showed a general decrease in metabolite abundance under monochromatic light compared to WL, with the R treatment inducing the highest number of significantly upregulated metabolites. Integrated KEGG pathway analysis of differential transcripts and metabolites highlighted the enrichment of secondary metabolic pathways, including diterpenoid, monoterpenoid, and phenylpropanoid biosynthesis. Notably, quantitative HPLC analysis confirmed that UV, R, and FR light significantly promoted the accumulation of dihydrotanshinone I and tanshinone IIA, while decreasing salvianolic acid A content. Metagenomic analysis revealed that monochromatic light, especially B light, reduced rhizosphere microbial alpha diversity and altered the abundance of specific bacterial families and species. Functional gene annotation also showed treatment-specific shifts in microbial metabolic potential and virulence factors. In conclusion, short-term monochromatic light culture, particularly R and FR, effectively modulates the transcriptome and metabolome of S. miltiorrhiza, enhancing the accumulation of key bioactive tanshinones, while simultaneously reshaping its rhizosphere microbial community. These findings offer a potential light-based strategy for improving the quality of S. miltiorrhiza.}, }
@article {pmid42299582, year = {2026}, author = {Yu, Y and Wang, C and Pan, X and Ding, C and Chen, J}, title = {Metagenomic profiling of biliary microbiota reveals distinct microbial and functional features in cholelithiasis and cholecystic polyps.}, journal = {Medicine}, volume = {105}, number = {24}, pages = {e49251}, pmid = {42299582}, issn = {1536-5964}, support = {2022YFC2804205//National key research and development program of China/ ; }, mesh = {Humans ; *Cholelithiasis/microbiology ; *Metagenomics/methods ; *Polyps/microbiology ; *Microbiota/genetics ; Female ; *Bile/microbiology ; Male ; *Metagenome ; Middle Aged ; Aged ; }, abstract = {Cholelithiasis and cholecystic polyps are common gastrointestinal conditions, and recent studies suggest that biliary microbiota dysbiosis may be closely associated with their pathogenesis. In this small cohort (n = 11), bile samples were aseptically collected during surgery from 6 patients with cholelithiasis and 5 patients with cholecystic polyps. Metagenomic sequencing was performed to investigate differences in the microbial composition and functional profiles between the 2 groups. The results revealed that the microbial α diversity of bile from patients with cholelithiasis was significantly greater than that of the polyp group, with significant differences in the Richness, Chao1, ACE, and Shannon indices (P < .05). β-diversity analysis further revealed distinct differences in microbial community composition across the groups. Linear discriminant analysis effect size analysis revealed Pseudomonadota as the only phylum enriched in the polyp group, whereas the cholelithiasis group was enriched with multiple phyla, such as Campylobacterota, Bacillota, and Fusobacteriota, and 35 genera, such as Bacteroides, Mucilaginibacter, and Pedobacter. Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis indicated that the microbial community in the cholelithiasis group was significantly associated with neurodegenerative disease-related pathways, while the microbial community in the polyp group was enriched in pathways related to ribosomes and fluid shear stress. This study highlights the potential role of biliary microecological imbalances in the development of biliary diseases and provides a theoretical basis for exploring pathogenesis and microbiota-based therapeutic strategies.}, }
@article {pmid42300105, year = {2026}, author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG}, title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.}, journal = {Food &amp; function}, volume = {17}, number = {15}, pages = {6868-6881}, doi = {10.1039/d6fo00158k}, pmid = {42300105}, issn = {2042-650X}, mesh = {Humans ; *Polyphenols/metabolism ; Female ; Adult ; Male ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Cross-Sectional Studies ; Middle Aged ; *Gastrointestinal Microbiome ; Diet ; Young Adult ; }, abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.}, }
@article {pmid42300737, year = {2026}, author = {Bueno de Mesquita, CP and Stallard-Olivera, E and Fierer, N}, title = {Predicting oxygen levels in microbial habitats using a metagenome-based approach.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0054526}, pmid = {42300737}, issn = {2379-5077}, support = {/WT_/Wellcome Trust/United Kingdom ; #W911-NF-23-1-0311//Army Research Office/ ; 313162/Z/24/Z/WT_/Wellcome Trust/United Kingdom ; NNF24SA0092560//Novo Nordisk Fonden/ ; }, mesh = {*Oxygen/analysis/metabolism ; *Metagenome ; Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/metabolism ; *Microbiota ; Humans ; Ecosystem ; }, abstract = {Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats.IMPORTANCEOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.}, }
@article {pmid42300757, year = {2026}, author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y}, title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.}, journal = {Food &amp; function}, volume = {17}, number = {13}, pages = {6062-6079}, doi = {10.1039/d6fo01565d}, pmid = {42300757}, issn = {2042-650X}, mesh = {Animals ; *Kefir/microbiology/analysis ; *Colitis/chemically induced ; Dextran Sulfate/adverse effects ; Intestinal Barrier Function ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Fermentation ; Tibet ; Mice, Inbred C57BL ; Inflammation ; RAW 264.7 Cells ; Bacteria/classification/genetics/isolation &amp; purification ; Milk ; Cultured Milk Products ; }, abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.}, }
@article {pmid42300931, year = {2026}, author = {Medouni-Haroune, L and Medouni-Adrar, S and Messaoudene, L and Negrichi, S and Bouiche, C and Sahraoui-Remini, Y and Allam, A and Meghlaoui, Z and Mouhoubi, K and Abbou, A and Brahimi, N and Mellal, MK and Sari, Z and Madani, K}, title = {Animal-based diets and the human gut microbiota: an integrative review combining metagenomic profiling and graphical synthesis of diet-microbiota associations.}, journal = {Food &amp; function}, volume = {17}, number = {14}, pages = {6294-6314}, doi = {10.1039/d6fo00371k}, pmid = {42300931}, issn = {2042-650X}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; *Diet ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Animal Feed/analysis ; }, abstract = {This review examines the relationships between animal-based diets, gut microbiota architecture, and human health by integrating insights from metagenomic studies and literature-based graphical representations. The gut microbiota is a complex microbial ecosystem, whose organization is closely linked to intestinal homeostasis and host health. Drawing on published metagenomic datasets, the review synthesizes patterns of dominant microbial groups and their organization within the gut, providing a framework for interpreting diet-related microbial variations across different geographic and cultural contexts. Evidence from the literature on animal-derived foods is integrated through graphical visualization to illustrate associations between specific foods and gut microbial taxa. These visualizations highlight distinct association patterns and microbial responses to various animal-based dietary components. The review discusses these patterns in relation to intestinal health, disease susceptibility, and potential dietary interventions. Overall, this work provides a structured, integrative perspective on the impact of animal-based diets on gut microbiota architecture, emphasizing the relevance of combining metagenomic insights with literature-based synthesis to inform nutritional science and public health strategies.}, }
@article {pmid42301089, year = {2026}, author = {Wang, H and Liang, Y and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {12}, pages = {e72059}, doi = {10.1096/fj.202601343R}, pmid = {42301089}, issn = {1530-6860}, support = {2025M780240//China Postdoctoral Science Foundation/ ; 2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, mesh = {Animals ; *Glutamates/pharmacology/administration &amp; dosage ; Female ; *Lactobacillus/drug effects/metabolism ; Signal Transduction/drug effects ; Swine ; *Proto-Oncogene Proteins c-akt/metabolism ; *Reproduction/drug effects ; *Dietary Fiber/pharmacology/administration &amp; dosage ; *Phosphatidylinositol 3-Kinases/metabolism ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; }, abstract = {The aim of this study was to investigate the combined effects of a high-fiber diet supplemented with N-carbamylglutamate (NCG) (H + N) on the gut microbiota, metabolites, and transcriptome in Landrace × Yorkshire sows using a multi-omics approach. Sows were allocated to four groups in a 2 × 2 design: Low-fiber or high-fiber diets, each with or without 0.05% NCG supplementation. The H + N treatment significantly increased litter weight at weaning. Metagenomic analysis revealed H + N significantly altered gut microbiota composition and function, particularly enriching Lactobacillus at multiple taxonomic levels from order to species (including Lactobacillus sp. 910 589 175). Plasma metabolomics identified two key lipid mediators, L-α-glycerylphosphorylcholine and taurocholic acid, whose abundances were significantly elevated by H + N and positively correlated with the enriched Lactobacillus. Transcriptomic profiling showed activation of the PI3K-Akt signaling pathway in response to H + N, which was associated with observed improvement in litter weight at weaning. Collectively, the multi-omics study uncovered a novel synergistic axis wherein H + N modulated the gut microbiome (specifically Lactobacillus enrichment), which in turn shaped the lipid metabolome to activate the PI3K-Akt pathway, ultimately enhancing sow reproductive efficiency.}, }
@article {pmid42301503, year = {2026}, author = {Bao, W and Li, X and Pan, H and Gao, Y and Zhao, L and Liu, J and Wang, S and Zhang, Y}, title = {Detoxification mechanisms of black soldier fly larvae against microcystin-LR.}, journal = {Functional &amp; integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42301503}, issn = {1438-7948}, mesh = {Animals ; *Microcystins/toxicity/metabolism ; Marine Toxins ; Larva/microbiology/metabolism/growth &amp; development/drug effects/genetics ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; Inactivation, Metabolic ; *Simuliidae/microbiology/metabolism/genetics/growth &amp; development/drug effects ; }, abstract = {This study aimed to elucidate the detoxification mechanisms of black soldier fly larvae (BSFL) against microcystin-LR (MC-LR). Using concentration-gradient exposure (0 - 400 µg/L) and integrated metagenomic and transcriptomic analyses, we investigated the growth responses, gut microbiota alterations, and synergistic detoxification mechanisms of BSFL. The results revealed that the growth performance of BSFL was not significantly affected even at high MC-LR concentrations (400 µg/L). However, significant alterations occurred in the gut microbial composition, with increased relative abundances of Actinobacteria and Firmicutes, along with increased species richness and diversity, which correlated with increasing exposure concentrations. Functional analysis revealed that functions related to carbohydrate metabolism, energy metabolism, and substrate transport were significantly enriched in the exposed groups. Transcriptomic data further indicated that MC-LR induced intestinal oxidative stress, with significant upregulation of antioxidant-related genes (superoxide dismutase, isocitrate dehydrogenase, and peroxiredoxin 6) as well as key xenobiotic metabolism genes (carboxylesterase, glutathione S-transferase, and UDP-glucuronosyltransferase). Additionally, heat shock proteins and the Toll signaling pathway were activated. We speculate that BSFL maintains gut microbial homeostasis against MC-LR toxicity through the coordinated regulation of gut microbial communities, host antioxidant systems, xenobiotic metabolism pathways, and immune responses, providing a theoretical foundation for safe resource utilization of cyanobacteria.}, }
@article {pmid42302279, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Rachid, D}, title = {From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42302279}, issn = {1477-4054}, support = {//University Mohammed VI Polytechnic (UM6P), Morocco/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Biomarkers ; *Colorectal Neoplasms/microbiology/genetics ; Machine Learning ; *Precision Medicine ; Causality ; Mendelian Randomization Analysis ; Metagenomics ; }, abstract = {Human gut microbiome research has generated many disease associations, yet few translate into clinical applications. A central obstacle is not a lack of data, but the limited integration of causal reasoning, as most studies report correlations without establishing directionality, confounding control, or mechanistic evidence. We propose a unified causal inference framework that integrates directed acyclic graphs, Mendelian randomization, double machine learning, mediation analysis, and tests of causal reversibility into a single decision-aware workflow. Unlike prior applications of these tools in isolation, our framework explicitly separates assumption mapping, causal identification, effect estimation, and mechanistic interpretation, introducing "assumption guardrails" that constrain interpretation at each stage and prevent overinterpretation of observational findings. Using a colorectal cancer case study with public metagenomic data, we demonstrate how the framework operates under real-world constraints, transforming observational associations into testable, mechanism-based hypotheses. The contribution is architectural in that it organizes existing tools into a disciplined, integrated pipeline that clarifies the strength of evidence at each stage. This operational blueprint provides a reproducible path from correlation to causation in microbiome research and toward precision interventions.}, }
@article {pmid42302785, year = {2026}, author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X}, title = {Power and sample-size estimation in human microbiome research.}, journal = {Med (New York, N.Y.)}, volume = {7}, number = {7}, pages = {101174}, doi = {10.1016/j.medj.2026.101174}, pmid = {42302785}, issn = {2666-6340}, mesh = {Humans ; *Microbiota ; Sample Size ; *Research Design ; Metagenomics/methods ; Models, Statistical ; }, abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.}, }
@article {pmid42307633, year = {2026}, author = {Carasso, S and Kasher-Dvora, M and Gefen, T and Geva-Zatorsky, N}, title = {Phase variation-mediated bacterial functional plasticity as a lens for understanding microbe‒host interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687913}, doi = {10.1080/19490976.2026.2687913}, pmid = {42307633}, issn = {1949-0984}, mesh = {Humans ; *Host Microbial Interactions ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/physiology ; *Bacterial Physiological Phenomena ; Animals ; }, abstract = {The human gut microbiome represents a dynamic microbial ecosystem profoundly influencing host physiology, immune development, and disease susceptibility. While metagenomic approaches have advanced our understanding of microbial composition and functional potential, they remain insufficient to capture the real-time molecular events governing host‒microbe interactions. Taxonomic abundance and genomic content alone do not reflect active gene expression or phenotypic output, and functional roles cannot be reliably inferred from phylogenetic identity, given the substantial heterogeneity observed even within species. Central to bridging this gap is the concept of bacterial functional plasticity, with a focus on phase-mediated functional plasticity, the intrinsic capacity of microbes to rapidly remodel their activity and phenotype in response to environmental and host-derived cues. This review highlights phase variation as a prominent and evolutionarily conserved mechanism underlying plasticity, encompassing DNA inversions, short-sequence repeat modifications, and broader structural genomic variation. Emerging evidence demonstrates not only the prevalence of phase-variable mechanisms across diverse gut taxa but also their significant regulatory, ecological, and immunological consequences. These findings reframe the microbiome from a static consortium of species to a functionally dynamic system capable of rapid rewiring in response to environmental pressures. By integrating genomic, ecological, and host-response data, this review lays the groundwork for mechanistic frameworks that could explain how flexible microbial strategies influence bacterial behavior and host outcomes. Moving beyond cataloging microbial composition toward deciphering the logic of functional adaptation will be essential for translating microbiome research into predictive, diagnostic, and therapeutic applications.}, }
@article {pmid42307846, year = {2026}, author = {Gomes, RF and García, GJY and Cardoso, MS and Dutra, JDCF and de Abreu Waldow, V and Akamine, RN and de Sousa, MP and Groposo, C and Brenig, B and Figueiredo, H and de Carvalho Azevedo, VA and Góes-Neto, A}, title = {Metagenomics and metatranscriptomics of prokaryotic and fungal microbiomes in produced water associated with petroleum degradation and pipeline corrosion from an oil terminal in Brazil.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42307846}, issn = {1573-0972}, mesh = {*Fungi/genetics/classification/metabolism/isolation &amp; purification ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Petroleum/metabolism/microbiology ; *Metagenomics ; Biodegradation, Environmental ; Corrosion ; Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Water Microbiology ; Hydrocarbons/metabolism ; Phylogeny ; }, abstract = {The prokaryotic microbial communities involved in hydrocarbon degradation and associated with oil pipeline corrosion have been extensively studied. Nonetheless, fungi can perform significant metabolic activities in these environments. Studies evaluating metabolically active microbial communities in oil reservoirs are limited. Our study investigated the total/DNA and active/RNA communities of Archaea, Bacteria, and Fungi in produced water samples from an onshore terminal in Brazil. DNA and RNA were sequenced using the Illumina HiSeq 2500 platform, and the meta-omics sequences were analyzed. Shannon alpha diversity (taxonomic and functional) revealed that total communities were more diverse than metabolically active ones, with Bacteria showing higher diversity than Archaea and Fungi. The bacterial genera Syntrophotalea (sulfur reducer) and Pseudodesulfovibrio (sulfate reducer) were most prominent in total communities, while Halanaerobium (acid producing) dominated active communities. These results confirm the presence of Microbially Influenced Corrosion (MIC); however, the aprAB and dsrABC genes showed very low expression. Methanogenic Archaea Methanocalculus, Methanoplanus, and Methanothrix were frequent in both total and active communities, and mcrABDG genes were significantly expressed in metatranscriptomic sequences. Fungal genera Absidia, Penicillium, and Rhizopus were dominant in DNA samples, whereas Saccharomycodes, Pichia, Coemansia, and Schizosaccharomyces dominated RNA samples. These fungi can remediate environments contaminated with recalcitrant hydrocarbons. Despite the limited information obtained from fungal functional profile, an in-depth investigation of their activities and interrelation with Archaea and Bacteria in oil reservoirs is crucial for monitoring and mitigating oil biodegradation and pipeline biocorrosion processes.}, }
@article {pmid42307995, year = {2026}, author = {Laiton, L and Acevedo, FE}, title = {Gut microbiome of the grape berry moth, Paralobesia viteana (Lepidoptera: Tortricidae) larvae through the grape ripening process revealed by high-throughput 16S and 18S rRNA sequencing.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42307995}, issn = {2057-5858}, mesh = {Animals ; *Vitis/parasitology/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; *Moths/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {The grape berry moth (GBM) Paralobesia viteana (Lepidoptera: Tortricidae) is an important pest of grapes in eastern North America. The larvae damage grape clusters by direct feeding and by increasing susceptibility to fungal and bacterial pathogens. In this study, we sequenced the V3-V4 region of the 16S rRNA gene and the V4 region of the 18S rRNA gene to characterize the composition and diversity of GBM larval gut bacterial and fungal communities when fed on immature and mature 'Concord' grapes. The data were analysed with QIIME 2, and downstream analyses included taxonomic composition, differential abundance, phylogenetic, functional and alpha/beta diversity analyses. While overall bacterial community diversity did not differ significantly between treatments, differential abundance analysis identified specific bacterial taxa enriched in each larval group. Ninety-three per cent of the bacterial communities belonged to the phylum Proteobacteria, and some may play roles in amino acid and carbohydrate metabolism in the insect gut. Analyses of the 18S rRNA region showed significant taxon-level compositional differences in fungal communities between larvae grown on grapes at different ripening stages. Ascomycota was the dominant phylum (98%) present in the guts of larvae fed on mature grapes, while larvae fed on immature grapes mainly contained fungi within the Cryptomycota (51%). Larvae fed on ripe grapes had a 10-fold higher fungal abundance and were enriched in Saccharomycetales yeasts. Several of the identified microbial taxa in larval guts are commonly found in grapes, which suggests they might be transient insect residents that are ingested with the diet. In conclusion, diet strongly shaped GBM gut-associated fungal communities; specific bacterial taxa also differed between larval groups despite similar overall bacterial diversity. These results contribute to basic knowledge of gut-associated microbes in fruit-feeding insects.}, }
@article {pmid42308119, year = {2026}, author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P}, title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42308119}, issn = {2057-5858}, mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation &amp; purification/genetics ; Metagenomics/methods ; Proteomics ; }, abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.}, }
@article {pmid42308739, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Hoerr, FJ and Robinson, K and Hauck, R}, title = {Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107215}, pmid = {42308739}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/microbiology ; Male ; *Dietary Fiber/administration &amp; dosage/metabolism ; Diet/veterinary ; *Transcriptome/drug effects ; Animal Feed/analysis ; *Jejunum/pathology/microbiology/drug effects ; Dietary Supplements/analysis ; *Poultry Diseases/microbiology/pathology/parasitology ; *Metagenome/drug effects ; Random Allocation ; Eimeria/physiology ; *Gastrointestinal Microbiome/drug effects ; *Clostridium Infections/veterinary/microbiology ; Dose-Response Relationship, Drug ; Avena/chemistry ; Intestinal Mucosa ; Beta vulgaris/chemistry ; }, abstract = {This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 d-old YP x Ross 708 male broilers were assigned to eight treatments. These included an unchallenged control and a challenged control, followed by six dietary treatments applied to challenged broilers. The dietary treatments consisted of fiber supplementation with oat hulls (OH) or soy hulls (SH), either alone or in combination with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. While the enteric challenge induced significant histopathological changes, fiber combinations including OH-WM and OH-SBP significantly (P < 0.05) reduced cumulative pathology scores. The challenge caused a shift toward Lactobacillus crispatus dominance in the microbiome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis. Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes APOB, DSEL, and ENPP7, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. These findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.}, }
@article {pmid42308920, year = {2026}, author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC}, title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {201}, number = {}, pages = {119656}, doi = {10.1016/j.biopha.2026.119656}, pmid = {42308920}, issn = {1950-6007}, mesh = {*Synbiotics/administration &amp; dosage ; Animals ; *Antioxidants/pharmacology/therapeutic use/administration &amp; dosage ; Male ; Humans ; Disease Progression ; Mice, Inbred C57BL ; Pilot Projects ; Liver/metabolism/drug effects/pathology ; Diet, High-Fat ; Mice ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; Gastrointestinal Microbiome/drug effects ; *Fatty Liver/drug therapy/metabolism ; Drug Synergism ; Middle Aged ; Feces/microbiology ; }, abstract = {BACKGROUND &amp; AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.<br><br>METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n&#x202f;=&#x202f;27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.<br><br>RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p&#x202f;<&#x202f;0.05), and increased the respiratory exchange ratio (p&#x202f;<&#x202f;0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p&#x202f;<&#x202f;0.05), while antioxidants primarily reduced adipose tissue (p&#x202f;<&#x202f;0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p&#x202f;<&#x202f;0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p&#x202f;<&#x202f;0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.<br><br>CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.}, }
@article {pmid42309017, year = {2026}, author = {Yang, X and Liu, W and Mao, Y and Wang, H}, title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.}, journal = {Ecotoxicology and environmental safety}, volume = {320}, number = {}, pages = {120390}, doi = {10.1016/j.ecoenv.2026.120390}, pmid = {42309017}, issn = {1090-2414}, mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Metabolome/drug effects ; *Plant Roots/drug effects/metabolism/microbiology ; *Soil Pollutants/toxicity ; *Cuminum/drug effects/metabolism/microbiology ; *Lead/toxicity ; Soil Microbiology ; Stress, Physiological ; Soil/chemistry ; }, abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.}, }
@article {pmid42311675, year = {2026}, author = {Zhang, H and Fan, B and Ma, R and Jiang, R and Qin, Z and Qu, X and Wang, J and Xue, J and Wang, C and Liu, X and Guo, L}, title = {Gut microbiota and sepsis-associated acute kidney injury: a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1724266}, pmid = {42311675}, issn = {1664-3224}, mesh = {Humans ; *Acute Kidney Injury/microbiology/etiology/therapy/immunology ; *Sepsis/complications/microbiology/immunology ; Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Intestinal Barrier Function ; Signal Transduction ; }, abstract = {BACKGROUND: Sepsis-associated acute kidney injury (SA-AKI) carries high morbidity and mortality, yet its pathogenesis remains incompletely understood. Emerging evidence underscores the gut-kidney axis as a critical pathway in SA-AKI development.<br><br>OBJECTIVE: This review aims to synthesize current knowledge on how sepsis-driven gut dysbiosis compromises intestinal barrier integrity and contributes to SA-AKI, and to explore potential therapeutic strategies targeting the gut microbiota.<br><br>METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus databases for publications between 2005 and 2026. Studies focusing on gut-kidney crosstalk mechanisms in sepsis/AKI were included. Key findings from human and animal studies were summarized.<br><br>RESULTS: Sepsis induces marked gut dysbiosis characterized by loss of microbial diversity and expansion of pathobionts. This dysbiosis compromises intestinal barrier integrity, facilitating translocation of bacterial products such as lipopolysaccharide (LPS). Upon entering circulation, these mediators activate systemic inflammation and renal signaling cascades, including the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-&#x3ba;B) pathway, leading to tubular injury and impaired renal function. Recent human metagenomic studies have identified specific microbial signatures associated with AKI, such as increased Clostridium asparagiforme and decreased Roseburia spp., alongside elevated uremic toxin-producing bacteria like Gordonibacter pamelaeae. Additionally, gut-derived metabolites including indoxyl sulfate, p-cresol sulfate, and trimethylamine N-oxide (TMAO) have been implicated in promoting renal inflammation and fibrosis. Importantly, renal dysfunction further disrupts gut homeostasis, establishing a pathological gut-kidney feedback loop. Targeting the gut-kidney axis via fecal microbiota transplantation, probiotic supplementation, or short-chain fatty acid administration may offer novel therapeutic avenues.<br><br>CONCLUSIONS: Sepsis induces gut microbiota dysregulation play an important role in the development of SA-AKI. The intestine-kidney crosstalk may provide a basis for the treatment of sepsis-induced organ injury and also provide new ideas for the treatment of SA-AKI.}, }
@article {pmid42312035, year = {2026}, author = {Radzieta, M and Malone, M and Schwarzer, S and Bergamin, E and Whitely, G and Jensen, S}, title = {Anaerobe-associated microbial shifts at infection onset in diabetes-related foot ulcers revealed by longitudinal metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812721}, pmid = {42312035}, issn = {2235-2988}, mesh = {Humans ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Bacteria, Anaerobic/classification/genetics/isolation &amp; purification ; *Microbiota ; Longitudinal Studies ; Male ; Female ; Aged ; Middle Aged ; Metagenome ; }, abstract = {INTRODUCTION: Diabetes-related foot infections (DRFIs) are a major cause of hospitalisation and carry a significantly increased risk of lower extremity amputation. To date there is a lack of longitudinal studies examining within-patient microbiome dynamics during the transition from non-infected to infected diabetes-related foot ulcers (DRFUs).<br><br>METHODS: We used shotgun metagenomic sequencing to longitudinally profile the wound microbiome of 6 patients with DRFUs who developed clinical infections, utilising taxonomic profiling, metagenome assembly and binning and strain level analysis to characterise within-patient microbial shifts.<br><br>RESULTS: DRFUs with no signs of clinical infection were colonised by virulent pathogens including Staphylococcus aureus, Streptococcus agalactiae, Enterococcus faecalis, Enterobacter hormaechei and Pseudomonas aeruginosa. In most patients, infection onset was associated with a decrease in pathogen abundance and a significant increase in obligate anaerobes including Prevotella spp, Peptoniphilus spp, Porphyromonas spp and Anaerococcus spp.<br><br>CONCLUSION: These findings highlight the potential importance of anaerobes and hypoxia in DRFIs and may support monitoring of tissue oxygen saturation as a predictor of infection onset.}, }
@article {pmid42313157, year = {2026}, author = {Cardenas Alegria, OV and Torres, MC and Breyer, GM and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Ramos, RTJ and Dorn, M and Kich, JD and Siqueira, FM}, title = {Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42313157}, issn = {1432-0991}, mesh = {Animals ; Swine ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Soil Microbiology ; *Manure/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ponds/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Soil/chemistry ; Metagenomics ; Genes, Bacterial ; *Microbiota ; }, abstract = {The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.}, }
@article {pmid42313512, year = {2026}, author = {Han, M and Zhao, H and Lai, J and Zhao, S and Dong, B and Xi, H}, title = {Succession and Functional Adaptation of Bacterial and Fungal Communities in Biological Soil Crusts Responding to Uranium Stress.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70359}, doi = {10.1111/1462-2920.70359}, pmid = {42313512}, issn = {1462-2920}, support = {22106182//National Natural Science Foundation of China/ ; 2022YFC3702500//National Key Research and Development Program of China/ ; SKLNBC2023-03//State Key Laboratory of NBC Protection for Civilian/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification/genetics ; Adaptation, Physiological ; Biodegradation, Environmental ; *Soil Pollutants, Radioactive/metabolism ; *Microbiota ; Stress, Physiological ; }, abstract = {Uranium (U) mining causes severe radioactive contamination threatening ecosystems. Biological soil crusts (BSCs), as pioneer communities in degraded habitats, show strong heavy metal accumulation potential, yet their adaptive mechanisms under U stress remain unclear. In this study, BSCs from a uranium tailings dam in Hunan Province were exposed to simulated U stress. Results showed that BSCs exhibited exceptionally high U accumulation capacity (up to 4131 mg/kg), and effectively immobilised U by converting it into residual and organic-bound fractions (collectively > 70%) via carboxyl complexation and microbial mineralisation, thus significantly reducing environmental mobility. U stress caused damage to the photosynthetic and antioxidant systems of the BSCs. Microbial community complexity decreased, with tolerant taxa including Proteobacteria and Bacilli significantly enriched. Metagenomics revealed distinct cross-kingdom functional adaptation strategies: bacteria upregulated energy metabolism and acetaldehyde metabolism to facilitate efflux detoxification, while fungi strengthened lipid homeostasis and antioxidant metabolism. Several U-tolerant strains (Bacillus, Aspergillus and Penicillium) closely associated with U immobilisation were further isolated and verified. This study systematically reveals the synergistic tolerance mechanisms of BSCs under U stress and provides key microbial resources and theoretical support for the in situ bioremediation of U-contaminated sites.}, }
@article {pmid42313858, year = {2026}, author = {Meijer, S and Hugerth, LW and Nouri, M and Erlandsson, L and Lavasani, S and Hansson, SR}, title = {Comparative analysis of gut microbiome alterations in early- and late-onset preeclampsia: A case control study.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0348943}, pmid = {42313858}, issn = {1932-6203}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Dysbiosis/microbiology ; Metagenomics ; Bacteria/classification/genetics ; }, abstract = {Preeclampsia (PE) is a complication during pregnancy characterized by hypertension, organ damage, and systemic inflammation. Increasing evidence suggests that the gut microbiome may play a role in the pathophysiology of PE. However, previous studies on the gut microbiome have generally overlooked the distinction between subgroups of PE, although clinical manifestations may differ. Also, most studies have not used deep sequencing techniques. Therefore, this study aimed to explore further potential differences in gut dysbiosis in different PE subgroups compared to controls using shotgun metagenomics. We studied the bacterial gut microbiome using shotgun metagenomic sequencing in 37 pregnant patients in the third trimester from a Swedish cohort, separating patients according to subtype (healthy controls N = 21, late-onset PE N = 8, early-onset PE N = 8). Differential relative abundances and alpha diversity were evaluated using Wilcoxon rank sum test, and beta diversity was evaluated using PERMANOVA. Multiple linear regression was used to study associations between gut microbiome composition differences and clinical parameters. Late-onset PE and early-onset PE were both associated with significantly different beta diversity compared to controls. Differences remained significant after adjusting for age, and were not affected by gestational age, BMI or parity. Alpha diversity was lower in late-onset PE compared to controls. While no significant differences in taxonomic abundances were seen after correcting for multiple testing, several interesting leads were identified, including a higher abundance of genus Blautia in late-onset PE, and lower abundance of Coprococcus catus and unclassified Lachnospiraceae in early-onset PE. Functional analysis did not reveal any significant differences after false discovery rate (FDR) correction. In conclusion, our results showed subgroup-specific gut microbiome differences in PE with more pronounced associations in late-onset PE, despite limited power due to the observational design and small cohort. Accordingly, our results highlight the importance of subgroup analysis when studying PE.}, }
@article {pmid42314322, year = {2026}, author = {Zhang, P and Zhu, Y and Wang, Z and Yu, P and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Tan, C and Wu, F and Peng, Q}, title = {Initial exploration of the health effects on Qinghai-Tibetan Plateau yaks following short-term exposure to polystyrene microplastics: Analysis of rumen microbiota, host metabolism, antioxidant function and inflammatory responses.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142707}, doi = {10.1016/j.jhazmat.2026.142707}, pmid = {42314322}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Rumen/microbiology/drug effects/metabolism ; *Polystyrenes/toxicity ; *Antioxidants/metabolism ; Inflammation/chemically induced ; *Microplastics/toxicity ; *Gastrointestinal Microbiome/drug effects ; Tibet ; Cytokines ; Metabolomics ; }, abstract = {Microplastics (MPs) are ubiquitous across environments including the Qinghai-Tibet Plateau. Most existing MPs studies focus on aquatic animals and rodents, while MPs influences on yaks (Bos grunniens) remain poorly understood. Using yaks as animal models, we combined metagenomics and metabolomics to explore short-term polystyrene-MPs (PS-MPs) impacts on ruminal microbiota, metabolism, antioxidant capacity and inflammation. Seven-day PS-MPs exposure reshaped rumen microbiota and elevated β-diversity. Four KEGG pathways (peptidoglycan synthesis, vitamin B6/riboflavin metabolism, terpenoid backbone biosynthesis) were enriched alongside altered extracellular polysaccharides composition. Serum metabolomics revealed elevated L-glutamine and indole-3-propionic acid, coupled with reduced 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and indole-3-lactic acid post-exposure. Urinary metabolomics revealed decreased D-erythrose 4-phosphate, dimethyl allyl pyrophosphate, and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate, collectively indicating inhibited terpenoid backbone biosynthesis in yaks. Additionally, PS-MPs triggered inflammatory responses, evidenced by elevated levels of pro-inflammatory cytokines (interferon-γ, interleukin-1β, interleukin-6, interleukin-17, interleukin-22, tumor necrosis factor-α, transforming growth factor-α), yet antioxidant function indexes (total antioxidant capacity, superoxide dismutase, glutathione peroxidase, catalase and malondialdehyde) showed no significant changes. Multi-omics suggested Prevotella ruminicola may help resist PS-MPs invasion. In summary, rumen microbes may alleviate PS-MPs adverse effects, explaining yaks' mild responses to short-term PS-MPs exposure. Long-term MPs effects, tissue deposition and related molecular mechanisms warrant further study.}, }
@article {pmid42315257, year = {2026}, author = {Cramer, C and Marshall, IPG and Abramson, MJ and Jõgi, NO and Khomich, M and Peddada, SD and Skottvoll, BS and Schlünssen, V and Bertelsen, RJ}, title = {Role of oral bacteria composition and functional gene profiles in respiratory diseases.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, pmid = {42315257}, issn = {2052-4439}, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; *Asthma/microbiology ; *Mouth/microbiology ; Adult ; Middle Aged ; *Rhinosinusitis/microbiology ; Norway/epidemiology ; Australia/epidemiology ; Estonia/epidemiology ; Nitric Oxide ; Fractional Exhaled Nitric Oxide Testing ; *Bacteria/isolation &amp; purification/genetics ; Chronic Disease ; Spirometry ; }, abstract = {INTRODUCTION: The oral microbiome has been shown to be associated with respiratory health, primarily in adult case studies or among children. This relationship has been scarcely investigated in adult population-based cohorts.<br><br>OBJECTIVES: To investigate the association between oral microbiome and respiratory health, more specifically asthma, chronic rhinosinusitis (CRS), lung function and fractional exhaled nitric oxide (FeNO) in a population-based cross-continental multicentre study among adults.<br><br>METHODS: Subgingival samples from 355 adult European Community Respiratory Health Survey participants from Norway, Australia and Estonia underwent metagenomic sequencing. Respiratory disease was defined from questionnaires and sensitisation from specific immunoglobulin E (IgE)/skin prick tests. Spirometry and FeNO were measured. The associations between alpha diversity and disease status were evaluated in cross-sectional analyses using logistic regression adjusting for sex, smoking and study centre. Differential abundance analyses were performed using analysis of compositions of microbiomes with bias correction.<br><br>RESULTS: Alpha diversity differed by study centre and sensitisation status and was associated with non-allergic CRS (richness: 1.12, 95%&#x2009;CI 1.03 to 1.22). A similar though not statistically significant pattern was seen for forced vital capacity (FVC) below the lower limit of normal (LLN). Lachnospiraceae and Xanthomonas were more abundant in the oral microbiome of non-asthmatics and individuals without CRS, respectively, as compared with asthmatics and CRS patients. Several functional genes (1477-3391)&#x2009;and genera (54-98) were only present in the non-case groups, whereas individuals with affected respiratory health had 0-74&#x2009;unique functional genes, but no unique genera present only in their respective groups.<br><br>CONCLUSION: Increased alpha diversity was associated with non-allergic CRS and a similar trend was seen for FVC below LLN. Bacterial composition and functional profiles of the oral microbiome differed by respiratory health status. This study is novel in exploring functional gene profiling in relation to asthma and FeNO.}, }
@article {pmid42315843, year = {2026}, author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, DM and Teixeira, M and Earl, AM and Worby, CJ and Kong, HH and Huang, SS and Segre, JA}, title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42315843}, issn = {2041-1723}, support = {R01 HS024286/HS/AHRQ HHS/United States ; U19 AI172725/AI/NIAID NIH HHS/United States ; ZIA HG200382/ImNIH/Intramural NIH HHS/United States ; ZIA-HG200382-14//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Anti-Bacterial Agents/pharmacology/therapeutic use ; California ; Drug Resistance, Multiple, Bacterial/genetics ; Escherichia coli/isolation &amp; purification/genetics ; Metagenome ; Metagenomics ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification/genetics ; Nursing Home Residents ; *Nursing Homes ; *Skin/microbiology ; Skin Microbiome ; Staphylococcus epidermidis/isolation &amp; purification/genetics ; Clinical Trials, Phase IV as Topic ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; }, abstract = {Antimicrobial resistance (AMR) is a health threat disproportionately affecting nursing home (NH) residents. Surveillance and infection control in NHs are restricted to nares or perirectal cultures, overlooking skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here, within the PROTECT trial NCT03118232, we show, that NH residents' skin serves as a reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using metagenomics, culturing, and genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including 4 (10.5%) with ESBL-producing Escherichia coli sequence type (ST)131/ST648 and 7 (18.4%) with methicillin-resistant Staphylococcus aureus. Skin microbiome analysis by metagenome-assembled genomes identified broader MDRO colonization, including 27 (71.1%) with E. coli ST93, 14 (36.8%) with Staphylococcus epidermidis ST2, 16 (42.1%) with Proteus mirabilis, 7 (18.4%) with Providencia stuartii, 7 (18.4%) with Enterococcus faecalis, and 5 (13.2%) with Pseudomonas aeruginosa. Colonization persisted after bathing. Clonal E. coli ST93 was shared by 27 residents across 9 facilities, and 5 resident pairs carried clonally related strains of ≥2 MDRO species, suggesting polymicrobial transmission. We confirmed skin as a reservoir of MDROs, utilizing metagenomics to detect colonization and transmission pathways, supporting AMR surveillance in long-term care.}, }
@article {pmid42316154, year = {2026}, author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y}, title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42316154}, issn = {1479-5876}, support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Probiotics/therapeutic use/pharmacology ; *Dysbiosis/microbiology/complications ; Animals ; *Respiratory Distress Syndrome, Newborn/microbiology/complications ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; *Translational Research, Biomedical ; Female ; Male ; Feces/microbiology ; Mice ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.<br><br>METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n&#x2009;=&#x2009;45), fecal samples collected within 48&#xa0;h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n&#x2009;=&#x2009;25), infants with RDS who did not receive SRT (RDS(S-) group, n&#x2009;=&#x2009;7), and infants with RDS who received SRT (RDS(S+) group, n&#x2009;=&#x2009;13). In the probiotic discovery cohort (n&#x2009;=&#x2009;40), gut microbiota of infants without RDS (CON group, n&#x2009;=&#x2009;17) and infants with RDS (RDS group, n&#x2009;=&#x2009;23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.<br><br>RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.<br><br>CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.}, }
@article {pmid42316350, year = {2026}, author = {Zhao, J and Su, Q and Wang, S and Li, Q and Chen, L and Kang, X and Xu, Q and Liu, C and Zhao, H}, title = {Differentiating hemorrhagic shock and organophosphate poisoning through integrated skin microbiome-metabolome signatures.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42316350}, issn = {1471-2180}, support = {2024B04J0022//Guangzhou Science and technology planning project/ ; 82371901//National Natural Science Foundation of China/ ; 2023JC36//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; }, mesh = {Animals ; *Organophosphate Poisoning/diagnosis/microbiology/metabolism ; *Skin Microbiome ; *Metabolome ; *Shock, Hemorrhagic/microbiology/diagnosis/metabolism ; Mice ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metabolomics ; *Skin/microbiology ; Metagenomics ; Disease Models, Animal ; }, abstract = {Accurate determination of cause of death and estimation of postmortem interval (PMI) are critical yet challenging tasks in forensic science, particularly in cases with rapid demise and absence of obvious morphological abnormalities. We employed an integrative multi-omics approach to characterize postmortem microbial succession and metabolic alterations on facial skin in mouse models of hemorrhagic shock (HS) and organophosphorus poisoning (OP) across three decomposition stages: bloating (2 days), active decay (8 days), and advanced decay (16 days). Metagenomic profiling revealed significantly reduced α-diversity in HS compared with OP throughout all stages (p < 0.001), accompanied by stage-dependent compositional shifts, including early enrichment of Firmicutes in HS and Proteobacteria in OP. A total of 237 differential taxa were identified, with Providencia and Morganella predominating in OP, whereas Staphylococcus and Corynebacterium dominated bloating stage of HS. Untargeted metabolomics uncovered distinct cause-of-death-linked metabolites, notably elevated 2'-deoxycytidine-5'-diphosphate in early OP and persistent cholic acid/cholate accumulation in HS at later PMI. Functional analysis highlighted histidine and phosphate/phosphonate metabolism as key discriminatory pathways, exhibiting stage-specific oscillations and strong correlations with characteristic taxa. These findings demonstrate that skin-based metagenomic-metabolomic integration provides robust, mechanistically informed biomarkers for both PMI estimation and cause-of-death differentiation, offering a minimally invasive and temporally dynamic tool for forensic investigations.}, }
@article {pmid42316995, year = {2026}, author = {Gu, Y and Li, L and Zhang, H and Ye, T and Zhu, Q and Zhao, X and Xie, K and Ge, R and Han, J and Qin, Y}, title = {Dietary purple sweet potato anthocyanin extracts attenuate intestinal barrier decline in naturally aged mice via the microbiota-autophagy-stem cell axis.}, journal = {Food &amp; function}, volume = {17}, number = {13}, pages = {6227-6245}, doi = {10.1039/d6fo00039h}, pmid = {42316995}, issn = {2042-650X}, mesh = {Animals ; *Anthocyanins/pharmacology ; *Ipomoea batatas/chemistry ; Mice ; *Aging/drug effects ; *Stem Cells/drug effects/metabolism ; *Plant Extracts/pharmacology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Male ; Intestinal Mucosa/drug effects/metabolism ; Dietary Supplements ; }, abstract = {Age-related deterioration of the intestinal epithelial barrier exacerbates systemic metabolic and functional decline, highlighting the gut as a key target for dietary interventions in healthy aging. Here, using naturally aged mice and intestinal organoids, we demonstrate that supplementation with purple sweet potato anthocyanins (PSPAs) alleviates systemic aging phenotypes, including impaired motor coordination, hepatic lipid dysregulation, insulin resistance, and cellular senescence, while concurrently restoring intestinal barrier integrity. PSPAs enhanced tight junction protein expression and epithelial architecture, independently of inflammation resolution, and promoted the proliferative and differentiation capacity of intestinal stem cells (ISCs). Metagenomic profiling revealed that PSPAs remodeled aging-associated gut microbiota composition and functions. Fecal microbiota transplantation established the causal contribution of microbiota remodeling to ISC rejuvenation, while luminal content-organoid assays confirmed the role of microbial metabolites. Integrative metabolomics identified metabolic changes linked to autophagy-related processes, including altered SCFA profiles, while transcriptomic analysis highlighted PI3K-AKT signaling as a major pathway associated with microbial and metabolic remodeling. Collectively, this multi-omics study establishes a mechanistic framework in which PSPAs alleviate aging-associated barrier decline through a "microbiota-autophagy-stem cell" axis, providing important insights into polyphenol-based strategies for gut-centered healthy aging.}, }
@article {pmid42317351, year = {2026}, author = {Lou, Y and Ma, D and Gan, Q and Xu, X and Xiao, Y and Wang, J and Li, Z and Zhang, T and Qi, L and Feng, S}, title = {Inflammatory protein mediators linking gut microbiota to degenerative lumbar spine disorders: cross-disease genetic evidence.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1855966}, pmid = {42317351}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Intervertebral Disc Degeneration/genetics/microbiology/immunology/metabolism ; Humans ; *Lumbar Vertebrae/pathology ; Rats ; Mendelian Randomization Analysis ; *Inflammation Mediators/metabolism ; *Spondylolisthesis/genetics/microbiology ; Biomarkers ; *Spinal Stenosis/genetics/microbiology ; Disease Models, Animal ; }, abstract = {BACKGROUND: Degenerative lumbar spine disorders (DLSD), including intervertebral disc disorders (IDD), degenerative spondylolisthesis, and lumbar spinal stenosis (LSS), are major contributors to low back pain and disability. Associations among gut microbiota (GM), inflammatory proteins, and DLSD have been demonstrated in prior studies. Yet, two key questions persist: whether specific circulating inflammatory proteins (IPs) mediate this association, and whether such mediation is shared across different diseases.<br><br>METHODS: We performed two-sample Mendelian randomization (MR) to evaluate causal associations among 473 GM taxa, 91 circulating IPs, and three DLSD outcomes using FinnGen R12 summary statistics. Causal estimates were obtained using inverse-variance weighted MR with complementary sensitivity analyses, pleiotropy and heterogeneity testing, and bidirectional MR. Two-step MR mediation was applied to quantify indirect effects of GM through IPs. Experimental validation was performed using rat models, with qPCR and ELISA assessing inflammatory markers in lumbar tissues and metagenomic sequencing evaluating gut microbiota profiles.<br><br>RESULTS: Genetically predicted GM taxa were associated with LSS (28 taxa), spondylolisthesis (20 taxa), and IDD (41 taxa). IP MR identified risk-increasing associations for LSS (4E-BP1 and interleukin-4), spondylolisthesis (CXCL1, CXCL5, FGF-5, IL-15RA, and IL-4) and IDD (IL-20RA and IL-6), while IL-18 showed a protective association with IDD that remained robust after multiple-testing correction. Mediation analyses identified 13 genetically supported putative GM-IPs-DLSD pathways, highlighting convergent mediators including PD-L1 for spondylolisthesis and IL-6 and IL-18 for IDD, with mediation proportions ranging from 7.55% to 13.22% across key pathways. Experimental results showed inflammatory activation and gut microbiota alterations in disease models, with partial concordance with the MR findings.<br><br>CONCLUSIONS: These findings support a genetically determined microbiota-inflammation axis in DLSD. Furthermore, they identify circulating inflammatory proteins as mediators to prioritize mechanistic studies and guide translational follow-up research.}, }
@article {pmid42319454, year = {2026}, author = {Xie, M and Jie, Y}, title = {From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42319454}, issn = {1432-0991}, support = {82371022//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; *Dry Eye Syndromes/microbiology/diagnosis ; Bacteria/genetics/classification/isolation &amp; purification ; *Eye/microbiology ; Fungi/isolation &amp; purification/genetics/classification ; Tears/microbiology ; }, abstract = {Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.}, }
@article {pmid42320776, year = {2026}, author = {Cho, MS and Lee, IS and Kim, J and Park, JW and Kim, J and Ko, SJ}, title = {Multi-herb formulations modulating gut microbiota: A systematic review and data-driven analysis.}, journal = {Journal of ethnopharmacology}, volume = {370}, number = {}, pages = {122082}, doi = {10.1016/j.jep.2026.122082}, pmid = {42320776}, issn = {1872-7573}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plant Preparations/pharmacology ; Data Analytics ; }, abstract = {Multi-herb formulations, characterized by their complex synergistic compositions, are widely used in traditional medicine to modulate the gut microbiota. However, identifying reproducible herb-microbiota associations across disparate clinical settings remains a significant methodological challenge.<br><br>AIM OF THE STUDY: This study aims to systematically synthesize human clinical evidence to map the modulation patterns of multi-herb formulations on the gut microbiota and to identify the herbal components associated with reported directional microbial shifts.<br><br>MATERIALS AND METHODS: We conducted a systematic review and data-driven analysis of 29 clinical trials involving 954 participants in multi-herb formulation groups. To integrate findings from heterogeneous clinical settings, we employed a binarization strategy focused on statistically significant directional shifts (+1 for increase, -1 for decrease). An extreme gradient boosting (XGBoost) learning framework combined with SHapley Additive exPlanations (SHAP) was used to deconstruct these formulations and explore the predictive importance of individual constituents. To ensure the highest level of scientific integrity and prevent data leakage, the model's generalizability was rigorously validated using Leave-One-Study-Out (LOSO) cross-validation at the independent study level.<br><br>RESULTS: The LOSO validation yielded a mean accuracy of 0.84 and a macro F1-score of 0.42, indicating limited but informative cross-study pattern recognition despite the inherent heterogeneity of clinical data. Our analysis identified recurrent directional associations: formulas containing Scutellaria baicalensis Georgi were associated with reported reductions in genus-level taxa such as Escherichia-Shigella within neuropsychiatric disease contexts. Formulas containing Zingiber officinale Roscoe were associated with reported increases and decreases in selected genus-level taxa across heterogeneous disease contexts.<br><br>CONCLUSIONS: This study provides a comprehensive, evidence-based map of how multi-herb formulations modulate the human gut microbiota. By prioritizing rigorous validation and accounting for the complexity of synergistic preparations, we have identified hypothesis-generating patterns that transcend individual study variations. These findings provide a realistic foundation for future high-resolution metagenomic research and the development of standardized ethnopharmacological therapies.}, }
@article {pmid42321844, year = {2026}, author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H}, title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42321844}, issn = {1479-5876}, support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology/genetics/immunology ; *Lung Neoplasms/microbiology/pathology/genetics/immunology ; *Microbiota/genetics ; Neoplasm Staging ; Pilot Projects ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; ROC Curve ; Middle Aged ; Aged ; *Bronchoalveolar Lavage ; Bacteria/genetics ; }, abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.<br><br>METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.<br><br>RESULTS: Dokdonia (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;5.704) and Cocleimonas (q&#x2009;=&#x2009;0.026, LDA&#x2009;=&#x2009;5.329) were enriched in the early-stage group, whereas Barnesiella (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.784), Pedobacter (q&#x2009;=&#x2009;0.040, LDA&#x2009;=&#x2009;4.913) and unclassified Bacteroides (q&#x2009;=&#x2009;0.046, LDA&#x2009;=&#x2009;4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.926), rfaD (q&#x2009;<&#x2009;0.001, LDA&#x2009;=&#x2009;3.918), nudF (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;4.283) and sfsA (q&#x2009;=&#x2009;0.004, LDA&#x2009;=&#x2009;3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8&#x207a; T lymphocytes (q&#x2009;<&#x2009;0.001), whereas it showed a lower proportion of CD4&#x207a; T cells and a decreased CD4/CD8 ratio (q&#x2009;<&#x2009;0.001; q&#x2009;<&#x2009;0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q&#x2009;=&#x2009;0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.<br><br>CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.}, }
@article {pmid42323145, year = {2026}, author = {Zhang, S and Lv, H and Cui, B and Zhou, D}, title = {Low-substrate nitrogen drives functional succession toward a cooperative Candidatus Brocadia consortium in anammox systems.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135206}, doi = {10.1016/j.biortech.2026.135206}, pmid = {42323145}, issn = {1873-2976}, mesh = {*Nitrogen/metabolism/pharmacology ; *Microbial Consortia ; Bioreactors/microbiology ; *Bacteria/metabolism/genetics ; Oxidation-Reduction ; *Anaerobic Ammonia Oxidation ; }, abstract = {Mainstream anammox treatment is promising but limited by slow acclimation and unstable performance under low nitrogen. Community succession is often observed, but it is usually explained by kinetic differences among anammox bacteria, which cannot fully account for competitive outcomes. Here, we operated an anammox biofilter under sustained low‑nitrogen stress and combined metagenomics, metatranscriptomics, co‑occurrence networks, and SMETANA to identify ecological adaptation mechanisms. During early acclimation, Ca. Kuenenia reduced the expression of costly biosynthetic pathways, including aromatic amino acid synthesis by 25.6%-38.8%. In contrast, Ca. Brocadia showed broad transcriptional activation, with anammox genes upregulated by ∼18-fold. During long-term operation, the community shifted to a multispecies Ca. Brocadia assemblage characterized by complementary model-inferred auxotrophies, stronger positive associations around the dominant Brocadia species (68.0%), and lower predicted metabolic resource overlap than that observed in the high-nitrogen system (0.66 ± 0.12 vs. 0.77 ± 0.10). Ultimately, Ca. Brocadia replaced Ca. Kuenenia as the dominant functional lineage, increasing from 1.0% to 44.7% in relative abundance and contributing 71.5% of total transcriptional activity. These findings suggest that low-nitrogen stress favors a metabolically complementary and potentially cooperative Ca. Brocadia assemblage rather than a single superior competitor, offering ecological guidance for stabilizing anammox processes in low-strength wastewater.}, }
@article {pmid42323523, year = {2026}, author = {Hatwar, N and Qureshi, A}, title = {Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42323523}, issn = {1432-0991}, support = {UGC August 2021-Grant Number -191620062301//UGC/ ; }, mesh = {*Polyvinyl Chloride/metabolism/chemistry ; Biodegradation, Environmental ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/enzymology/isolation &amp; purification ; Composting ; *Microbiota ; Soil/chemistry ; *Plastics/metabolism ; }, abstract = {Polyvinyl chloride (PVC) plastic films accumulate in the environment and cause ecological damage due to their persistent, high-density polymeric nature. To mitigate PVC pollution, a sustainable bioremediation approach needs to be designed. Biodegradation of PVC using pure bacterial cultures has been reported as a sustainable option. However, PVC biodegradation studies in the presence of a soil/compost indigenous microbiome have not been conducted. In the present study, attempts have been made to understand and show the biodeterioration and biodegradation of PVC under soil and compost burial conditions. The study revealed that the PVC films, when buried under soil and compost at different conditions (ambient, sun-exposed, and 37 °C conditions), resulted in gravimetric weight loss with CO2 release. Under soil burial at 37 °C, PVC films showed 13.32 ± 0.10% weight reduction with 9.9 ± 0.9% CO2 evolution in 90 days, whereas compost conditions resulted in 6.89 ± 0.11% weight reduction. Another unique feature of the study is the metagenomic profiling of PVC buried soil/compost microbiomes, which revealed Proteobacteria and Actinobacteria as dominant phyla with Bacillus, Staphylococcus, Streptomyces, Arthrobacter, and Exiguobacterium as predominant genera. Also, the bioinformatics analysis revealed that these microbes possess potential metabolic capability associated with PVC biodeterioration and biodegradation (laccases, peroxidases, and oxidoreductases). Overall, the novelty reflects integrating metagenomic, spectroscopic, and morphological characterization of buried PVC plastic and linking microbial community dynamics with their enzymatic machinery and physico-chemical transformations of PVC. These multi-analytical approaches provided mechanistic evidence that the soil/compost microbial community initiates the PVC biodegradation process, offering a scientific basis for designing sustainable plastic waste management and remediation practices.}, }
@article {pmid42324270, year = {2026}, author = {Ma, Y and Yang, M and Xu, A and Zhao, X and Dong, X and Li, W and Tu, H and Guo, Y and Song, Z and Wu, X}, title = {Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42324270}, issn = {2055-5008}, support = {K20230085//Healthy Zhejiang One Million People Cohort/ ; 2020E10004//Zhejiang Key Laboratory of Intelligent Preventive Medicine/ ; 2019R01007//the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2020C03002//Cancer Center, Zhejiang University and Key Research and Development Program of Zhejiang Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Cross-Sectional Studies ; *Fatty Liver/microbiology/metabolism ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Adult ; Metagenome ; Metabolic Networks and Pathways ; }, abstract = {This cross-sectional study compared the gut microbiota between metabolic dysfunction associated steatotic liver disease (MASLD) patients and healthy controls. A total of 1401 participants, including 392 MASLD patients and 1009 healthy controls, were enrolled from one project site of the Healthy Zhejiang One Million People Cohort (HOPE) between January 2022 and June 2023. Shotgun metagenomic sequencing was conducted to compare the composition and functional profiles of the gut microbiome between MASLD patients and healthy controls. Compared to the control group, MASLD patients exhibited significant alterations in both alpha and beta diversity, along with reduced connectivity and robustness of the gut microbial network. We identified significant changes in the abundance of 12 microbial strains between the two groups with two strains (t_SGB4749 and t_SGB4753) enriched and ten strains depleted in MASLD patients. In comparison to the control group, MASLD patients demonstrated distinct differences in the genomic potential related to increased glycolysis, decreased pyruvate metabolism, and elevated lipopolysaccharide (LPS) biosynthesis in both metagenomic functional profiling and single-strain genome analysis. These findings suggest that alterations in specific microbial strains and metabolic pathways may contribute to MASLD pathogenesis.}, }
@article {pmid42324618, year = {2026}, author = {Hernandez, JB and Abiodun, M and Hayer, SS and Dickson, T and Ayayee, P and Clayton, JB}, title = {Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687925}, pmid = {42324618}, issn = {1949-0984}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Metagenome/drug effects ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Callithrix/microbiology ; Metagenomics ; Shotgun Sequencing ; Real-Time Polymerase Chain Reaction ; Genome, Bacterial ; Feces/microbiology ; }, abstract = {Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.}, }
@article {pmid42328867, year = {2026}, author = {Wang, Y and Sheng, P and Wang, S and Zhong, X and Cao, H and Li, D and Yan, J and Yang, J and Wang, Y and Peng, J and Sun, F and Wang, S and Feng, Y and Sun, J and Zhang, F}, title = {Gut microbiota translocation contributes to early islet apoptosis in streptozotocin-induced diabetes.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0017226}, pmid = {42328867}, issn = {2379-5077}, support = {2022YFF1100601//National Key Research and Development Program of China/ ; LCYJ202347//Wuxi Translational Medicine Research Institute/ ; 2023YFF1104305//National Key Research and Development Program of China/ ; 82370809//National Natural Science Foundation of China/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; BK20221204//Funding for Leading Talents in Medical and Health Profession in Wuxi Taihu Lake Talent Plan/ ; CXTD2021003//Key Discipline Construction Program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; HB2023063//Medical Key Discipline Program of Wuxi Health Commission/ ; }, mesh = {Animals ; *Apoptosis ; *Diabetes Mellitus, Experimental/pathology/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Mice ; *Islets of Langerhans/pathology/metabolism ; Male ; Fecal Microbiota Transplantation ; Streptozocin ; Intestinal Barrier Function ; *Bacterial Translocation ; Dysbiosis ; Mice, Inbred C57BL ; }, abstract = {Dysbiosis of the gut microbiota and impaired intestinal barrier are associated with diabetes development. The translocation of gut microbiota induced by streptozotocin (STZ) has been confirmed to damage pancreatic islets. However, it remains uncertain whether dysregulated gut microbiota plays an essential role in the translocation leading to pancreatic injury. In specific pathogen-free (SPF) and germ-free (GF) mice treated with STZ, we measured glucose metabolism levels, pancreatic islet damage, intestinal barrier integrity, and bacterial content in the pancreas to investigate the role of gut microbiota translocation in diabetes development. Shotgun metagenomic sequencing was used to analyze the impact of STZ on gut microbiota structure and function. Fecal microbiota transplantation was performed to explore if gut microbiota translocation depends on STZ-induced structural dysregulation. STZ induced intestinal damage in SPF mice, resulting in gut microbiota translocation to the pancreas, pancreatic apoptosis, and dysregulated glucose metabolism. Despite inherent intestinal barrier damage, absence of pancreatic apoptosis in GF mice further indicates that gut microbiota translocation is an essential prerequisite for STZ-induced pancreatic islet apoptosis. STZ significantly altered mouse gut microbiota composition and function. Transplantation of fecal microbiota from STZ-treated or saline-treated mice into STZ-induced GF mice also resulted in microbial translocation and pancreas apoptosis. Apoptosis of β cells in STZ-treated mice results from gut microbiota translocating to the pancreas through impaired intestinal barrier caused by STZ treatment independent of alterations in the gut microbial community.IMPORTANCEIn our study, the apoptosis of β cells in STZ-treated mice is the result of the translocation of gut microbiota to the pancreas through the impaired intestinal barrier induced by STZ, independent of alterations in the gut microbiota. These findings proposed the potential role of compounds in impairing the intestinal barrier integrity, promoting microbiota migration and finally damaging pancreatic islets.}, }
@article {pmid42328985, year = {2026}, author = {Pallotti, S and Nigro, ME and Albini, E and Russo, E and Carpi, FM and Falconi, M and Torbidoni-Baldassari, B and Giuliodori, AM and Petrelli, D and Beccacece, L and Pezzotti, G and Magistrali, CF and Massacci, FR and Napolioni, V}, title = {Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0156226}, pmid = {42328985}, issn = {2165-0497}, support = {RC 004/2022//Ministero della Salute/ ; }, mesh = {Abattoirs ; *Wastewater/microbiology ; Metagenomics ; *Microbiota/genetics ; Italy ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Animals ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota, along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation-flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.IMPORTANCEAntimicrobial resistance is a growing global health concern that extends beyond clinical settings into agricultural and environmental systems. Slaughterhouses represent critical interfaces where microbial communities from livestock, processing environments, and wastewater converge, creating opportunities for the persistence and dissemination of antimicrobial resistance genes. Despite the widespread use of physicochemical treatments to reduce organic load and suspended solids in slaughterhouse wastewater, their impact on microbial communities and resistome remains poorly characterized. By applying long-read metagenomic sequencing, this study provides a comprehensive characterization of the microbiome and resistome in slaughterhouse wastewater before and after treatment. Our findings show that commonly applied coagulation-flocculation treatments do not substantially alter the relative structure of microbial communities or the diversity of resistance genes. These results highlight the potential role of slaughterhouse wastewater as an environmental reservoir for antimicrobial resistance and emphasize the need for improved treatment technologies and systematic surveillance strategies to mitigate the environmental dissemination of resistance determinants in line with the One Health approach.}, }
@article {pmid42329047, year = {2026}, author = {Villanelo, SAR and Vestergaard, SZ and Liu, L and Yang, Y and Pedersen, IS and Nielsen, PH and Dueholm, MKD}, title = {Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0147726}, pmid = {42329047}, issn = {2165-0497}, support = {NNF22OC0071498//Novo Nordisk Fonden/ ; }, mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation &amp; purification/classification/genetics/drug effects ; Phylogeny ; DNA, Bacterial/genetics ; Wastewater/microbiology ; Microbiota/drug effects ; }, abstract = {The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation properties are essential for retaining active biomass while producing a clarified effluent. Understanding the microbial composition of AS and the functions of individual taxa is crucial for improving wastewater treatment practices and developing new treatment technologies. Although DNA-based studies have identified abundant taxa and inferred their metabolic roles, many of these organisms remain uncultured, limiting experimental validation of genome-based predictions. Here, we investigated whether antibiotics can transiently reduce community complexity and alleviate competitive exclusion during cultivation, thereby facilitating isolation of previously uncultured activated sludge bacteria. Dispersed single cells from AS were cultivated on agarose plates containing filter-sterilized AS fluid and 1 of 11 antibiotics at three concentrations. Full-length 16S rRNA gene amplicon sequencing indicated that antibiotics reduced microbial diversity and altered community composition in an antibiotic- and concentration-dependent manner. Two antibiotic conditions were selected for pure-culture isolation, resulting in 74 isolates that represented 28 different species based on genomic average nucleotide identity. These include 13 putatively novel species based on GTDB classification, and 19 species belonging to nine globally abundant AS core genera. Although several isolates belonged to genera with cultured representatives, they likely represent distinct species with potentially different ecological functions and physiological traits. These findings demonstrate that antibiotics can function as ecological selectors during cultivation and aid the targeted isolation of ecosystem-relevant activated sludge bacteria.IMPORTANCEBiological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.}, }
@article {pmid42330834, year = {2026}, author = {Cabrera, C and Carrión, N and Mateo, D and Heredia, L and Pino, M and Galvez, S and Forcadell-Ferreres, E and Vicens, P and Torrente, M}, title = {Shotgun metagenomic profiling of the gut microbiota in Parkinson's disease dementia and dementia with Lewy bodies.}, journal = {Parkinsonism &amp; related disorders}, volume = {149}, number = {}, pages = {108400}, doi = {10.1016/j.parkreldis.2026.108400}, pmid = {42330834}, issn = {1873-5126}, mesh = {Humans ; *Parkinson Disease/microbiology/complications/physiopathology ; Female ; Male ; *Lewy Body Disease/microbiology/physiopathology ; Aged ; Cross-Sectional Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Aged, 80 and over ; Case-Control Studies ; Metagenomics ; *Dementia/microbiology ; *Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are related α-synucleinopathies that share Lewy pathology, but they differ clinically. Increasing evidence links gut microbiota (GMB) dysbiosis and microbially derived metabolites to Parkinsonian disorders yet reported associations remain heterogeneous across cohorts and the Lewy body dementia syndromes are comparatively under characterized. This study integrated clinical characterization and GMB profiling in Parkinson's disease dementia (PDD), DLB, and healthy controls (HC) to identify shared and syndrome specific features, and to relate these patterns to cognitive, neuropsychiatric, and functional outcomes.<br><br>METHODS: The present cross-sectional case-control study in Spain included 76 adults aged 60 to 85 years (HC&#x202f;=&#x202f;38, PDD&#x202f;=&#x202f;27, DLB&#x202f;=&#x202f;11). Stool samples underwent shotgun metagenomic sequencing, with species-level taxonomic profiling using Kraken2. Community diversity was assessed using observed species and Chao1 richness, Shannon alpha diversity, and Bray-Curtis dissimilarity for beta diversity. LEfSe and multivariate linear modeling with MaAsLin2 were performed to identify GMB species associated with PDD and DLB and their clinical correlates.<br><br>RESULTS: PDD showed higher richness compared with HC. Shannon alpha diversity did not differ between groups. Bray-Curtis differed by separation of HC from both PDD and DLB, with no significant difference between Lewy body dementia syndromes. LEfSe identified 19 significantly differential taxa. Furthermore, several taxa showed significant multivariable associations with clinical outcomes.<br><br>CONCLUSIONS: PDD and DLB shared a broadly similar GMB alteration away from HC, with multivariable associations between several taxa and clinical outcomes. Longitudinal and functional studies are needed to clarify causality and biomarker potential.}, }
@article {pmid42331262, year = {2026}, author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R}, title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.}, journal = {Genomics}, volume = {118}, number = {4}, pages = {111282}, doi = {10.1016/j.ygeno.2026.111282}, pmid = {42331262}, issn = {1089-8646}, mesh = {Humans ; *Cholesteatoma/microbiology ; *Ear Canal/microbiology/pathology ; Metagenomics ; *Microbiota ; *Metagenome ; Actinobacteria/genetics/isolation &amp; purification ; Bacillota/genetics/isolation &amp; purification ; Proteobacteria/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.<br><br>METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.<br><br>RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).<br><br>CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.}, }
@article {pmid42335476, year = {2026}, author = {Valentino, V and De Filippis, F and Ercolini, D}, title = {Fermented foods: lessons learned from metagenomics.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103545}, doi = {10.1016/j.copbio.2026.103545}, pmid = {42335476}, issn = {1879-0429}, mesh = {*Metagenomics/methods ; *Fermented Foods/microbiology ; *Food Microbiology ; Fermentation ; Microbiota ; Multiomics ; Probiotics ; }, abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.}, }
@article {pmid42335503, year = {2026}, author = {Liu, LM and Fang, HB and Wang, YF and Zhang, YL and Yu, QQ and Zhang, WY and Liu, J and Miao, H and Zhao, YY}, title = {Niaoduqing particles ameliorated tubulointerstitial fibrosis by suppressing IκB/NF-κB signalling pathway via inhibiting host- and gut microbiota-mediated tryptophan co-metabolism.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128592}, doi = {10.1016/j.micres.2026.128592}, pmid = {42335503}, issn = {1618-0623}, mesh = {Animals ; *Signal Transduction/drug effects ; Rats ; *Tryptophan/metabolism ; *NF-kappa B/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Fibrosis/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Rats, Sprague-Dawley ; Disease Models, Animal ; *I-kappa B Proteins/metabolism ; Bacteria/classification/genetics/drug effects ; Renal Insufficiency, Chronic/drug therapy ; Metabolomics ; Feces/microbiology ; Ureteral Obstruction ; }, abstract = {Tubulointerstitial fibrosis (TIF) is an inevitable outcome of progressive chronic kidney disease (CKD). Niaoduqing particles (NDQ) were developed for the treatment of CKD. However, the molecular mechanisms underlying the effect of NDQ on TIF remain unclear. Fecal gut microbiota (GM) and serum metabolites were analyzed using metagenomics and metabolomics in unilateral ureteral obstruction (UUO)-induced TIF rats. NDQ treatment attenuated UUO-induced TIF in rats in a dose- and time-dependent manner. The increased abundance of eight pathogenic bacteria, including Bacillus wiedmannii, Enterococcus mundtii and Fusobacterium varium, showed strong positive correlations with TID scores, whereas the reduced abundance of two probiotic bacteria, Ruminococcus flavefaciens and Clostridium celatum, showed strong negative correlations with tubulointerstitial damage (TID) scores. NDQ treatment reversed these aberrant microbial alterations, indicating its capacity to remodel GM dysbiosis. TID scores were strongly correlated with host- and GM-mediated tryptophan co-metabolites, including indoxyl sulfate, tryptamine and indole-3-acetic acid, in both TIF- and NDQ-treated TIF rats, and NDQ intervention normalized these metabolic disturbances. Notably, Fusobacterium varium and Enterococcus faecium exhibited strong linear correlations with indoxyl sulfate, indole-3-acetic acid, and indole-3-aldehyde in the TIF rat model. Furthermore, NDQ suppressed IκB/NF-κB signaling pathway in both TIF rats and TGF-β1-induced NRK-52E cells. These inhibitory effects were partially reversed by NF-κB p65 knockdown. This study is the first to demonstrate that NDQ alleviates TIF by reshaping microbial dysbiosis and modulating host- and GM-mediated tryptophan metabolism. These findings support that NDQ mitigates TIF by suppressing IκB/NF-κB signaling pathway through regulation of host-microbiota-derived tryptophan metabolism.}, }
@article {pmid42335822, year = {2026}, author = {He, T and Liu, J and Li, Y and Ohgami, N and Wei, X and Peng, T and Zhang, X and Zhang, R and Du, J and Deng, Y and Jiang, H and Zhang, P and Zhang, Y}, title = {Long-term groundwater arsenic exposure is associated with altered arsenic methylation capacity and gut microbiota composition in a rural Chinese population.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142658}, doi = {10.1016/j.jhazmat.2026.142658}, pmid = {42335822}, issn = {1873-3336}, mesh = {Humans ; *Arsenic/urine/toxicity/metabolism/analysis ; *Groundwater/chemistry ; China ; Methylation ; *Water Pollutants, Chemical/urine/toxicity/metabolism/analysis ; Adult ; *Gastrointestinal Microbiome/drug effects ; Female ; Rural Population ; Male ; *Environmental Exposure/analysis ; Middle Aged ; Feces/microbiology ; Bacteria ; East Asian People ; }, abstract = {This study investigated the relationship between long-term groundwater arsenic exposure, arsenic methylation capacity, and gut microbiota in adults from rural northern China. Arsenic detoxification relies in part on methylation processes, and growing evidence suggests that the gut microbiome may participate in arsenic biotransformation, yet population-based data integrating exposure, metabolism, and microbial profiles remain scarce. We recruited 258 participants from two neighboring villages supplied by centralized wells with contrasting arsenic levels (control, n = 138; exposure, n = 120). Total urinary arsenic was measured in all participants, and arsenic species were quantified in a subgroup (n = 60) to derive primary and secondary methylation indices (PMI and SMI). Fecal metagenomes were sequenced to characterize taxonomic composition and functional potential based on KEGG and GO annotations. Individuals in the exposure village showed higher levels of urinary inorganic arsenic and methylated metabolites. While PMI was comparable between groups, SMI was significantly reduced among exposed individuals, indicating impaired secondary methylation. Arsenic exposure was also associated with pronounced alterations in gut microbial diversity and community structure. Several anaerobic taxa, largely linked to fermentative metabolism, were positively associated with SMI after multivariable adjustment. Functional analyses further revealed differences in pathways related to transport, environmental sensing, and metabolism. These findings suggest that chronic arsenic exposure is associated with reduced methylation efficiency and shifts in gut microbial composition and function, and that the gut microbiome may contribute to interindividual variability in arsenic metabolism and toxicity.}, }
@article {pmid42337243, year = {2026}, author = {Hoskinson, C and Dai, DLY and Petersen, C and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Turvey, SE}, title = {Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42337243}, issn = {2041-1723}, support = {[274CHI] and [EC1-144621]//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; [274CHI] and [EC1-144621]//AllerGen (AllerGen National Center of Excellence)/ ; [274CHI] and [EC1-144621]//Genome Canada (G&#xe9;nome Canada)/ ; }, mesh = {Humans ; *Malassezia/genetics/isolation &amp; purification/physiology ; Infant ; Feces/microbiology ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Mycobiome ; Male ; Female ; Child, Preschool ; *Food Hypersensitivity/microbiology/immunology ; Child ; Metagenome ; Metagenomics ; *Hypersensitivity/microbiology ; }, abstract = {While early-life gut bacterial microbiota maturation has been well studied and linked to childhood disease, the development of the gut mycobiome remains poorly understood. Few studies have defined fungal succession in infancy, and even fewer have integrated fungal and bacterial maturation, allowing interkingdom analysis within the same individuals. In this study, we analyzed a subset of the CHILD Study Cohort (n = 1409 participants) and generated both ITS2 amplicon and shotgun metagenomic sequencing data from infant stool samples (n = 2256 samples). We hypothesized that the infant mycobiome follows predictable developmental trajectories that influence childhood health outcomes. We found that fungi are reliable biomarkers for gut maturation, with the notable emergence of Saccharomyces and Malassezia as some of the strongest indicators across both fungi and bacteria. Fungal composition was strongly associated with infant age (R = 0.79, p < 0.001) and with the later development of both atopic dermatitis (adj. p = 0.029) and food allergy (adj. p = 0.013). Further, differences in fungal development coincided with changes in key gut immune-modulating metabolites such as butyrate and glycerol, indicating the functional importance of infant gut mycobiome maturation in early-life immune development. Together, these results highlight the early life mycobiome as a potential therapeutic target to mitigate allergic disease development.}, }
@article {pmid42338488, year = {2026}, author = {Chen, B and Chen, J and Feng, Z and Lv, H and Lin, Q and Jiang, G}, title = {Gut microbiota reconstruction after liver transplantation and its association with early postoperative infections in patients with liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1845273}, pmid = {42338488}, issn = {2235-2988}, mesh = {Humans ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Retrospective Studies ; *Postoperative Complications/microbiology ; Dysbiosis/microbiology ; Male ; *Liver Failure/surgery/complications ; Probiotics/administration &amp; dosage/therapeutic use ; Middle Aged ; Metagenomics ; Feces/microbiology ; Adult ; *Bacterial Infections/microbiology/epidemiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Postoperative infection remains a major cause of morbidity after liver transplantation (LT) in patients with liver failure. Increasing evidence suggests that gut microbiota dysbiosis may contribute to infection risk, but its dynamic changes after LT are not fully understood.<br><br>METHODS: This retrospective study included 60 patients with liver failure who underwent LT and developed postoperative infection-related risk. Patients were divided into a probiotic group and a non-probiotic group. Fecal samples were collected before transplantation and on postoperative days 7, 14, 21, and 28. Metagenomic sequencing was performed to analyze gut microbial composition, diversity, and antibiotic resistance genes.<br><br>RESULTS: The probiotic group showed a significantly lower rate of postoperative bacterial infection, especially intra-abdominal infection. After LT, gut microbiota gradually recovered in both groups, but restoration was faster in the probiotic group. The non-probiotic group showed persistent dysbiosis, characterized by enrichment of opportunistic pathogens such as Enterococcus and Klebsiella, whereas beneficial genera including Bifidobacterium and Lactobacillus were more abundant in the probiotic group. Antibiotic resistance genes were also more enriched in the non-probiotic group.<br><br>CONCLUSION: Early postoperative gut microbiota reconstruction is closely associated with infectious complications after LT, and modulation of gut microbiota may help improve postoperative outcomes.}, }
@article {pmid42338489, year = {2026}, author = {Tang, C and Li, B and Chen, J and Liu, X and She, C}, title = {Causal relationship between gut microbiota and adenomyosis: metagenomics sequencing and Mendelian randomization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1772864}, pmid = {42338489}, issn = {2235-2988}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Adenomyosis/microbiology/etiology ; *Mendelian Randomization Analysis ; *Metagenomics/methods ; Middle Aged ; Adult ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in the pathogenesis of adenomyosis (AM); however, whether this association is causal and through which mechanisms it operates remain largely unknown.<br><br>METHODS: To interrogate potential causal relationships, we performed a two-sample Mendelian randomization (MR) analysis leveraging inverse-variance weighting (IVW) as the primary estimator, complemented by MR-Egger, weighted median, and weighted mode approaches, to evaluate the causal effects of gut microbial taxa and microbiota-derived metabolic pathways on AM. We further conducted mediation analyzes to delineate the role of circulating immune-cell phenotypes in this process. In parallel, in an independent clinical cohort, 22 patients with AM and 23 age-matched healthy controls recruited from the health-screening center of our institution were enrolled according to stringent inclusion and exclusion criteria (including antibiotic-use history and long-term local residency) and subjected to shotgun metagenomic sequencing. Significant differences in the types of bacterial communities were observed between the AM group and the control group. Subsequently, the results were cross-compared with those of the MR study using the Linear Discriminant Analysis Effect Size (LEfSe) method, and further verified using the ANCOM-BC method to determine the common microbial characteristics.<br><br>RESULTS: MR analysis identified ten microbial taxa and ten metabolic pathways with evidence of potential causal associations with AM. Of these, nine taxa and five pathways were associated with a reduced risk of AM, including Alistipes indistinctus (OR&#xa0;=&#xa0;0.847, 95% CI&#xa0;=&#xa0;0.754-0.951, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), Ruminococcus torques (OR&#xa0;=&#xa0;0.818, 95% CI&#xa0;=&#xa0;0.712-0.941, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), class Deltaproteobacteria (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), family Desulfovibrionaceae (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), order Desulfovibrionales (OR&#xa0;=&#xa0;0.780, 95% CI&#xa0;=&#xa0;0.629-0.967, p&#xa0;=&#xa0;0.024, p~FDR~ > 0.05), Parasutterella excrementihominis (OR&#xa0;=&#xa0;0.875, 95% CI&#xa0;=&#xa0;0.784-0.977, p&#xa0;=&#xa0;0.017, p~FDR~ > 0.05), Ruminococcus bromii (OR&#xa0;=&#xa0;0.836, 95% CI&#xa0;=&#xa0;0.718-0.972, p&#xa0;=&#xa0;0.020, p~FDR~ > 0.05), Bacteroides finegoldii (OR&#xa0;=&#xa0;0.919, 95% CI&#xa0;=&#xa0;0.855-0.987, p&#xa0;=&#xa0;0.020, p~FDR~ > 0.05), and the genus Parasutterella (OR&#xa0;=&#xa0;0.886, 95% CI&#xa0;=&#xa0;0.797-0.986, p&#xa0;=&#xa0;0.026, p~FDR~ > 0.05); the five protective pathways comprised dTDP-L-rhamnose biosynthesis (OR&#xa0;=&#xa0;0.819, 95% CI&#xa0;=&#xa0;0.674-0.995, p&#xa0;=&#xa0;0.045, p~FDR~ > 0.05), lactose and galactose degradation (OR&#xa0;=&#xa0;0.818, 95% CI&#xa0;=&#xa0;0.689-0.972, p&#xa0;=&#xa0;0.022, p~FDR~ > 0.05), the reductive TCA cycle (OR&#xa0;=&#xa0;0.919, 95% CI&#xa0;=&#xa0;0.851-0.993, p&#xa0;=&#xa0;0.032, p~FDR~ > 0.05), allantoin degradation to glyoxylate (OR&#xa0;=&#xa0;0.907, 95% CI&#xa0;=&#xa0;0.830-0.991, p&#xa0;=&#xa0;0.030, p~FDR~ > 0.05), and glycolysis I (from glucose-6-phosphate) (OR&#xa0;=&#xa0;0.850, 95% CI&#xa0;=&#xa0;0.747-0.967, p&#xa0;=&#xa0;0.013, p~FDR~ > 0.05).Conversely, one taxon and five pathways were associated with an increased risk of AM: the genus Lactobacillus (OR&#xa0;=&#xa0;1.083, 95% CI&#xa0;=&#xa0;1.008-1.164, p&#xa0;=&#xa0;0.030, p~FDR~ > 0.05), degradation of glucose and glucose-1-phosphate (OR&#xa0;=&#xa0;1.202, 95% CI&#xa0;=&#xa0;1.056-1.369, p&#xa0;=&#xa0;0.005, p~FDR~ > 0.05), peptidoglycan biosynthesis (in Enterococcus faecium) (OR&#xa0;=&#xa0;1.138, 95% CI&#xa0;=&#xa0;1.007-1.285, p&#xa0;=&#xa0;0.039, p~FDR~ > 0.05), pyruvate fermentation to acetone (OR&#xa0;=&#xa0;1.118, 95% CI&#xa0;=&#xa0;1.001-1.248, p&#xa0;=&#xa0;0.048, p~FDR~ > 0.05), glycerol degradation to butanol (OR&#xa0;=&#xa0;1.118, 95% CI&#xa0;=&#xa0;1.011-1.237, p&#xa0;=&#xa0;0.031, p~FDR~ > 0.05), and de novo pyrimidine deoxyribonucleotide biosynthesis (OR&#xa0;=&#xa0;1.216, 95% CI&#xa0;=&#xa0;1.063-1.390, p&#xa0;=&#xa0;0.004, p~FDR~ > 0.05).Mediation analysis revealed that the immune phenotype "CD24 on CD24[+]CD27[+] B cells" mediated the pathway from Ruminococcus bromii to AM, accounting for 32.91% of the total effect (p&#xa0;=&#xa0;0.020).Shotgun metagenomic profiling of the clinical cohort demonstrated no significant differences in &#x3b1;-diversity or &#x3b2;-diversity between the AM and control groups. At the phylum level, the relative abundance of Desulfobacterota was significantly decreased in the AM group (p<&#xa0;0.05), and at the genus level, Alistipes was similarly reduced (p<&#xa0;0.05). LEfSe analysis further indicated enrichment of Escherichia and Clostridium in the AM group, whereas Desulfobacterota and Rikenellaceae were enriched in the Control group. Matching the aforementioned results with the Mendelian randomization (MR) outcomes revealed that Desulfovibrionales and Desulfovibrionaceae constituted the shared microbial taxa. This finding was subsequently re-validated and confirmed using the ANCOM-BC method.<br><br>CONCLUSIONS: Integrating genetic causal inference with clinical metagenomic validation, this study provides convergent evidence that specific gut microbial taxa, their associated metabolic pathways, and immune-cell-mediated mechanisms may be causally implicated in the development of AM. These findings offer a framework for future microbiota-targeted preventive and therapeutic strategies against AM.}, }
@article {pmid42340399, year = {2026}, author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA}, title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42340399}, issn = {1432-184X}, mesh = {*Groundwater/virology/microbiology ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Metagenomics ; *Virome ; Genome, Viral ; *Bacteria/virology/genetics/classification ; Microbiota ; Phylogeny ; Ecosystem ; }, abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.}, }
@article {pmid42341025, year = {2026}, author = {Wohl, DL and Belder, PT and Mitchell, BD}, title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350558}, pmid = {42341025}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; }, abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.}, }
@article {pmid42341424, year = {2026}, author = {Tsuboi, I and Inoue, S and Hirayama, T and Mitsui, Y and Watanabe, M and Hirakawa, H and Sadahira, T}, title = {Gut, vaginal, and urinary microbiome alterations in women with genitourinary syndrome of menopause: A systematic review.}, journal = {Maturitas}, volume = {211}, number = {}, pages = {109031}, doi = {10.1016/j.maturitas.2026.109031}, pmid = {42341424}, issn = {1873-4111}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota ; Syndrome ; *Female Urogenital Diseases/microbiology ; *Menopause ; *Gastrointestinal Microbiome ; *Urinary Tract/microbiology ; Lactobacillus ; *Urine/microbiology ; }, abstract = {BACKGROUND AND OBJECTIVE: Genitourinary syndrome of menopause (GSM) is a chronic condition caused by estrogen deficiency, encompassing vaginal dryness, dyspareunia, and urinary symptoms. Alterations in the vaginal, urinary, and gut microbiome may contribute to GSM pathophysiology. We synthesize the evidence on microbiome composition and diversity across these compartments in postmenopausal women with GSM.<br><br>METHODS: PubMed, Scopus, and Embase were searched from inception to April 2026 for studies assessing the microbiome in postmenopausal women with GSM using 16S rRNA gene sequencing, metagenomics, or culture-based methods.<br><br>RESULTS: Twenty-three studies (5027 participants) were included: 15 examined the vaginal microbiome, seven the urinary microbiome, and one the gut microbiome. Postmenopausal women consistently showed reduced Lactobacillus abundance and increased microbial diversity. Estrogen therapy partially restored Lactobacillus dominance but did not uniformly improve symptoms. In the SWAN cohort (n&#xa0;=&#xa0;1320), sexual pain was the only GSM symptom independently associated with a specific community state type (CST IV-C1; OR 2.26, 95% CI 1.20-4.23). Specific species showed associations with distinct symptom domains: Prevotella with urinary symptoms, Finegoldia magna with recurrent urinary tract infection, and Streptococcus with sexual pain. Parallel Lactobacillus depletion and pathobiont enrichment across all three compartments pointed toward a vaginal-bladder-gut axis, potentially linked through estrobolome disruption and bacterial translocation.<br><br>CONCLUSION: The postmenopausal genitourinary microbiome is characterized by Lactobacillus depletion and increased diversity, but microbiome restoration alone does not predict symptom resolution. The shared microbial alterations across compartments suggest a vaginal-bladder-gut axis that may collectively drive GSM, but this requires multi-compartment longitudinal validation. PROSPERO registration: CRD420261335478.}, }
@article {pmid42341885, year = {2026}, author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L}, title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.}, journal = {Diabetes research and clinical practice}, volume = {238}, number = {}, pages = {113373}, doi = {10.1016/j.diabres.2026.113373}, pmid = {42341885}, issn = {1872-8227}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Atherosclerosis/epidemiology ; *Blood Glucose/metabolism ; Continuous Glucose Monitoring ; *Diabetes Mellitus, Type 1/blood/microbiology/complications/epidemiology ; *Dyslipidemias/epidemiology/blood/etiology ; *Fast Foods/adverse effects ; Food, Processed ; *Gastrointestinal Microbiome/physiology ; Glycated Hemoglobin/metabolism ; *Glycemic Control ; Italy/epidemiology ; }, abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).<br><br>METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n&#xa0;=&#xa0;103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.<br><br>RESULTS: Mean UPF intake was 15.5&#xa0;% of total food intake. Higher UPF intake was independently associated with higher triglycerides (&#x3b2; per 20&#xa0;g/1000&#xa0;kcal&#xa0;=&#xa0;3.62&#xa0;mg/dL; 95&#xa0;%CI 1.16-6.08) and lower HDL-cholesterol (&#x3b2;&#xa0;=&#xa0;&#xa0;-&#xa0;0.98&#xa0;mg/dL; 95&#xa0;%CI&#xa0;-&#xa0;1.72 to&#xa0;-&#xa0;0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).<br><br>CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.}, }
@article {pmid42342731, year = {2026}, author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H}, title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42342731}, issn = {2055-5008}, support = {100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 100572058//S&#xe4;chsische Aufbaubank/ ; 323134//Norges Forskningsr&#xe5;d/ ; 323134//Norges Forskningsr&#xe5;d/ ; }, mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.}, }
@article {pmid42343233, year = {2026}, author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM}, title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690689}, pmid = {42343233}, issn = {1949-0984}, mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration &amp; dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; }, abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.}, }
@article {pmid42343457, year = {2026}, author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X}, title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42343457}, issn = {2049-2618}, mesh = {*Populus/microbiology/growth &amp; development/metabolism ; *Rhizosphere ; *Microbiota ; *Carbon/metabolism ; Soil Microbiology ; *Phosphorus/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics ; Plant Roots/microbiology ; Soil/chemistry ; }, abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.<br><br>RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and&#x200b; a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in&#x200b; stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.<br><br>CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.}, }
@article {pmid42343765, year = {2026}, author = {Qiu, X and Lei, Z and Wang, J}, title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {42}, number = {5}, pages = {2103-2113}, doi = {10.13345/j.cjb.250783}, pmid = {42343765}, issn = {1872-2075}, support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; }, mesh = {*Solanum lycopersicum/growth &amp; development/drug effects ; *Plant Roots/growth &amp; development/drug effects ; *Seedlings/growth &amp; development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; }, abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.}, }
@article {pmid42346116, year = {2026}, author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M}, title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.}, journal = {Cells}, volume = {15}, number = {12}, pages = {}, pmid = {42346116}, issn = {2073-4409}, support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; }, mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; }, abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.}, }
@article {pmid42346775, year = {2026}, author = {He, Z and Nie, Y and Li, C and Sun, G and Zheng, W and Liu, H and Geng, M and Tian, J and Zhang, Y}, title = {GV-971 Ameliorates Chronic Restraint Stress-Induced Depression-like Phenotypes Accompanied by Reshaping of the Microbiota-Gut-Brain Axis.}, journal = {Marine drugs}, volume = {24}, number = {6}, pages = {}, pmid = {42346775}, issn = {1660-3397}, support = {2024CXPT029, 2025CXPT011//Key R&amp;D Program of Shandong Province, China/ ; ZR2024QH615//Shandong Provincial Natural Science Foundation/ ; SYS202205//Shandong Laboratory Program/ ; }, mesh = {Animals ; *Depression/drug therapy/etiology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Brain-Gut Axis/drug effects ; *Oligosaccharides/pharmacology ; Restraint, Physical ; Disease Models, Animal ; *Antidepressive Agents/pharmacology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; Phenotype ; Hippocampus/drug effects/metabolism ; Intestinal Barrier Function ; }, abstract = {Depression is increasingly linked to microbiota-gut-brain axis dysfunction, yet current monoaminergic antidepressants show limited efficacy. This study investigated the therapeutic potential and underlying mechanisms of GV-971, a marine-derived oligosaccharide, in a chronic restraint stress (CRS) mouse model. We first established that 8 h of daily restraint for 4-8 weeks induces a stable depression-like phenotype characterized by behavioral despair and significant reduction in peripheral monoamine neurotransmitters (5-HT and norepinephrine). GV-971 treatment robustly attenuated CRS-induced depression- and anxiety-like behaviors, restored hippocampal serotonin levels, reduced elevated plasma corticosterone concentrations, and ameliorated CRS-induced adrenal cortical hyperplasia. Mechanistically, GV-971 significantly suppressed neuroinflammation by inhibiting microglial hyperactivation in the prefrontal cortex and hippocampus. Concurrently, it repaired intestinal barrier dysfunction, evidenced by reduced permeability, restored mucosal integrity, and recovered goblet cell numbers. Crucially, integrated shot-gun metagenomics and plasma metabolomics revealed that GV-971 not only reshaped microbial taxonomy but also functionally recalibrated the gut ecosystem. It enriched beneficial taxa (e.g., Bifidobacterium pseudolongum, Bacteroides uniformis) and specific metabolic pathways, leading to increased short-chain fatty acids (valeric and caproic acids) and a significant reduction in plasma levels of tryptophan-kynurenine pathway metabolites, specifically the neurotoxic compounds kynurenine and quinolinic acid. Fecal microbiota transplantation (FMT) from GV-971-treated donors partially recapitulated the antidepressant and gut-protective effects in CRS recipients, confirming a causal role for the remodeled microbiota. Collectively, GV-971 exerts antidepressant effects by coordinately remodeling the gut microbiota, normalizing tryptophan and SCFA metabolism, restoring gut barrier integrity, and dampening central neuroinflammation, supporting its potential as a novel gut-brain axis-targeted therapy for depression.}, }
@article {pmid42347203, year = {2026}, author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ}, title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {42347203}, issn = {2076-0817}, mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration &amp; dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration &amp; dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration &amp; dosage ; }, abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.}, }
@article {pmid42347906, year = {2026}, author = {Liu, Y and Lin, H and Zhu, M and Chen, X and Yu, Z and Peng, D and Dong, G and Ni, Y and Fu, J}, title = {Gut microbiota dysbiosis and short-chain fatty acid alterations in pediatric new-onset type 1 diabetes with ketoacidosis.}, journal = {Journal of endocrinological investigation}, volume = {49}, number = {9}, pages = {2555-2569}, pmid = {42347906}, issn = {1720-8386}, support = {2023C03047//Key Research and Development Program of Zhejiang Province/ ; 2021YFC2701900//Key Technologies Research and Development Program/ ; 82370863//National Natural Science Foundation of China/ ; 82502105//National Natural Science Foundation of China/ ; LKLY25H180005//Natural Science Foundation of Zhejiang Province/ ; LQN25H040005//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 1/complications/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Dysbiosis/metabolism/microbiology/etiology/diagnosis ; Female ; *Diabetic Ketoacidosis/metabolism/microbiology/etiology ; Male ; *Gastrointestinal Microbiome ; Child ; Feces/microbiology/chemistry ; Adolescent ; Prognosis ; Follow-Up Studies ; Biomarkers/analysis ; Child, Preschool ; }, abstract = {PURPOSE: Diabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication in children with type 1 diabetes (T1D) and remains associated with considerable morbidity and mortality. Although gut dysbiosis has been reported in newly diagnosed T1D, the gut microbiota and microbial metabolites during DKA onset remain poorly characterized.<br><br>METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 96 newly diagnosed T1D children, including 32 presenting with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative and correlation analyses were conducted to explore differences in gut microbial composition, SCFA levels, and their association with clinical indicators of DKA severity.<br><br>RESULTS: Children with DKA exhibited distinct gut microbial compositions, with marked &#x3b2;-diversity separation from non-DKA individuals. The DKA group was characterized by an enrichment of potential pathogens and a significant depletion of SCFA-producing genera, including Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus. Correspondingly, fecal SCFA levels were significantly reduced in the DKA group. Moreover, SCFAs and their producing bacteria were strongly correlated with clinical indices of DKA severity. Mediation analysis suggested that reductions in SCFAs, particularly propionic acid and butyric acid, were associated with metabolic alterations linking SCFA-producing bacteria to DKA.<br><br>CONCLUSION: This study provides a comprehensive characterization of gut microbiota and SCFA alterations in T1D children at DKA onset. The depletion of SCFA-producing bacteria and their metabolites reflects metabolic disturbances associated with DKA, and highlights SCFAs and their producers as candidate metabolic features warranting further validation as biomarkers and therapeutic targets.}, }
@article {pmid42348335, year = {2026}, author = {Biswa, BB and Mori, H and Toyoda, A and Fujiwara, K and Kurokawa, K and Koide, T}, title = {Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {33}, number = {3}, pages = {}, pmid = {42348335}, issn = {1756-1663}, support = {JPMJSP2104//JST/ ; 19KK0177//JSPS/ ; 24K01951//JSPS/ ; //Research Organization of Information and Systems/ ; }, mesh = {Animals ; Male ; Female ; *Limosilactobacillus reuteri/isolation &amp; purification/genetics ; Mice ; Oxytocin/blood ; *Behavior, Animal ; *Gastrointestinal Microbiome ; Feces/microbiology ; Selective Breeding ; Pyruvic Acid/blood ; }, abstract = {Domestication alters animal behaviour, particularly tameness. We previously established 2 tamed mouse groups by selective breeding for active tameness-defined as the motivation to approach a human hand-from genetically heterogeneous wild-derived mouse stock, together with 2 nonselected control groups. Genetic analyses identified loci associated with active tameness, but their low heritability suggested contributions from nongenetic factors. We therefore hypothesized that the gut microbiota, which has been shown to influence brain function, contributes to behavioural changes associated with active tameness. To test this hypothesis, we conducted shotgun metagenomic analyses of faecal samples from 10 males and 10 females (80 individuals total) from the 2 tamed and 2 nonselected groups. Tamed mice exhibited markedly higher levels of active tameness, accompanied by elevated blood concentrations of oxytocin and pyruvate. While overall taxonomic and functional diversity of the gut microbiota was largely unchanged, the abundance of Limosilactobacillus reuteri was significantly increased in the tamed mice. Administration of a pyruvate-secreting L. reuteri strain to nonselected mice elevated blood oxytocin levels and enhanced active tameness, although plasma pyruvate levels were not increased. These findings suggest that L. reuteri is associated with behavioural modulation, potentially via oxytocin-related pathways, and provide mechanistic insight into microbial contributions to animal domestication.}, }
@article {pmid42348560, year = {2026}, author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S}, title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0352336}, pmid = {42348560}, issn = {1932-6203}, mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; }, abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.}, }
@article {pmid42349523, year = {2026}, author = {Muqaddas, K and Mahnoor,  and Hayat, O and Islam, A and Khan, R and Naz, S}, title = {Cutaneous leishmaniasis promotes skin microbial dysbiosis and exacerbation of local inflammatory responses.}, journal = {Microbial pathogenesis}, volume = {218}, number = {}, pages = {108655}, doi = {10.1016/j.micpath.2026.108655}, pmid = {42349523}, issn = {1096-1208}, mesh = {Humans ; *Leishmaniasis, Cutaneous/pathology/microbiology/parasitology ; Skin Microbiome ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Female ; *Skin/microbiology/pathology/parasitology ; *Bacteria/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Leishmania tropica/isolation &amp; purification/genetics ; DNA, Bacterial/genetics/chemistry ; *Inflammation/pathology ; Microbiota ; Adult ; DNA, Ribosomal Spacer/genetics/chemistry ; Phylogeny ; }, abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.}, }
@article {pmid42350342, year = {2026}, author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T}, title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].}, journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology}, volume = {42}, number = {6}, pages = {499-510}, pmid = {42350342}, issn = {1007-8738}, mesh = {Animals ; *HLA-B27 Antigen/genetics/metabolism ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/genetics/metabolism ; Mice, Transgenic ; Humans ; Mice ; *Inflammation ; Female ; Dextran Sulfate ; }, abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.}, }
@article {pmid42352268, year = {2026}, author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE}, title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, pmid = {42352268}, issn = {2218-273X}, mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; }, abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.}, }
@article {pmid42352384, year = {2026}, author = {Brown, JL and Mahadevan, P and Middlebrooks, M}, title = {Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea Slug Elysia papillosa.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, pmid = {42352384}, issn = {2218-273X}, support = {OURI//University of Tampa/ ; }, mesh = {Animals ; *Gastropoda/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Phylogeny ; }, abstract = {Certain sacoglossan sea slugs, often known as "solar-powered sea slugs", are a group of marine gastropods that have the unique ability to photosynthesize by stealing functional chloroplasts from algae. The sacoglossan Elysia papillosa can maintain functional chloroplasts for up to two weeks after feeding. The microbiome of these slugs may play a crucial role in their metabolism, immunity, development, but more importantly their photosynthesis. Shotgun metagenomic sequencing was conducted on four samples of E. papillosa in order to characterize their microbiome. Sequences were classified and relative abundance was quantified with Centrifuger and functional data was examined using SqueezeMeta. Bacteria were analyzed by taxonomic groups and hypothesized function to the sea slug was determined with literature analysis. All samples were dominated by phyla Actinomycetota, Bacillota, Patescibacteriota, and Pseudomonadota. The presence of the phyla Bacteroidota and Bacillota was notable in all samples, which contain species known to produce enzymes that break down polysaccharides. It is possible that these bacteria could assist in degradation of the polysaccharide xylan found in the cell walls of Penicillus, the algal food source of E. papillosa. One species that was found in all samples was Cutibacterium acnes which has been shown to be an important component of the gut microbiota in other marine invertebrates and may provide the host with vitamin B12 and other beneficial nutrients. Many of these bacteria may be opportunistic rather than commensal. As a result, more research is required to describe the interactions between the slug and its microbiome, but this preliminary report provides a valuable starting point for identifying the microbiome make-up to further understanding of these relationships.}, }
@article {pmid42353029, year = {2026}, author = {Xu, HJ and Liu, QL and Zhang, YF and Cuan, SN and Jia, Z and Qiao, D}, title = {Metagenomic Insights into Gut Microbiota Alterations Following Dendrobium huoshanense Water Extract Intervention in Streptozotocin-Induced Type 1 Diabetic Rats.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, pmid = {42353029}, issn = {1422-0067}, support = {no//the platform of the Traditional Chinese Medicine Institute of Anhui Dabie Mountain/ ; }, mesh = {Animals ; *Dendrobium/chemistry ; Rats ; *Plant Extracts/pharmacology/chemistry ; *Diabetes Mellitus, Experimental/drug therapy/microbiology ; *Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenomics/methods ; *Hypoglycemic Agents/pharmacology ; Rats, Sprague-Dawley ; Streptozocin ; Water/chemistry ; Metagenome ; }, abstract = {Dendrobium huoshanense water extract (DHWE) exhibits hypoglycemic effects in streptozotocin-induced type 1 diabetic (STZ-T1D) rats. However, its regulatory impact on the gut microbiota of T1D rats remains largely unclear. In this study, metagenomic sequencing was employed to characterize alterations in the gut microbiota of STZ-T1D rats following DHWE intervention, aiming to explore associations between DHWE-mediated gut microbial changes and T1D-related phenotypes. The results showed that 1300 mg/kg·BW/day DHWE did not significantly affect gut microbial α-diversity (p > 0.05), but drove the β-diversity structure toward that of normal rats. Meanwhile, DHWE significantly reduced the Bacteroidota/Bacillota ratio (p < 0.05), Megamonas (p < 0.01), Megamonas funiformis (p < 0.01), and notably increased the relative abundances of Adlercreutzia (p < 0.01), Adlercreutzia equolifaciens (p < 0.01) in STZ-T1D rats. Furthermore, functional annotation revealed that DHWE enriched multiple metabolic pathways, including streptomycin biosynthesis, ansamycins biosynthesis, galactose metabolism, ether lipid metabolism, and caprolactam degradation. Collectively, these findings demonstrate that DHWE reshapes gut microbiota composition and function in STZ-T1D rats, offering new clues regarding how gut microbial changes may contribute to the modulatory effects of Dendrobium huoshanense in T1D conditions.}, }
@article {pmid42353070, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Koralnik, IJ}, title = {Cross-Compartment Virome Profiling in Human Immunodeficiency Virus Infection and Substance Use Disorder Reveals Brain-CSF-Periphery Discordance and Hepatitis B Virus in Central Nervous System.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, pmid = {42353070}, issn = {1422-0067}, support = {DP1 DA048493/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Brain/virology ; *HIV Infections/virology/cerebrospinal fluid/complications ; *Substance-Related Disorders/virology/cerebrospinal fluid/complications ; *Virome ; *Hepatitis B virus/genetics/isolation &amp; purification ; Female ; *Central Nervous System/virology ; Male ; *Hepatitis B/virology/cerebrospinal fluid ; Viral Load ; Adult ; }, abstract = {The diversity and abundance of the brain virome is an active field of investigation. However, how the brain virome relates to the presence of viruses outside of the nervous system remains unclear. The rationale for this study is that analyses across multiple biologically linked compartments within the same individuals provide an important opportunity to evaluate virome discordance and viral burden. To characterize viral prevalence and burden across anatomical compartments, we applied the targeted viral enrichment method ViroFind to matched postmortem brain (n = 66), cerebrospinal fluid (CSF; n = 24), and peripheral samples (spleen, peripheral blood mononuclear cells, and lymph nodes; n = 66) from individuals with and without human immunodeficiency virus (HIV) infection and substance use disorder (SUD) in the National NeuroAIDS Tissue Consortium. We detected nucleic acids from 27 viruses representing 12 taxa. Several viruses, including adenovirus, torque teno virus, Epstein-Barr virus, human herpesvirus 6 and 7, cytomegalovirus, parvovirus, and JC polyomavirus, showed significant inter-compartment differences in prevalence or burden. CSF exhibited lower overall viral diversity than brain or peripheral samples, whereas peripheral samples showed the highest viral burden. CNS viral detection was more likely when the same virus was also detected in the periphery. We also detected HBV and HCV in CNS samples despite them not being classically regarded as neurotropic. Broader virome profiling showed greater peripheral viral burden and diversity in HIV-positive than HIV-negative individuals, whereas SUD was not associated with overall viral burden differences. These findings highlight important cross-compartment differences in viral detection, including occurrence of occult HBV infection within the CNS, and support the value of CNS-periphery comparisons in virome studies. These findings can contribute to improved diagnosis and management of viral infections.}, }
@article {pmid42358948, year = {2026}, author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G}, title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1849216}, pmid = {42358948}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; }, abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.<br><br>METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.<br><br>RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.<br><br>CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.}, }
@article {pmid42359485, year = {2026}, author = {Addy, HPK and Amedorme, D and Osei-Poku, P and Kwarteng, A}, title = {Predicted Functional Potentials of Bacterial Communities in Fermented Maize Products From Ghana, Nigeria, and Benin via 16S rRNA Amplicon Sequencing and PICRUSt2.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70272}, pmid = {42359485}, issn = {2045-8827}, mesh = {RNA, Ribosomal, 16S/genetics ; *Zea mays/microbiology ; *Fermented Foods/microbiology ; Ghana ; Nigeria ; Benin ; *Microbiota/genetics ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Sequence Analysis, DNA ; Phylogeny ; Lactobacillus/genetics/metabolism ; DNA, Bacterial/genetics ; }, abstract = {Fermented maize products are integral to the diets of many African communities. Despite their cultural significance and health benefits, little is known about the metabolic potential of their microbial populations. This study utilized 16S rRNA amplicon sequencing data from the NCBI to characterize the functional capabilities of microbiomes in six maize-based fermented foods. Quality assessment and taxonomic classification were performed using QIIME2 with the SILVA 138 database, while functional predictions were generated with PICRUSt2 and analyzed in R. Taxonomic profiling revealed that Firmicutes dominated all samples, reaching peak abundance in Mawe (94.9%) and S37_Fermented_Maize (91.4%). Proteobacteria were elevated in S19_Fermented_maize (up to 36.5%) and S38_Dehulled_Maize (16.0%). At the genus level, Lactobacillus was most abundant in S5_Mawe (82.2%) and S6_Mawe (79.6%), while Acetobacter peaked in S19_Fermented_maize (32.7%). Regarding functional predictions, Lactobacillus appeared to drive key KEGG Orthologs and pathways, specifically ABC transporters, transcriptional regulation, and DNA replication mechanisms. In contrast, Weissella and Streptococcus contributed notably to peptide/nickel transport, L-lactate dehydrogenase (EC 1.1.1.27), and nucleotide biosynthesis. Acetobacter was prominent in Ogi, showing a connection with site-specific methylation (EC 2.1.1.72) and phospholipid synthesis (PHOSLIPSYN-PWY). Notably, commercial Mawe samples exhibited higher predicted activities related to transposase activity (K07496), energy metabolism, and peptidoglycan maturation (PWY0-1586). These findings demonstrate that while traditional fermentation processes maintain a consistent set of metabolic functions predominantly driven by Lactobacillus, distinct variations exist depending on product type and production approach. These predicted functions provide a baseline for further experimental validation of the metabolic contributions of microbial communities in fermented maize products.}, }
@article {pmid42359789, year = {2026}, author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ}, title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2691334}, pmid = {42359789}, issn = {1949-0984}, mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth &amp; development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth &amp; development/metabolism ; }, abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.}, }
@article {pmid42361932, year = {2026}, author = {Ying, Y and Zheng, X and Yang, J and Ye, H and Dong, Z and Ji, Y and Li, S and Tan, X and Zhang, W}, title = {Tong-Xie-Yao-Fang ameliorates IBS-D: Potential role of Alistipes finegoldii-associated gut tryptophan indole metabolism.}, journal = {Journal of ethnopharmacology}, volume = {371}, number = {}, pages = {122061}, doi = {10.1016/j.jep.2026.122061}, pmid = {42361932}, issn = {1872-7573}, mesh = {Animals ; *Irritable Bowel Syndrome/drug therapy/metabolism/microbiology ; *Tryptophan/metabolism ; Mice, Inbred C57BL ; Male ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Indoles/metabolism ; *Gastrointestinal Microbiome/drug effects ; Colon/metabolism/drug effects/microbiology ; Mice ; Receptors, Aryl Hydrocarbon/metabolism ; Disease Models, Animal ; Indoleacetic Acids/metabolism ; Basic Helix-Loop-Helix Proteins/metabolism ; *Diarrhea/drug therapy/metabolism/microbiology ; Humans ; }, abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent chronic gastrointestinal condition characterized by visceral hypersensitivity, low-grade mucosal inflammation, and impaired epithelial barrier integrity. Current therapies remain limited, highlighting the need for more alternative strategies. Tong-Xie-Yao-Fang (TXYF), a classical Chinese herbal formula, has shown clinical efficacy in IBS-D, however, the mechanisms underlying its therapeutic effects remain unclear.<br><br>AIM OF THE STUDY: This study aimed to investigate whether and how TXYF exerts therapeutic effects by modulating colonic tryptophan metabolism, with a particular focus on the gut microbiota.<br><br>MATERIALS AND METHODS: IBS-D model was induced by combining chemical irritation and wrap restraint stress in C57BL/6J mice, and multi-omics approaches were employed to identify specific microbiota and metabolites modulated by TXYF. The multi-omics findings were further verified in vivo and in vitro.<br><br>RESULTS: TXYF treatment significantly alleviated IBS-D symptoms in our model. Non-targeted metabolomics identified the tryptophan-indole pathway as a key axis modulated by TXYF, with indole-3-acetic acid (IAA) emerging as a prominent differential metabolite in colonic tissue. Western blot analysis showed that TXYF activated the aryl hydrocarbon receptor (AhR) in the colon. Integrative metagenomic and metabolomic analyses revealed a strong association between Alistipes finegoldii and colonic indole and IAA levels. Consistent with these findings, transplantation of A. finegoldii combined with tryptophan supplementation, or administration of IAA alone, recapitulated the therapeutic effects of TXYF against IBS-D. In vitro, both IAA and faecal supernatant from TXYF-treated mice protected against tumour necrosis factor-induced epithelial barrier disruption in an AhR-dependent manner.<br><br>CONCLUSION: Collectively, the present study suggests that the therapeutic efficiency of TXYF against IBS-D is closely associated with its ability to modify microbiota-derived colonic IAA production, with gut microbiota member Alistipes finegoldii playing a key role in this effect.}, }
@article {pmid42362546, year = {2026}, author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE}, title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42362546}, issn = {2041-1723}, support = {R21 AG089348/AG/NIA NIH HHS/United States ; R01 AG092220/AG/NIA NIH HHS/United States ; R01 AG083883/AG/NIA NIH HHS/United States ; R01 DK143650/DK/NIDDK NIH HHS/United States ; R01 AG070973/AG/NIA NIH HHS/United States ; }, mesh = {*Alzheimer Disease/pathology/metabolism/genetics/microbiology/blood ; *Imidazoles/blood/metabolism ; Animals ; Humans ; Male ; *Gastrointestinal Microbiome/physiology ; Glycogen Synthase Kinase 3 beta/metabolism/antagonists &amp; inhibitors ; tau Proteins/metabolism ; Mice ; Female ; Neurons/metabolism/drug effects/pathology ; Phosphorylation ; Aged ; *Propionates/metabolism/blood ; Mice, Inbred C57BL ; Feces/microbiology ; Biomarkers/blood ; Brain/pathology/metabolism ; }, abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.}, }
@article {pmid42362550, year = {2026}, author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R}, title = {Remodelling of the gut virome after long-term fasting.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42362550}, issn = {2055-5008}, mesh = {*Fasting ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/genetics/classification/isolation &amp; purification ; Humans ; Metagenomics/methods ; Bacteria/virology/classification ; Feces/virology/microbiology ; Bacteroides/virology ; Faecalibacterium/virology ; }, abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.}, }
@article {pmid42362787, year = {2026}, author = {Sinha, B and Khandeparker, L}, title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42362787}, issn = {1573-2959}, mesh = {*Plastics/analysis ; Seasons ; *Biofilms ; *Environmental Monitoring ; *Microbiota ; Estuaries ; Bacteria/classification ; }, abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.}, }
@article {pmid42364169, year = {2026}, author = {Pan, P and Zhou, NY}, title = {Metabolic interactions enable aerobic degradation of the environmental pollutant BDE-47.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42364169}, issn = {1751-7370}, support = {JYB2025XDXM906//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; 2024YFA0919000//National Key R&amp;D Program of China/ ; }, mesh = {*Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; Aerobiosis ; *Environmental Pollutants/metabolism ; Metabolic Networks and Pathways ; Wastewater/microbiology ; Microbial Consortia ; }, abstract = {As a prevalent congener of polybrominated diphenyl ethers (PBDEs), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) poses significant environmental and health risks due to its persistence and bioaccumulation. However, the limited understanding of the microbial degradation mechanism of BDE-47 has hindered the development of effective bioremediation strategies. Here, we decipher an aerobic catabolic pathway of BDE-47 mediated by metabolic relay within a synthetic consortium composed of two environmental isolates, Rhizorhabdus wittichii YL-JM2C and Cupriavidus necator JMP134. Bioaugmentation with this consortium achieved complete removal of BDE-47 in real wastewater samples. The molecular basis underlying this cooperative degradation was elucidated through the heterologous expression and functional characterization of key enzymes involved. Namely, the dioxygenase TcsAaAb from strain YL-JM2C catalyzed the initial conversion of BDE-47 into 2,4-dibromophenol (2,4-DBP) and 3,5-dibromocatechol (3,5-DBC). As a dead-end intermediate in strain YL-JM2C, the former (2,4-DBP) was subsequently transformed into the latter (3,5-DBC) by the hydroxylase TfdB from strain JMP134. The resulting 3,5-DBC was catabolized through the downstream ortho-cleavage pathway present in both strains. These key enzymes for BDE-47 degradation coexist across diverse environments, including soil, seawater, and marine sediments. Global marine metagenomic profiling revealed a significant enrichment of these catabolic signatures in the Mariana Trench, implying that microorganisms in the hadal zone possess the genetic potential for PBDE catabolism. This study unveils previously unrecognized aerobic catabolic mechanisms for BDE-47 within natural ecosystems, offering promising bioremediation strategies for PBDE-contaminated environments.}, }
@article {pmid42364424, year = {2026}, author = {Chambers, LM and Spakowicz, D and Chalif, J and O'Connor, R and Kistenfeger, Q and Mehra, Y and Mohssen, M and Abdeen, C and Haight, P and Nagel, C and Neff, R and Cohn, D and Copeland, LJ and Backes, F and Cosgrove, C and Hays, J and Dravillas, C and McLaughlin, E and O'Malley, D}, title = {PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy.}, journal = {Gynecologic oncology}, volume = {211}, number = {}, pages = {74-78}, doi = {10.1016/j.ygyno.2026.06.016}, pmid = {42364424}, issn = {1095-6859}, mesh = {Humans ; Female ; Double-Blind Method ; *Probiotics/administration &amp; dosage/therapeutic use ; *Ovarian Neoplasms/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Vagina/microbiology ; Middle Aged ; Adult ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Microbiota/drug effects ; Aged ; Cisplatin/administration &amp; dosage ; }, abstract = {BACKGROUND: PRO-PLATINUM evaluates whether a 5-strain probiotic formulation can favorably modulate the gut microbiome during platinum-based chemotherapy in ovarian cancer (OC), while assessing feasibility, safety, and translational correlates of response and toxicity.<br><br>PATIENTS AND METHODS: PRO-PLATINUM is an IRB-approved, randomized, double-blind, placebo-controlled trial enrolling 124 patients with stage II-IV or platinum-sensitive recurrent high-grade OC receiving platinum-based chemotherapy. The study opened to enrollment in February 2026. Participants are randomized 1:1 to a 5-strain probiotic (WBF-038) or placebo, stratified by newly diagnosed advanced versus recurrent disease. The intervention contains inulin and five microbial strains: Akkermansia muciniphila, Anaerobutyricum hallii, Clostridium beijerinckii, Clostridium butyricum, and Bifidobacterium infantis, and is administered orally twice daily beginning within seven days of cycle 1 and continuing through seven days after the completion of cycle 6. Eligible patients must have ECOG performance status 0-2, adequate organ function, and no major probiotic-related contraindications. Stool, blood, and vaginal samples are collected at baseline, cycle 3, and cycle 6; tumor tissue is collected at surgery when available. The primary endpoint is change in gut microbiome composition by whole-genome metagenomic sequencing. Secondary endpoints include intervention adherence, biospecimen feasibility, recurrence-free survival, and overall survival. Exploratory endpoints include toxicity, postoperative infections, stool consistency, diet, medication and antibiotic exposure, quality of life, symptom burden, serum metabolomic and immune profiling, vaginal and tumor microbiome composition, and associations between microbial features and clinical outcomes.<br><br>CONCLUSIONS: PRO-PLATINUM will evaluate treatment feasibility and safety and generate prospective translational data to inform future microbiome-directed strategies to improve treatment tolerance, quality of life, and outcomes in OC patients.}, }
@article {pmid42364737, year = {2026}, author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M}, title = {The lung microbiome in hematopoietic stem cell transplantation: immune interactions, clinical consequences, and emerging interventions.}, journal = {Respiratory medicine}, volume = {261}, number = {}, pages = {109004}, doi = {10.1016/j.rmed.2026.109004}, pmid = {42364737}, issn = {1532-3064}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Microbiota/immunology ; *Lung/microbiology/immunology ; Graft vs Host Disease/immunology ; Dysbiosis/immunology ; *Lung Diseases/microbiology/immunology/etiology ; }, abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.}, }
@article {pmid42366019, year = {2026}, author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J}, title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70367}, doi = {10.1111/1462-2920.70367}, pmid = {42366019}, issn = {1462-2920}, support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation &amp; purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; }, abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.}, }
@article {pmid42366665, year = {2026}, author = {Kuzbekov, SR}, title = {[Microbiota and microbiome of the lacrimal drainage system].}, journal = {Vestnik oftalmologii}, volume = {142}, number = {3}, pages = {91-100}, doi = {10.17116/oftalma202614203191}, pmid = {42366665}, issn = {0042-465X}, mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.}, }
@article {pmid42367778, year = {2026}, author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y}, title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1868704}, pmid = {42367778}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; }, abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.<br><br>METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.<br><br>RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P&#xa0;<&#xa0;0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P&#xa0;=&#xa0;0.003) and depletion of Roseburia (1.05% vs. 3.77%, P&#xa0;=&#xa0;0.005) and Ruminococcus (5.98% vs. 7.85%, P&#xa0;=&#xa0;0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P&#xa0;=&#xa0;0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.<br><br>CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably&#xa0;Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.}, }
@article {pmid42367784, year = {2026}, author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X}, title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1859206}, pmid = {42367784}, issn = {1664-3224}, mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; }, abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.}, }
@article {pmid42370706, year = {2026}, author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, M&#xd8;}, title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0057726}, pmid = {42370706}, issn = {2379-5077}, support = {NNF20OC0061313//Novo Nordisk Fonden/ ; NOD-AOL 101125376/ERC_/European Research Council/International ; 295910//Norges Forskningsr&#xe5;d/ ; NNF20OC0061165//Novo Nordisk Fonden/ ; }, mesh = {*Lignin/metabolism ; *Lakes/microbiology ; *Denitrification ; *Geologic Sediments/microbiology ; *Microbial Consortia ; Bacteria/metabolism/genetics/classification ; Nitrates/metabolism ; Eutrophication ; Metagenome ; }, abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.}, }
@article {pmid42370713, year = {2026}, author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ}, title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0113625}, pmid = {42370713}, issn = {2379-5077}, support = {18-ERD-041//Lawrence Livermore National Laboratory/ ; SCW1632//U.S. Department of Energy/ ; }, mesh = {*Virion/genetics/isolation &amp; purification ; *Grassland ; *Soil Microbiology ; *Virome/genetics ; *Metagenomics/methods ; Genome, Viral ; Soil/chemistry ; }, abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.}, }
@article {pmid42370731, year = {2026}, author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L}, title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0040726}, pmid = {42370731}, issn = {2379-5077}, support = {R56 AG079586/AG/NIA NIH HHS/United States ; R56AG079586/AG/NIA NIH HHS/United States ; }, mesh = {*Microbiota ; *Machine Learning ; Humans ; Multivariate Analysis ; }, abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.}, }
@article {pmid42370747, year = {2026}, author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE}, title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.}, journal = {mBio}, volume = {17}, number = {8}, pages = {e0338225}, pmid = {42370747}, issn = {2150-7511}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; DE-FOA-0001858//Advanced Research Projects Agency - Energy/ ; R01-ES030316/NH/NIH HHS/United States ; EF-2025217//National Science Foundation/ ; OCE-1837116//National Science Foundation/ ; }, mesh = {Animals ; Polyphenols/metabolism ; Polysaccharides/metabolism ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; *Seaweed/metabolism/chemistry ; *Bacteria/metabolism/classification/genetics ; Biotransformation ; }, abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.}, }
@article {pmid42371112, year = {2026}, author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X}, title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42371112}, issn = {1436-6215}, support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; }, mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; }, abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.<br><br>METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500&#xa0;ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).<br><br>RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P&#x2009;<&#x2009;0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.<br><br>CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.<br><br>CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).}, }
@article {pmid42371206, year = {2026}, author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T}, title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42371206}, issn = {1573-0972}, support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; }, mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth &amp; development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenome ; China ; Microbiota/genetics ; }, abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.}, }
@article {pmid42372926, year = {2026}, author = {Kwon, CY and Choi, YH and Kim, H and Han, K and Jang, D and Hwangbo, H}, title = {Gut microbial signature for frailty discrimination: a metagenomic meta-analysis of 28 independent cohorts.}, journal = {Experimental gerontology}, volume = {222}, number = {}, pages = {113223}, doi = {10.1016/j.exger.2026.113223}, pmid = {42372926}, issn = {1873-6815}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Frailty/microbiology/diagnosis ; Metagenomics ; Biomarkers ; Dysbiosis/microbiology ; Aged ; Random Forest ; Cohort Studies ; }, abstract = {Frailty, a clinical syndrome of multisystem decline and homeostatic vulnerability, is a critical public health priority. While the gut microbiome regulates immune and metabolic signaling, current evidence remains fragmented. We performed a metagenomic meta-analysis of 955 individuals from 28 independent cohorts across 24 countries to identify universal microbial signatures and develop a generalizable discriminative model. Frailty was determined using a Proxy Frailty Index based on the deficit accumulation model. Following refinement to isolate signatures from disease-specific dysbiosis, we used Firth's penalized regression for biomarker discovery and validated a Random Forest (RF) model via leave-one-study-out cross-validation. Shannon diversity exhibited a significant and sharp decline during the transition from robust to pre-frail states (p = 0.0006), manifesting at the earliest stages of physiological decline. We identified 16 microbial biomarkers characterized by the progressive attrition of core symbionts, such as Coprococcus eutactus, and the opportunistic expansion of pathobionts, including Enterococcus gallinarum. Sensitivity analysis in a healthy sub-cohort (n = 499) confirmed that these shifts occur independently of chronic clinical diagnoses and their associated confounding effects (p = 0.036). The 16-species RF model, predominantly driven by Collinsella massiliensis, achieved a corrected mean area under the receiver operating characteristic curve of 0.7572 across 5 eligible cohorts. Gut microbial restructuring is a sentinel biological hallmark of frailty that occurs independently of aging-related diseases. This study establishes a microbial signature broadly applicable across European and East Asian populations that serves as a high-fidelity, non-invasive metric for precision geriatric assessment.}, }
@article {pmid42372963, year = {2026}, author = {Cui, Q and Wang, F and Shan, X and Ding, L and Qiu, X and Zhang, B and Li, X and Liang, X and Guo, X}, title = {Biodegradable polylactic acid microplastics affect nutrient cycling during the entire crop growth cycle: Implications for soil ecosystem multifunctionality.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {406}, number = {}, pages = {128664}, doi = {10.1016/j.envpol.2026.128664}, pmid = {42372963}, issn = {1873-6424}, mesh = {*Polyesters ; *Soil Microbiology ; Soil/chemistry ; *Soil Pollutants/metabolism/toxicity ; *Microplastics/metabolism ; Ecosystem ; Microbiota ; Biodegradation, Environmental ; *Crops, Agricultural/growth &amp; development ; Zea mays/growth &amp; development ; Nitrogen ; }, abstract = {While microplastics (MPs) have been extensively studied for their effects on soil nutrient cycling, their influence on ecosystem multifunctionality (EMF) across the entire crop growth cycle remains poorly understood. This study systematically investigated the impacts of a model biodegradable MP, polylactic acid (PLA), on soil microbiomes and EMF across different maize incubation periods. Results of 16S rRNA amplicon sequencing and metagenomic analysis revealed that PLA-MPs decreased bacterial community α-diversity, co-occurrence network complexity, and stability throughout the 120-day incubation period. Particularly, PLA-MPs exerted more pronounced effects at early incubation stages (30 and 60 days), and these effects were intensified with increasing PLA-MP concentrations. PLA-MPs suppressed anaerobic carbon fixation (porA, porB, frda) and pyruvate metabolism (ppdk), while promoting fermentation (L-lactate dehydrogenase), nitrogen fixation (nifD, nifH, nifK, anfG), and microbial phosphorus (P) acquisition (phoD, phn cluster). Over the entire incubation period, PLA-MP-induced shifts in nutrient cycling enhanced soil carbon (C) function by 37.6-569%, while decreasing nitrogen (N) and P functions by 8.40-22.4% and 16.8-56.2%, respectively. Path analysis revealed that PLA-MPs altered soil properties and bacterial community diversity, which in turn regulated functional genes and these individual soil functions, thereby reducing EMF by 2.05-27.0% (R[2] = 0.923), with bacterial community diversity as the primary driver of EMF (standardized path coefficient of 0.978). These findings underscore the impacts of PLA-MPs on EMF in the soil-crop system throughout the entire maize growth cycle, advancing the understanding of the agroecological safety of biodegradable MPs.}, }
@article {pmid42374590, year = {2026}, author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB}, title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42374590}, issn = {2049-2618}, support = {Heritage_2020-005_RESTOROMIC//&#xd6;sterreichischen Akademie der Wissenschaften/ ; }, mesh = {Austria ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Sodium Chloride ; Transcriptome ; Salinity ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.<br><br>RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.<br><br>CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.}, }
@article {pmid42376319, year = {2026}, author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S}, title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1828012}, pmid = {42376319}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; }, abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.<br><br>METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.<br><br>RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p&#xa0;=&#xa0;0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p&#xa0;=&#xa0;0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.}, }
@article {pmid42376710, year = {2026}, author = {Arguelles, EDLR and Mugikura, K and Sato, S}, title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.}, journal = {Journal of phycology}, volume = {62}, number = {4}, pages = {1221-1239}, pmid = {42376710}, issn = {1529-8817}, support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; }, mesh = {*Diatoms/physiology ; *Microbiota ; *Biofilms/growth &amp; development ; *Zeatin/metabolism ; *Introduced Species ; *Rivers/microbiology ; Japan ; Bacteria/metabolism ; Eutrophication ; }, abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.}, }
@article {pmid42377028, year = {2026}, author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K}, title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.}, journal = {mSystems}, volume = {11}, number = {7}, pages = {e0048926}, pmid = {42377028}, issn = {2379-5077}, support = {081901/21-25//Bundesinstitut f&#xfc;r Sportwissenschaft (BISp)/ ; 01EA1707 &amp; 01EA1708//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; EXC2151-390873048//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Young Adult ; *Athletes ; *Bacteria/classification/genetics ; *Gastrointestinal Microbiome/genetics ; Germany ; Metagenomics ; }, abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.}, }
@article {pmid42377624, year = {2026}, author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C}, title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42377624}, issn = {1573-0972}, mesh = {*Wastewater/microbiology ; *Microalgae/growth &amp; development/microbiology ; Phylogeny ; *Bacteria/isolation &amp; purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; }, abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.}, }
@article {pmid42378712, year = {2026}, author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M}, title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.}, journal = {Journal of Crohn's &amp; colitis}, volume = {20}, number = {6}, pages = {}, pmid = {42378712}, issn = {1876-4479}, support = {//Takeda Pharmaceutical Company Ltd/ ; }, mesh = {Humans ; *Crohn Disease/complications/genetics/microbiology ; *Rectal Fistula/genetics/microbiology/etiology/pathology/metabolism ; Multiomics ; Female ; Male ; Adult ; Epithelial-Mesenchymal Transition/genetics ; Transcriptome ; Middle Aged ; Intestinal Mucosa/pathology/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; Metabolomics ; }, abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.<br><br>DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n&#x2009;=&#x2009;23) or CgF (n&#x2009;=&#x2009;17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.<br><br>RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.<br><br>CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.}, }
@article {pmid42378973, year = {2026}, author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B}, title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.}, journal = {Water research}, volume = {304}, number = {}, pages = {126351}, doi = {10.1016/j.watres.2026.126351}, pmid = {42378973}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; Cefpirome/metabolism ; *Cephalosporins/metabolism ; *Microbial Consortia ; Bacteria/metabolism ; }, abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.}, }
@article {pmid42379260, year = {2026}, author = {Alamri, MM and Proctor, G and Garcia-Guevara, F and Guennec, AL and Mainas, G and Shoaie, S and Nibali, L}, title = {Multiomics analyses in young grade C molar incisor pattern periodontitis.}, journal = {Journal of dentistry}, volume = {174}, number = {}, pages = {106871}, doi = {10.1016/j.jdent.2026.106871}, pmid = {42379260}, issn = {1879-176X}, mesh = {Humans ; Multiomics ; Female ; *Periodontitis/microbiology/metabolism ; Dental Plaque/microbiology ; Male ; Saliva/microbiology/chemistry ; Young Adult ; Microbiota ; Adolescent ; Adult ; Case-Control Studies ; Metabolome ; Metagenomics ; }, abstract = {OBJECTIVE: To explore the microbial profiles in plaque and saliva and metabolic profiles in saliva and serum collected from young patients (≤25 years old) with grade C molar incisor pattern periodontitis (C/MIP), to compare them to age-matched controls and integrate both omics to elucidate C/MIP pathogenesis.<br><br>MATERIAL AND METHOD: Thirty-one young patients with C/MIP and 31 periodontally healthy age-matched controls were recruited. Bacterial profiles were investigated in unstimulated saliva and subgingival plaque using shotgun sequencing metagenomics while metabolic profiles were assessed in saliva using nuclear magnetic resonance and serum using mass spectrometry. Data from both omics analyses were integrated and visualised as interaction networks using Cytoscape software.<br><br>RESULTS: C/MIP showed significantly lower levels of several salivary (e.g., dimethylamine, proline, glycine) and serum metabolites, and higher levels of others including methyl indole-3-acetate and sulfosalicylic acid, compared to controls (P < 0.001). Fifteen bacteria, of which twelve were associated with C/MIP, were differentially prevalent between groups. The plaque microbiome in C/MIP was enriched with pathogenic species such as D. oralis, C. rectus, T. denticola, and P. endodontalis, while health-associated bacteria like R. mucilaginosa and L. hongkongensis were more prevalent in controls. D. oralis and GGB10485-SGB49305 emerged as potential microbial biomarkers. Notably, metabolites such as DL-glutamine and taurine were significantly associated with periodontal pathogens.<br><br>CONCLUSION: C/MIP is marked by a distinct dysbiotic microbiome and altered metabolic profile. While key pathogens and metabolites likely contribute to disease progression, the underlying mechanisms remain only partially understood due to the complexity and incomplete characterisation of many associated factors.<br><br>CLINICAL SIGNIFICANCE: This study highlighted the multifactorial nature of C/MIP, driven by microbial dysbiosis, immune disturbances, and metabolic alterations. A comprehensive multi-omics approach offered a foundation for understanding microbial-metabolite dynamics in young patients, and highlighted candidate biomarkers for future diagnostics and therapeutics.}, }
@article {pmid42381048, year = {2026}, author = {Porcel Sanchis, D and Pola, M and Engelberts, JP and Guerra-Font, O and Messer, L and Alberola-Mora, I and Escobar Sáez, L and Pérez Gómez, N and Portolés Campo, &#xc1; and Valero-Tebar, J and Naya Garmendia, LM and Preciado Barahona, JC and Gil García, R and Arnau, V and McIlroy, SJ and Džunková, M}, title = {Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42381048}, issn = {2049-2618}, mesh = {Animals ; *Symbiosis ; *Metagenomics/methods ; Phylogeny ; *Microbiota/genetics ; *Gastropoda/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenome ; }, abstract = {BACKGROUND: Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.<br><br>RESULTS: Using ethanol-preserved specimens archived for up to 30&#xa0;years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.<br><br>CONCLUSIONS: Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.}, }
@article {pmid42381379, year = {2026}, author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA}, title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690687}, pmid = {42381379}, issn = {1949-0984}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.}, }
@article {pmid42383698, year = {2026}, author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO}, title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {32}, number = {9}, pages = {972-984}, pmid = {42383698}, issn = {1477-0970}, support = {R01 NS087226/NS/NINDS NIH HHS/United States ; R01 NS121928/NS/NINDS NIH HHS/United States ; R21 NS126866/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Tryptophan/metabolism/blood ; *Bile Acids and Salts/metabolism/blood ; Male ; *Multiple Sclerosis/metabolism/blood ; Female ; Adult ; Middle Aged ; *Tobacco Smoking/adverse effects/metabolism ; *Gastrointestinal Microbiome/physiology ; Indoles/metabolism/blood ; }, abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.<br><br>OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.<br><br>METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N&#x2009;=&#x2009;266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.<br><br>RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).<br><br>CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.}, }
@article {pmid42384485, year = {2026}, author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ}, title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {116334}, doi = {10.1016/j.celrep.2025.116334}, pmid = {42384485}, issn = {2211-1247}, mesh = {Humans ; *Indians, North American ; Bacteria/genetics/classification ; Archaea/genetics/classification ; Metagenome ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Microbiota ; }, abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.}, }
@article {pmid42384916, year = {2026}, author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA}, title = {Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {7}, pages = {}, pmid = {42384916}, issn = {1367-4811}, support = {//Lawrence Livermore National Laboratory/ ; }, mesh = {*Metadata ; *Metagenomics/methods ; Humans ; *Databases, Genetic ; *Metagenome ; *Microbiota/genetics ; Biocuration ; Software ; }, abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.<br><br>AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.}, }
@article {pmid42385223, year = {2026}, author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A}, title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.}, journal = {MicrobiologyOpen}, volume = {15}, number = {4}, pages = {e70359}, pmid = {42385223}, issn = {2045-8827}, mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; }, abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.}, }
@article {pmid42385828, year = {2026}, author = {Yin, Z and Zhang, Y and Song, S and Li, C and Shi, J and Yin, Y and Cai, Y}, title = {Co-contamination of antimony and arsenic reshapes resistome, virulome, and virome in poultry feces near the world's largest antimony mine.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {406}, number = {}, pages = {128684}, doi = {10.1016/j.envpol.2026.128684}, pmid = {42385828}, issn = {1873-6424}, mesh = {Animals ; Mining ; *Arsenic/analysis ; *Antimony/analysis ; *Feces/microbiology/virology ; *Virome ; Poultry ; Drug Resistance, Microbial/genetics ; Microbiota ; }, abstract = {The poultry microbiome and virome are integral to the One Health framework, with significant implications for ecosystem and human health, but their responses to arsenic (As) and antimony (Sb) exposure remain overlooked. Here, we conducted a comprehensive metagenomic characterization of the metal resistome, antibiotic resistome, virulome, and virome in poultry feces collected from the world's largest antimony mining area. We found that As and Sb co-contamination was significantly associated with elevated resistance and virulence. The abundance of metal resistance genes (MRGs) was 1.8-fold higher in the high-Sb group than in the low-Sb group (15,022.27 ± 3538.47 vs 8370.24 ± 4502.07 TPM, P = 0.008), with arsR, arsB, and arsC dominating the MRG profiles. Similarly, antibiotic resistance genes (ARGs) abundance was 1.6-fold higher in the high-Sb group than in the low-Sb group (7251.00 ± 1844.34 vs 4478.95 ± 2302.69 TPM, P = 0.026), with multidrug resistance genes being the predominant class (8.09% - 58.48%). Metagenome-assembled genomes (MAGs) analysis and contig analysis suggest co-selection of MRGs, ARGs, and virulence factor genes (VFGs). We identified 100,819 viral contigs clustered into 91,004 viral operational taxonomic units (vOTUs), revealing a highly diverse viral community. Members of Enterobacteriaceae (e.g., Klebsiella) and Enterococcaceae (i.e., Enterococcus) were identified as key drivers mediating resistance and virulence dynamics, acting as resistome supercarriers, opportunistic pathogens, and viral hosts. These findings suggest that As-Sb co-contamination is an overlooked but potentially important driver of poultry antimicrobial resistance and pathogenicity, and highlight potential ecological and public health risks in mining-impacted poultry-associated environments.}, }
@article {pmid42385873, year = {2026}, author = {Chen, P and Si, H and Wang, J and Xie, J and Gu, C and Ma, W and Liu, X and Sun, Q}, title = {Metagenomic insights into microbial responses to soil amendments and oat cultivar identity in saline-alkali soils.}, journal = {Environmental research}, volume = {306}, number = {Pt 2}, pages = {125147}, doi = {10.1016/j.envres.2026.125147}, pmid = {42385873}, issn = {1096-0953}, mesh = {*Avena/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Metagenomics ; Rhizosphere ; *Microbiota ; Bacteria/genetics/classification ; Manure ; }, abstract = {Host cultivar identity can influence rhizosphere microbiomes, yet its relative importance compared with soil amendment regime in saline-alkali farmland remains insufficiently resolved. Here, we compared how two oat (Avena sativa) cultivars shape soil microbial communities and functions under contrasting amendment regimes. In a field experiment, two oat cultivars, Tianyan 60 (TY60) and Musite (MST), were grown under five treatments: control, bacterial agent, organic manure, silica fume, and their combination. Soil physicochemical properties, enzyme activities, and metagenomic sequencing were used to characterize microbial taxonomic and functional profiles. Amendment regimes strongly altered soil nutrient and enzyme variables, whereas cultivar identity explained more variation than amendment regime in microbial community structure and beta diversity under the tested field conditions. Taxonomically, TY60 showed stronger amendment-associated reassembly, including enrichment of Bacteroidota, Pseudomonadota, and Ascomycota under selected treatments, whereas MST retained a comparatively more stable higher-rank backbone. Network analysis further indicated cultivar-associated differences in microbial community organization. Functionally, organic manure and the combination treatments (MIX3) produced the broadest shifts in C, N, P, and S cycling gene modules, particularly in TY60-associated soils. Null-model analyses showed that stochastic assembly dominated overall, but the dominant stochastic component differed among kingdoms, with bacteria mainly governed by drift, archaea by homogeneous dispersal, and fungi by a more balanced contribution of the drift and homogeneous dispersal. These results indicate that cultivar identity played a stronger role than amendment regime in shaping amendment-associated microbiome and functional shifts in this two-cultivar comparison, highlighting the potential value of combining cultivar choice with organic-microbial inputs to improve rhizosphere multifunctionality in saline-alkali agroecosystems.}, }
@article {pmid42386249, year = {2026}, author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J}, title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {124}, number = {1}, pages = {101323}, doi = {10.1016/j.ajcnut.2026.101323}, pmid = {42386249}, issn = {1938-3207}, mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; }, abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).<br><br>OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.<br><br>METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.<br><br>RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.<br><br>CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.}, }
@article {pmid42387381, year = {2026}, author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B}, title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42387381}, issn = {1471-2180}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; }, abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.<br><br>RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq.&#xa0;Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.<br><br>CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.}, }
@article {pmid42387604, year = {2026}, author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY}, title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.}, journal = {Infectious diseases of poverty}, volume = {15}, number = {1}, pages = {}, pmid = {42387604}, issn = {2049-9957}, support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; }, mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; }, abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.<br><br>METHODS: Female BALB/c mice and Sprague Dawley rats (n&#x2009;=&#x2009;10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.<br><br>RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P&#x2009;<&#x2009;0.05) while Bacteroidetes increased (P&#x2009;<&#x2009;0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P&#x2009;<&#x2009;0.05) but decreased in rats (P&#x2009;<&#x2009;0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P&#x2009;<&#x2009;0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.<br><br>CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.}, }
@article {pmid42389510, year = {2026}, author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F}, title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1760700}, pmid = {42389510}, issn = {2235-2988}, mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation &amp; purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; }, abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.<br><br>METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).<br><br>KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.<br><br>CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.}, }
@article {pmid42390233, year = {2026}, author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X}, title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.}, journal = {mSphere}, volume = {11}, number = {7}, pages = {e0036926}, pmid = {42390233}, issn = {2379-5042}, mesh = {*Geologic Sediments/microbiology ; *Salinity ; *Hydrocarbons/metabolism ; *Bacteria/genetics/metabolism/classification ; Metagenomics ; *Adaptation, Physiological ; *Microbiota/genetics ; Biodegradation, Environmental ; Phylogeny ; Genome, Bacterial ; }, abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.}, }
@article {pmid42390352, year = {2026}, author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Jingjing, X and Lianyi, H and Wang, B and Li, Y and Roeselers, G and Gong, S}, title = {Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.}, journal = {Food &amp; function}, volume = {17}, number = {14}, pages = {6596-6607}, doi = {10.1039/d6fo02082h}, pmid = {42390352}, issn = {2042-650X}, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; China ; Infant, Newborn ; Female ; Feces/microbiology ; *Metabolome ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Child, Preschool ; Bifidobacterium ; Prebiotics ; Breast Feeding ; Infant Formula ; East Asian People ; }, abstract = {The neonatal period is a critical stage of development during which the gut microbiome profoundly influences both short- and long-term health and nutrition. Its maturation from infancy to childhood is shaped by interacting environmental factors, including feeding mode, birth mode, and geographic location. A clinical study of 445 infants and toddlers (aged 0-24 months) from six socioeconomically diverse regions in China investigated age-related trajectories of gut microbiome and metabolomic development, with a particular focus on feeding mode. The study included a breastfed reference group and a formula-fed group that received an open-label formula containing a prebiotic mixture of short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS, 9 : 1). Longitudinal fecal samples were analyzed using shotgun metagenomic and metabolomic approaches. Feeding mode was strongly associated with variations in gut microbiome structure and function, along with birth mode and geographic location. Bifidobacterium and Bacteroides were the dominant taxa in both groups and exhibited dynamic abundance trajectories over time. Increased Bifidobacterium abundance was correlated with gene functions involved in starch and fatty acid metabolism as well as the fructose-6-phosphoketolase pathway (Bifid shunt). Comparative metabolomic analyses of amino acids and bile acids revealed highly similar metabolic profiles between the two groups. These findings highlight the association between feeding mode with the developing gut microbiome and describe age-dependent trajectories in Chinese children.}, }
@article {pmid42390679, year = {2026}, author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F}, title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.}, journal = {Ecotoxicology (London, England)}, volume = {35}, number = {6}, pages = {}, pmid = {42390679}, issn = {1573-3017}, support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; }, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; }, abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.}, }
@article {pmid42391940, year = {2026}, author = {Wang, J and Guo, C and Pu, X}, title = {Metabolic filtering as a putative mechanism linking soil metabolome and microbial community assembly along a lake expansion gradient.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128601}, doi = {10.1016/j.micres.2026.128601}, pmid = {42391940}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Metabolome ; *Lakes/microbiology ; *Soil/chemistry ; *Microbiota/physiology ; Ecosystem ; Multiomics ; Bacteria/classification/metabolism/genetics ; Metabolomics ; Metagenomics ; Tibet ; Salinity ; }, abstract = {Climate-driven lake expansion across the Qinghai-Tibet Plateau induces profound edaphic shifts, but how these abiotic changes shape soil microbial assembly remains unclear. Soil metagenomics and metabolomics were integrated along a 0-10 km spatial gradient at Gahai. Redundancy analysis (RDA) identified moisture (NDWI) and salinity (SI) as primary ecosystem drivers. Structural equation modeling (SEM) provided exploratory evidence consistent with a mediation pathway (P = 0.64, CFI = 1, RMSEA = 0), in which environmental factors potentially influenced microbial community structure indirectly, via reshaping the soil metabolome rather than through a direct path. Moisture availability exerted a strong negative effect on soil metabolic profiles (λ = -0.93), leading to a pronounced negative correlation between the metabolome and microbial community (λ= -0.97). Multi-omics integration attributed this pattern to stress-induced accumulation of defensive metabolites, including Feruloylputrescine and 3-Methylthiopropyl-desulfoglucosinolate. These compounds showed significant negative correlations with dominant genera (e.g., Candidatus Kryptobacter). This "metabolic filtering" is hypothesized to selectively limit the presence of non-adapted taxa based solely on correlational SEM and network analyses, supporting our tentative hypothesis that increasing environmental stress may promote a transition from competitive interactions toward patterns consistent with stronger deterministic filtering. Our exploratory findings suggest that the soil metabolome acts as a functional interface mediating microbial adaptation and strategic resource allocation to lake expansion in this high-altitude saline-alkali system. However, due to regional heterogeneity, these patterns provide a theoretical baseline for plateau lake ecosystems and should be applied with caution to broader geographic areas.}, }
@article {pmid42391942, year = {2026}, author = {Castellano-Hinojosa, A and de Freitas, J and de Carvalho, DU and Monus, BD and González-López, J and Strauss, SL and Albrecht, U}, title = {Compartmental and functional responses of the citrus microbiome and resistome to the systemic delivery of oxytetracycline by trunk injection.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128613}, doi = {10.1016/j.micres.2026.128613}, pmid = {42391942}, issn = {1618-0623}, mesh = {*Oxytetracycline/administration &amp; dosage/pharmacology ; *Microbiota/drug effects ; *Citrus/microbiology/drug effects ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizobiaceae/drug effects ; Plant Roots/microbiology ; Rhizosphere ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; Plant Leaves/microbiology ; Liberibacter/drug effects ; Bacteria/classification/genetics/drug effects ; Soil Microbiology ; Fruit/microbiology ; }, abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely limits citrus production worldwide. We investigated how oxytetracycline (OTC) trunk injection affects the citrus holobiont, examining its ability to suppress CLas and improve tree performance while assessing compartment-specific responses of the microbiome and resistome. A field experiment was conducted in CLas-infected sweet orange trees, integrating qPCR pathogen quantification, fruit yield and juice quality measurements, functional pathway analysis, and genome-resolved profiling across leaves, bark, fibrous roots, and the rhizosphere at three time points after injection. OTC reduced CLas abundance in leaves and improved fruit yield and juice quality without altering microbial diversity. No clear OTC-associated shifts in microbial functional pathways were observed in aboveground compartments, and resistome profiles were strongly compartment-dependent but showed no detectable response to OTC treatment. However, pronounced functional shifts were detected in belowground compartments, with consistent reductions in carbon-, nitrogen-, and phosphorus-related pathways and declines in several taxa and metagenome-assembled genomes associated with nutrient turnover. In contrast, stress-tolerance and xenobiotic-responsive microorganisms were enriched. In addition, these belowground responses were associated with low-abundance, rare taxa rather than by changes in alpha diversity or the dominant community, revealing a hidden functional reconfiguration that was concentrated in the root and rhizosphere compartments most relevant to nutrient cycling and long-term soil health. These findings demonstrate that systemically delivered OTC induces targeted, compartment-specific reorganization of microbiome functions rather than broad disruption. By linking physiological improvement with functional and genome-resolved microbial responses, this study highlights the broader ecological consequences of antibiotic interventions in perennial crops.}, }
@article {pmid42392820, year = {2026}, author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY}, title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {51}, number = {9}, pages = {2652-2664}, doi = {10.19540/j.cnki.cjcmm.20260107.707}, pmid = {42392820}, issn = {1001-5302}, mesh = {Animals ; *Drugs, Chinese Herbal/administration &amp; dosage ; *Reperfusion Injury/metabolism/prevention &amp; control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; }, abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.}, }
@article {pmid42394335, year = {2026}, author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X}, title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {55}, number = {3}, pages = {491-498}, doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019}, pmid = {42394335}, issn = {1000-8020}, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; }, abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.<br><br>METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1&#x2236;1&#x2236;1 ratio) and Mix-B group(same bacterial strains, in a 10&#x2236;1&#x2236;1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 &#xd7; 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.<br><br>RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, &#x3b2;-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.<br><br>CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.}, }
@article {pmid42394341, year = {2026}, author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V}, title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.}, journal = {Journal of environmental quality}, volume = {55}, number = {4}, pages = {e70215}, pmid = {42394341}, issn = {1537-2537}, support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; }, mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; }, abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.}, }
@article {pmid42397430, year = {2026}, author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H}, title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42397430}, issn = {1436-6215}, mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.<br><br>METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.<br><br>RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.<br><br>CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.}, }
@article {pmid42397535, year = {2026}, author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK}, title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {21}, pages = {10626-10639}, pmid = {42397535}, issn = {1614-7499}, mesh = {*Feces/microbiology ; Humans ; Anaerobiosis ; Fatty Acids, Volatile ; Methane ; Microbiota ; Bacteria ; Archaea ; Hydrolysis ; }, abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.}, }
@article {pmid42397950, year = {2026}, author = {Karthik, Y and Nanjareddy, K and Arthikala, MK}, title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.}, journal = {Plant signaling &amp; behavior}, volume = {21}, number = {1}, pages = {2693436}, pmid = {42397950}, issn = {1559-2324}, support = {//General Directorate for Academic Personnel Affairs/ ; //National Autonomous University of Mexico/ ; }, mesh = {*Glycine max/microbiology/growth &amp; development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF &amp; PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.}, }
@article {pmid42398208, year = {2026}, author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z}, title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {159}, number = {}, pages = {158533}, doi = {10.1016/j.phymed.2026.158533}, pmid = {42398208}, issn = {1618-095X}, mesh = {Animals ; *Polysaccharides/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Orthomyxoviridae Infections/drug therapy ; Signal Transduction/drug effects ; *Abrus/chemistry ; *Antiviral Agents/pharmacology ; Interferon-beta/metabolism ; Female ; Mice, Inbred BALB C ; Influenza A Virus, H1N1 Subtype/drug effects ; Dogs ; Male ; }, abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.<br><br>PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.<br><br>METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-&#x3b2;) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-&#x3b2;, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).<br><br>RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of&#x2192;4)-&#x3b1;-D-Glcp-(1&#x2192;,&#x2192;4)-&#x3b2;-D-Galp-(1&#x2192;, and &#x2192;4,6)-&#x3b1;-D-Glcp-(1&#x2192; linkages and &#x3b1;-D-Glcp-(1&#x2192; branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-&#x3b2; antiviral pathway via microbial-derived acetate.<br><br>CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-&#x3b2; antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-&#x3b2; homeostasis, highlighting its potential for influenza prevention.}, }
@article {pmid42398246, year = {2026}, author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X}, title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130396}, doi = {10.1016/j.jenvman.2026.130396}, pmid = {42398246}, issn = {1095-8630}, mesh = {Animals ; Parks, Recreational ; *Snails/microbiology ; Dogs ; *Introduced Species ; *Drug Resistance, Microbial/genetics ; China ; Feces/microbiology ; Drug Resistance, Bacterial ; }, abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.}, }
@article {pmid42398311, year = {2026}, author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V}, title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128605}, doi = {10.1016/j.micres.2026.128605}, pmid = {42398311}, issn = {1618-0623}, mesh = {*Crops, Agricultural/microbiology/growth &amp; development ; *Microbiota/genetics/physiology ; Biotechnology/methods ; Agriculture/methods ; Bacteria/genetics ; Ecosystem ; Plants/microbiology ; Microbial Consortia ; }, abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.}, }
@article {pmid42398606, year = {2026}, author = {Liu, J and Liu, Y and Zheng, Y and Wang, H and Wang, J and Zhang, Y and Wang, K}, title = {Intestinal metabolic characteristics of Smilax china L. pectic polysaccharide and prediction of its gut microbiota-mediated mechanism.}, journal = {International journal of biological macromolecules}, volume = {374}, number = {}, pages = {153348}, doi = {10.1016/j.ijbiomac.2026.153348}, pmid = {42398606}, issn = {1879-0003}, mesh = {Animals ; *Smilax/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Pectins/metabolism/chemistry ; *Polysaccharides/metabolism/chemistry ; *Intestines/microbiology ; }, abstract = {This study aimed to investigate the intestinal metabolic characteristics and mechanisms of the pectic polysaccharide isolated from the medicinal plant Smilax china L. (SCLP). Firstly, in vitro simulated digestion confirmed that SCLP remained stable in simulated digestive fluids. Subsequently, in vivo real-time tracking of intestinal metabolism based on fluorescent labeling revealed that SCLP maintained its prototype in the small intestine and began to be degraded into fragments (Mw < 4000 Da) upon reaching the cecum and colon, where it was retained for prolonged periods. Pseudo-sterile mouse experiments indicated the mediating role of gut microbiota in SCLP metabolism. Furthermore, metagenomic sequencing suggested that SCLP increased the proportion of polysaccharide utilization loci (PULs) from Phocaeicola vulgatus and Bacteroides uniformis, elevated the gene numbers of carbohydrate-active enzymes (CAZymes) including GHs, GTs and CBMs, and activated pathways of carbohydrate metabolism. Finally, in vitro bacterial culture study verified the degradation and utilization of SCLP by Phocaeicola vulgatus and Bacteroides uniformis. In summary, this work elucidates the intestinal metabolic profile of SCLP, providing valuable insights for its further development and utilization.}, }
@article {pmid42399943, year = {2026}, author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W}, title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42399943}, issn = {1743-422X}, support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; }, abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.}, }
@article {pmid42400260, year = {2026}, author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S}, title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2695485}, pmid = {42400260}, issn = {1949-0984}, mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; }, abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.}, }
@article {pmid42402030, year = {2026}, author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W}, title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.}, journal = {mSphere}, volume = {11}, number = {7}, pages = {e0084825}, pmid = {42402030}, issn = {2379-5042}, support = {2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; }, mesh = {Animals ; *Spheniscidae/virology/classification ; *Virome ; Phylogeny ; Metagenomics ; Parvoviridae/genetics/classification/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; Cloaca/virology ; Microviridae/genetics/classification/isolation &amp; purification ; Caliciviridae/genetics/classification/isolation &amp; purification ; Anelloviridae/genetics/classification/isolation &amp; purification ; Circoviridae/genetics/classification ; Genome, Viral ; *Gastrointestinal Microbiome ; }, abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.}, }
@article {pmid42402034, year = {2026}, author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q}, title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0388925}, pmid = {42402034}, issn = {2165-0497}, support = {2022B02029//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; CARS-38//National Modern Agriculture Industry Technology System/ ; }, mesh = {Animals ; Sheep/growth &amp; development/microbiology/metabolism ; *Drugs, Chinese Herbal/metabolism/administration &amp; dosage ; Fermentation ; *Dietary Supplements/analysis ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects ; Rumen/microbiology/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Antioxidants/metabolism ; Diet ; Insulin-Like Growth Factor I/metabolism ; Superoxide Dismutase/metabolism ; }, abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.<br><br>IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.}, }
@article {pmid42404879, year = {2026}, author = {Dai, P and Feng, J and Cao, J and Fan, D}, title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1828633}, pmid = {42404879}, issn = {1664-3224}, mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.<br><br>METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.<br><br>RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-&#x3ba;B, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).<br><br>CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.}, }
@article {pmid42405768, year = {2026}, author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and May, KL and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH}, title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.}, journal = {mSphere}, volume = {11}, number = {7}, pages = {e0038626}, pmid = {42405768}, issn = {2379-5042}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; R35 GM156739/GM/NIGMS NIH HHS/United States ; R35GM136407/GM/NIGMS NIH HHS/United States ; Research Scholar Award//Southern Society for Clinical Investigation/ ; R35 GM136407/GM/NIGMS NIH HHS/United States ; AI175048//National Institute of Allergy and Infectious Diseases/ ; R35GM156739/GM/NIGMS NIH HHS/United States ; K23AI144036//National Institute of Allergy and Infectious Diseases/ ; U54CK000601/CC/CDC HHS/United States ; U54 CK000601/CK/NCEZID CDC HHS/United States ; R25 AI175048/AI/NIAID NIH HHS/United States ; }, mesh = {*Escherichia coli/virology/genetics ; Humans ; *O Antigens/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Bacteriophages/physiology ; *Coliphages/physiology ; Fecal Microbiota Transplantation ; Models, Theoretical ; }, abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.}, }
@article {pmid42409501, year = {2026}, author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D}, title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {240}, number = {}, pages = {119678}, doi = {10.1016/j.foodres.2026.119678}, pmid = {42409501}, issn = {1873-7145}, mesh = {Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Swine ; *Food Microbiology ; *Microbiota ; Bacteria/metabolism/classification/genetics ; *Red Meat/microbiology/analysis ; *Pork Meat/microbiology/analysis ; Food, Processed ; Food Handling/methods ; }, abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.}, }
@article {pmid42413135, year = {2026}, author = {Hernández-Velázquez, R and Bokulich, NA}, title = {Unlocking the biotechnological potential of traditional fermented food microbiomes.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103550}, doi = {10.1016/j.copbio.2026.103550}, pmid = {42413135}, issn = {1879-0429}, mesh = {*Biotechnology ; *Microbiota ; *Fermented Foods/microbiology ; Fermentation ; *Food Microbiology ; Multiomics ; Humans ; }, abstract = {Fermented foods are a globally important source of dietary microbes, cultural heritage, and functional diversity, yet current microbiome research captures only a narrow fraction of this richness. Public sequencing datasets are heavily skewed toward a limited set of regions and fermentation types, leaving vast areas of geographic, substrate, and process diversity underrepresented. This imbalance constrains the discovery of novel microbial species, enzymes, and biosynthetic capacities, and risks accelerating homogenization through standardized starter cultures. We argue that coordinated, ethically grounded global efforts integrating metagenomics, multi-omics, standardized metadata, and biobanking are urgently needed to document, preserve, and responsibly leverage fermented food microbial diversity for sustainable food systems and innovation.}, }
@article {pmid42413404, year = {2026}, author = {Cao, Z and Gong, H and Qin, H and Wei, T and He, X and Yang, K and Li, X and Wang, Y and Jia, Y and Lan, X and He, W and Jing, X and Long, R and Li, B and Mi, J}, title = {Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142862}, doi = {10.1016/j.jhazmat.2026.142862}, pmid = {42413404}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Escherichia coli/genetics/drug effects ; *Diarrhea/microbiology/veterinary ; *Dysbiosis/veterinary/microbiology ; Feces/microbiology ; *Cattle Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Escherichia coli Infections/veterinary/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.}, }
@article {pmid42414020, year = {2026}, author = {Clister, D and Chandra, QM and Tan, MW and Gunawan, MC and Bibi, A and Ahmed, A and Bastian, M and Meesakul, P and Cao, S and Kim, B and Nurkolis, F and Syahputra, RA}, title = {Microbiome-Based Precision Interventions in Type 2 Diabetes Mellitus: Mechanisms, Modulators, and Translational Opportunities.}, journal = {The Journal of nutrition}, volume = {156}, number = {7}, pages = {101596}, doi = {10.1016/j.tjnut.2026.101596}, pmid = {42414020}, issn = {1541-6100}, mesh = {*Diabetes Mellitus, Type 2/therapy/microbiology ; Humans ; *Precision Medicine ; Probiotics ; *Gastrointestinal Microbiome ; Prebiotics ; Fecal Microbiota Transplantation ; Synbiotics ; Dysbiosis ; Animals ; *Microbiota ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disease driven by insulin resistance, chronic low-grade inflammation, and impaired glucose regulation. Although pharmacological options have advanced, sustained glycemic control remains elusive due to heterogeneity in disease progression and therapeutic response. Precision medicine offers a framework to individualize interventions, with the gut microbiota emerging as a central determinant of host metabolic and immune regulation. Dysbiosis has been implicated in T2DM through altered microbial metabolites-including short-chain fatty acids, bile acids, branched-chain amino acids, and indole derivatives-that shape insulin sensitivity, inflammatory pathways, and glucose homeostasis. This review critically examined microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and personalized nutrition, alongside advances in metagenomics and machine learning for biomarker discovery. By integrating mechanistic and translational insights, we highlight opportunities and challenges in implementing microbiome-based precision interventions, underscoring their potential to transform T2DM management.}, }
@article {pmid42417706, year = {2026}, author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY}, title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {28}, pages = {22337-22347}, pmid = {42417706}, issn = {1520-5118}, mesh = {*Oryza/microbiology/growth &amp; development/chemistry/classification ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; Germination ; Fungi/genetics/classification/isolation &amp; purification ; *Seeds/microbiology/growth &amp; development/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.}, }
@article {pmid42418234, year = {2026}, author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC}, title = {Evolving strategies for virus discovery.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, pmid = {42418234}, issn = {2057-5858}, mesh = {*Viruses/genetics/isolation &amp; purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; }, abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.}, }
@article {pmid42418242, year = {2026}, author = {Robinson, JM and Guentas, L and Breed, MF}, title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001777}, pmid = {42418242}, issn = {2057-5858}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; }, abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.}, }
@article {pmid42418904, year = {2026}, author = {Yu, J and Wan, Y and Peng, Y and Liang, S and Chan, FKL and Ng, SC and Tun, HM}, title = {Multi-cohort evidence for impaired microbial support of the methionine cycle in children with autism spectrum disorder.}, journal = {Psychiatry research}, volume = {364}, number = {}, pages = {117317}, doi = {10.1016/j.psychres.2026.117317}, pmid = {42418904}, issn = {1872-7123}, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/metabolism ; *Methionine/metabolism ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/metabolism ; Child ; Cohort Studies ; Male ; }, abstract = {The contribution of gut microbiota to outcomes of autism spectrum disorders (ASD) has been increasingly appreciated in recent years. With the accumulating evidence on ASD-driven alterations of the gut microbiota, heterogeneities arise across different reports. To account for variabilities in gut microbiota, clinical representations of ASD and data processing approaches, as well as limitations in sample sizes among the existing gut microbiota studies for ASD, the present multi-cohort analysis applied a standard bioinformatic and statistical pipeline on the publicly available gut metagenomic sequencing data for 674 samples, including 326 TD and 348 ASD individuals, collected from eight studies across three main geographical regions. Throughout the analysis, we identified taxonomic profiles of the gut microbiota exhibited more pronounced dysbiosis associated with ASD and between-study variations compared to functional profiles. Differentially abundant taxonomic and pathway markers were identified and validated for their consistent response to ASD across different studies. Co-occurring deficits in microbial pathways for salvaging adenosylcobalamin and S-adenosyl-L-methionine and biosynthesis of methionine in children with ASD point to a reduced microbial support for the host methionine cycle. Species from Faecalibacterium, Bacteroides, Blautia and Bifidobacterium were identified as microbial contributors to ASD-deficient microbial pathways, particularly those related to the methionine cycle. Therefore, the generalisable ASD-deficient contributors to the methionine cycle, such as Blautia wexlerae, Bacteroides stercoris and Streptococcus thermophilus, could be further investigated for their role in therapeutic applications for ASD.}, }
@article {pmid42419222, year = {2026}, author = {Liang, Y and Gao, H and Chen, F and Sun, J and Sun, G and Wang, Z and Li, Y and Liu, H and Geng, M and Li, J and Zhang, Y}, title = {Bilateral intranigral α-synuclein seeding in A53T transgenic mice drives early Parkinsonism and concurrent gut dysbiosis.}, journal = {Biochemical and biophysical research communications}, volume = {830}, number = {}, pages = {154244}, doi = {10.1016/j.bbrc.2026.154244}, pmid = {42419222}, issn = {1090-2104}, mesh = {Animals ; *alpha-Synuclein/metabolism/administration &amp; dosage/genetics ; Mice, Transgenic ; *Dysbiosis/pathology ; Male ; Mice ; Gastrointestinal Microbiome ; Substantia Nigra/metabolism/pathology ; *Parkinsonian Disorders/pathology/genetics/metabolism ; Disease Models, Animal ; Female ; }, abstract = {Heterozygous A53T α-synuclein transgenic mice (M83 line) typically exhibit late-onset Parkinson's disease (PD) symptoms. This study established an accelerated PD model via bilateral intranigral injection of α-synuclein preformed fibrils (PFF) to characterize central and peripheral pathologies. Three-month-old heterozygous A53T mice received bilateral substantia nigra injections of α-synuclein PFF or PBS. Motor function was assessed monthly. Following the onset of motor deficits, the substantia nigra was harvested for immunohistochemistry and colons were harvested for H&amp;E, transcriptomic analysis and western blotting, while gut microbiota composition was assessed using metagenomic sequencing. Three months post-injection, PFF-treated mice exhibited significant motor deficits, dopaminergic neuron loss, and nigral α-synuclein aggregation, with no sex differences. Peripherally, mice displayed increased α-synuclein in colon, impaired gut motility, reduced Occludin expression indicating barrier damage, and colonic inflammation. Metagenomics identified gut dysbiosis characterized by a skewed Bacillota/Bacteroidota ratio, Lactobacillus depletion, and enrichment of inflammation-associated taxa. Bilateral intranigral α-synuclein PFF injection in A53T mice successfully induces an early-onset, progressive PD phenotype encompassing motor impairments, nigrostriatal neurodegeneration. Crucially, the model recapitulates key peripheral manifestations, including gastrointestinal dysfunction and microbial dysbiosis. These findings provide compelling evidence for a descending brain-to-gut pathological axis where central α-synuclein pathology drives distal gut alterations. This optimized model offers a valuable platform for investigating multi-system PD progression and bidirectional brain-gut communication mechanisms.}, }
@article {pmid42419262, year = {2026}, author = {Gelsinger, DR and Wang, HH}, title = {Toward precision microbiome therapeutics: From black box to blueprint.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {7}, pages = {1157-1161}, doi = {10.1016/j.chom.2026.06.014}, pmid = {42419262}, issn = {1934-6069}, mesh = {Animals ; Humans ; Bacteria/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Gene Editing ; Metagenomics ; Microbiota ; *Precision Medicine/methods ; }, abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.}, }
@article {pmid42419832, year = {2026}, author = {Chaurasia, A and Ponangi, K}, title = {The microbiome of the head and neck region.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {25-51}, doi = {10.1016/bs.ai.2026.03.002}, pmid = {42419832}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; }, abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.}, }
@article {pmid42419833, year = {2026}, author = {Jams, J and Jayasinghe, RD}, title = {Introduction.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {3-23}, doi = {10.1016/bs.ai.2026.03.005}, pmid = {42419833}, issn = {1557-8445}, mesh = {Humans ; *Microbiota ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Biofilms ; Animals ; *Head and Neck Neoplasms/microbiology/etiology/immunology ; Host Microbial Interactions ; Host-Pathogen Interactions ; }, abstract = {Microorganisms colonize nearly all anatomical sites of the human body, with the oral cavity hosting one of the most diverse, accessible, and densely populated microbial ecosystems. The oral microbiome comprises a complex consortium of bacteria, fungi, viruses, archaea, and protozoa that inhabit distinct ecological niches. Each niche provides unique physicochemical conditions that shape microbial composition, structure, and function. In addition to oral and dental sites, oral biofilms frequently develop on dental materials, appliances, and prostheses, where surface characteristics such as roughness, hydrophobicity, and chemical composition further influence microbial adhesion and biofilm maturation, leading to marked differences at species and strain levels. Advances in culture-independent molecular technologies, particularly 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics approaches, have greatly enhanced understanding of oral microbial diversity, functional capacity, and host-microbe interactions beyond the limitations of conventional culture-based methods. In health, the oral microbiome exists in a state of dynamic equilibrium, or eubiosis, which contributes to local and systemic homeostasis. This balance is modulated by host factors such as saliva composition, immune responses, and oral hygiene practices, as well as environmental influences including diet, tobacco use, and alcohol consumption. Disruption of this equilibrium, termed dysbiosis, has been increasingly implicated in the pathogenesis of head and neck cancers. Emerging evidence suggests that microbial dysbiosis may promote carcinogenesis through chronic inflammation, immune modulation, production of carcinogenic metabolites, and direct interactions with epithelial cells. Understanding the microbiology of head and neck cancer therefore provides critical insights into disease initiation, progression, and potential diagnostic and therapeutic strategies.}, }
@article {pmid42420265, year = {2026}, author = {Vilar Geraldi, M and Dwibedi, C and Jaiswal, R and Gregori, G and Zhou, X and Lv, B and Zheng, Y and Wang, X and Wu, H and Axelsson, KF and Bäckhed, F and Tremaroli, V and Lorentzon, M}, title = {Gut microbiota associates with frailty in older women.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42420265}, issn = {2041-1723}, support = {2023-01976, 2023-01976, 2022-06725, 2018-05973, 2024-03723,//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Lorentzon, 2023-2024//Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse (King Gustaf V and Queen Victoria's Foundation of Freemasons)/ ; 2024-0104//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; Lorentzon, 2016//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, mesh = {Humans ; Female ; Aged ; *Frailty/microbiology/mortality ; Aged, 80 and over ; *Gastrointestinal Microbiome/genetics/physiology ; Sweden/epidemiology ; Frail Elderly ; Bacteria/classification/genetics/isolation &amp; purification ; Cohort Studies ; }, abstract = {Frailty is a multifactorial geriatric condition linked to increased mortality and adverse health outcomes and is associated with gut microbiome features that differ from those observed in healthy ageing. We analyze gut metagenomic profiles in relation to estimated frailty severity and frailty-related clinical outcomes assessed with an internally developed and validated Frailty Mortality Index (FMI) in the SUPERB cohort, comprising 2,081 Swedish women aged 75-80 years. The FMI is a composite measure that integrates functional, physiological and psychological dimensions associated with frailty and mortality risk, and shows stronger associations with mortality compared to the Charlson Comorbidity Index in the SUPERB cohort. The FMI is inversely associated with microbial diversity, gene richness, and predicted functional capacity, which are linked to physical function, mortality and fall-related injuries. A total of 404 bacterial species are significantly associated with FMI, and most show concordant associations in a Chinese cohort of 1,448 older adults. Here we show microbial signatures linked to frailty and mortality across different continents.}, }
@article {pmid42421935, year = {2026}, author = {Memida, T and Jaar, JC and Chen, T and Cao, G and Kuriki, N and Abdolahinia, ED and Okamoto, M and Shindo, S and Yamashita, S and He, X and Suzuki, M and Vardar, S and Kawai, T and Han, X}, title = {Hyperglycemia and systemic inflammation differentially shape immune dysregulation, tissue destruction, and microbiota in experimental periodontitis and peri-implantitis in diabetic mice.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847456}, pmid = {42421935}, issn = {1664-3224}, mesh = {Animals ; *Peri-Implantitis/immunology/microbiology/pathology/etiology ; *Periodontitis/immunology/microbiology/pathology/etiology ; Mice ; *Hyperglycemia/immunology/microbiology ; *Microbiota/immunology ; *Diabetes Mellitus, Experimental/immunology/complications/microbiology ; *Inflammation/immunology ; Disease Models, Animal ; Cytokines/metabolism ; Male ; }, abstract = {AIM: To investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.<br><br>MATERIALS AND METHODS: After implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.<br><br>RESULTS: Liraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3[+] Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.<br><br>CONCLUSIONS: Diabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.}, }
@article {pmid42421950, year = {2026}, author = {Lu, W and Wang, Y and Zhang, J and Li, Y and Huang, L and Yang, W and Zhou, S and Zhou, M and Chen, Y and Wu, R and Wang, Y and Zhang, H and Wan, J and Xia, F and Zhang, Z and Shen, L}, title = {Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1871586}, pmid = {42421950}, issn = {1664-3224}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immunotherapy/adverse effects/methods ; *Metabolome ; Metabolomics ; Multiomics ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/metabolism/microbiology/immunology ; Treatment Outcome ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Immunotherapy-based total neoadjuvant therapy (iTNT) is a promising strategy for microsatellite-stable locally advanced rectal cancer (LARC), yet therapeutic response and treatment-related toxicity remain heterogeneous. Integrated fecal microbiome and metabolome profiling may provide non-invasive biomarkers and functional clues for optimizing iTNT.<br><br>METHODS: We conducted a longitudinal fecal multi-omics study using samples from patients with microsatellite-stable LARC enrolled in the TORCH trial (NCT04518280). A total of 102 fecal samples were collected before treatment, during treatment, and after completion of iTNT. Metagenomic sequencing and untargeted metabolomics were integrated to characterize longitudinal microbial and metabolic changes. We also examined baseline features associated with therapeutic response, and multi-omics signatures linked to hematologic and gastrointestinal toxicities. A murine tumor model treated with radiotherapy plus immunotherapy, with or without GABA supplementation, was used for functional testing of the response-associated metabolite.<br><br>RESULTS: iTNT induced longitudinal gut microbiome remodeling. This remodeling was characterized by altered community structure, increased alpha diversity, enhanced microbial network connectivity, enrichment of Firmicutes-associated taxa, and depletion of Bacteroidetes and Proteobacteria. Fecal metabolomic profiles also shifted during treatment, with prominent changes in amino acid-related pathways and significant concordance between microbial and metabolic profiles. Responders were enriched in several Firmicutes-associated genera, including Ruminococcus, Anaerostipes, and Coprobacillus. In contrast, non-responders showed enrichment of Klebsiella and response-associated metabolites including gamma-aminobutyric acid (GABA). Microbial functional and metabolomic pathway analyses showed convergent enrichment of arginine and proline metabolism, which includes an alternative GABA-related metabolic route. Functionally, GABA supplementation weakened the antitumor efficacy of radiotherapy plus immunotherapy and was accompanied by systemic T cell dysfunction. In addition, specific microbial taxa and fecal metabolic features were associated with hematologic toxicity and diarrhea severity, with baseline metabolites showing exploratory potential for toxicity stratification.<br><br>CONCLUSION: This study provides a longitudinal fecal microbiome-metabolome resource for iTNT in LARC and identifies candidate microbial and metabolic features associated with treatment response and toxicity. GABA was functionally supported as a response-associated immunomodulatory metabolite, while candidate microbial functional signals warrant further mechanistic validation.}, }
@article {pmid42424147, year = {2026}, author = {Ebel, ER and Kulkarni, AS and Mongad, DS and Olm, MR and Devi, SI and Mir, BA and Ozarkar, S and Sonnenburg, ED and Shouche, YS and Sonnenburg, JL and Dhotre, DP}, title = {Gut microbiomes of tribal communities in India vary with dairy and grain consumption.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2694242}, pmid = {42424147}, issn = {1949-0984}, support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; India ; Feces/microbiology ; *Diet ; *Edible Grain/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Dairy Products ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Tract/microbiology ; }, abstract = {Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%-47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.}, }
@article {pmid42424326, year = {2026}, author = {Brown, CR and Yacoub, MN and Bogan, JE and Buehler, MD and Hoffman, ML and Krumbeck, JA and Loughman, ZJ}, title = {Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0350824}, pmid = {42424326}, issn = {1932-6203}, mesh = {Animals ; *Cloaca/microbiology/parasitology ; *Cryptosporidium/isolation &amp; purification ; *Snakes/microbiology/parasitology ; *Microbiota ; *Cryptosporidiosis/microbiology/parasitology ; Animals, Wild/microbiology ; }, abstract = {The Eastern Indigo Snake (EIS; Drymarchon couperi), a federally threatened species native to the southeastern United States, serves as a valuable model for examining the effects of captivity and infection on gastrointestinal microbial composition in reptiles. As an alternative to direct gut sampling, we examined the cloacal microbiomes of EISs to evaluate changes in microbial community structure across our study groups. This study assessed the cloacal microbiome of wild and captive EISs using shotgun metagenomic sequencing. Samples were divided into three groups for comparative microbiome analysis: captive snakes positive for Cryptosporidium serpentis (C. serpentis), captive snakes negative for C. serpentis, and wild snakes. Alpha (Shannon index, paired Wilcoxon test) and beta diversity (Bray-Curtis dissimilarity, PERMANOVA, CAP) metrics were used to assess microbial diversity and community composition across groups. Furthermore, a linear discriminant analysis effect size (LEfSe) was used to identify microbial taxa significantly enriched in C. serpentis-positive versus C. serpentis-negative captive snakes. Bacterial, fungal, bacteriophage, nematode, and protozoan taxa were significantly enriched in C. serpentis-positive snakes compared with C. serpentis-negative captive snakes, based on a linear discriminant analysis (LDA) score ≥ 2.5 and p ≤ 0.05. Total taxa species Shannon diversity was consistent between C. serpentis-positive and negative captive snakes (p = 0.55) while wild snake samples were significantly more diverse (p = 0.026). Wild snakes also exhibited a significantly increased Shannon diversity of fungi (p = 0.044), protozoa (p = 0.012), and nematodes (p = 0.008) compared to their captive counterparts. This study offers the first in-depth characterization of the cloacal microbiome in reptiles, specifically in EISs, using shotgun metagenomic sequencing. The findings establish a foundation for exploring microbiota-host interactions with implications for reptile health, disease ecology, and conservation management.}, }
@article {pmid42425523, year = {2026}, author = {Post, SE and Ceisler, HS and Lal, RG and Singh, A and Deen, MA and Bonomo, LE and Cunic, LM and Brito, IL}, title = {Discovery of Novel Glycosidase-Derived Cell-Penetrating Peptides Encoded by Human Gut Commensals.}, journal = {ACS synthetic biology}, volume = {15}, number = {8}, pages = {3179-3192}, pmid = {42425523}, issn = {2161-5063}, support = {NA//David and Lucile Packard Foundation/ ; NA//Pew Charitable Trusts/ ; NA//Cornell College of Engineering Innovation and Entrepreneurship grant/ ; NA//Cornell Ignite Innovation Acceleration grant/ ; NA//Cornell University BRC Flow Cytometry Core Facility/ ; NA//Cornell University BRC Genomics Core Facility/ ; NA//Cornell University BRC Imaging Core Facility/ ; NA//National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Cell-Penetrating Peptides/metabolism/genetics/chemistry ; Escherichia coli/metabolism/genetics ; *Glycoside Hydrolases/metabolism/genetics/chemistry ; *Gastrointestinal Microbiome ; Fibronectins/metabolism ; Bacteroidetes/enzymology/genetics ; Endocytosis ; }, abstract = {Intracellular delivery of therapeutics remains a major challenge for modern medicine. To enhance intracellular uptake, therapeutics can be delivered with carrier proteins possessing an inherent cell-penetrating activity. There is an increasing need for new cell-penetrating carriers with diverse biophysical properties and mechanisms of action to transport a wide range of therapeutic cargo. As many cell-penetrating proteins and peptides derive from natural proteins, we sought to mine a previously unexplored community, the human gut microbiome, for cell-penetrating sequences. Here, we performed a high-throughput functional metagenomic screen to identify cell-penetrating protein fragments from the human gut microbiome. We identified protein fragments encoded within glycosidase enzymes from members of the Bacteroidetes phylum that mediate internalization into human cell lines when displayed on the surface of nonpathogenic, noninvasive Escherichia coli. We investigate one fragment, dubbed Gh_112, that adheres to human fibronectin, activates multiple endocytic pathways, and specifically promotes uptake of E. coli into multiple cancerous epithelial cell lines rather than healthy epithelial tissue in vitro. Overall, this work demonstrates that the human gut microbiome is a source of cell-penetrating sequences and expands the known repertoire of cell-penetrating carrier systems.}, }
@article {pmid42425637, year = {2026}, author = {Elsheshtawy, A and Clokie, BGJ and Saugh, S and Adler, KD and Michniewski, SM and MacKenzie, S and Clokie, MRJ and Sicheritz-Pontén, T and Albalat, A}, title = {Microbial succession and spoilage dynamics revealed by multi-omics in Norway lobster (Nephrops norvegicus) during ice storage.}, journal = {Food microbiology}, volume = {140}, number = {}, pages = {105151}, doi = {10.1016/j.fm.2026.105151}, pmid = {42425637}, issn = {1095-9998}, mesh = {Animals ; *Nephropidae/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Seafood/microbiology/analysis ; Food Storage ; Multiomics ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Shellfish/microbiology ; *Microbiota ; Ice ; Food Microbiology ; }, abstract = {The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.}, }
@article {pmid42426489, year = {2026}, author = {Dimri, A and Sharma, P and Vishvakarma, R and Sharma, S}, title = {Effect of Probiotics on the Gut-Mammary Pathway: Implications on Infant Microbiota Transfer and Development.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {42426489}, issn = {2161-3311}, mesh = {Humans ; *Probiotics/administration &amp; dosage/pharmacology ; Female ; *Gastrointestinal Microbiome ; Infant, Newborn ; Milk, Human/microbiology ; Lactobacillus ; Bifidobacterium ; Pregnancy ; Infant ; *Gastrointestinal Tract/microbiology ; Lactation ; *Mammary Glands, Human/microbiology ; }, abstract = {PURPOSE OF REVIEW: Transfer of microbiota from the maternal gut, during lactation, takes place via breastmilk, which establishes an intricate beneficial microbial ecosystem in the gut of the newborn. A healthy gut microbiota influences and enhances the neonatal health, and aids in multidimensional development-metabolically, immunologically, neurologically, and hormonally. Several microorganisms like Lactobacillus and Bifidobacterium get transferred to the infant gut and play a key role in its colonization and programming. Administration of such microbes, or probiotics, to the mother can assist in improving the benefits imparted by breastmilk to the infant, and can also provide health benefits to the mother. In recent years, there has been a focus on related metagenomic studies and the immunological effects of individual genera have also been studied in detail. In this review, we observe the gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios. We also analyze the level of evidence of potential of some promising probiotic strains in the transfer, establishment, and development of infant gut microbiota based on recently conducted studies.<br><br>RECENT FINDINGS: The analysis of recent metagenomic studies proved that strains like Bifidobacterium infantis, Lactobacillus rhamnosus, and Limosilactobacillus reuteri exibit a high level of evidence in benefitting the microbiota transfer as well as establishment, diversification, and development of the infant gut ecosystem. Hence, these strains in particular, can be given as supplements to mothers during pregnancy and lactation, in order to improve their inherent immunity and the overall health of the mother-infant dyad. With the advent of metagenomics, the roles, functions and effects of microbes in the gut-mammary pathway have been re-examined. This review, critically evaluates the recent studies related to gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios with particular emphasis on the strength and quality of their evidence.}, }
@article {pmid42428252, year = {2026}, author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y}, title = {The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.}, journal = {Environmental health perspectives}, volume = {134}, number = {3}, pages = {335-350}, pmid = {42428252}, issn = {1552-9924}, mesh = {Humans ; *Air Pollution/adverse effects/statistics &amp; numerical data ; *Gastrointestinal Microbiome/drug effects ; Aged ; Particulate Matter/adverse effects ; Ozone ; Male ; Female ; *Cognition/drug effects ; *Cognitive Dysfunction/epidemiology ; *Air Pollutants ; *Environmental Exposure/statistics &amp; numerical data ; }, abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway given their crucial role in the gut-brain axis.<br><br>OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circulating metabolites in the association of residential PM2.5 and O3 exposure with cognitive dysfunction.<br><br>METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated by using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-Mental State Examination and Hasegawa Dementia Scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes.<br><br>RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and l-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase.<br><br>CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation.}, }
@article {pmid42429456, year = {2026}, author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K}, title = {Exploring life's hidden majority: microbial dark matter symposium highlights.}, journal = {mSphere}, volume = {11}, number = {7}, pages = {e0058725}, pmid = {42429456}, issn = {2379-5042}, mesh = {Metagenomics ; *Microbiota ; Bacteria/genetics/classification ; Computational Biology ; Ecosystem ; }, abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.}, }
@article {pmid42429485, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Multi-omics analysis identify novel microbiome-metabolome signatures associated with obesity.}, journal = {Journal of applied microbiology}, volume = {137}, number = {7}, pages = {}, doi = {10.1093/jambio/lxag172}, pmid = {42429485}, issn = {1365-2672}, support = {2016YFC1201805//National Key R&amp;D Program of China/ ; 2017YFC1001100//National Key R&amp;D Program of China/ ; 201604020007//Science and Technology Program of Guangzhou, China/ ; 81770878//National Natural Science Foundation of China/ ; }, mesh = {*Obesity/microbiology/metabolism/blood ; Humans ; Multiomics ; Male ; *Metabolome ; Metabolomics ; Body Mass Index ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Cohort Studies ; }, abstract = {AIMS: Explore the potential microbiome and serum metabolome factors and their interactions associated with obesity.<br><br>METHODS AND RESULTS: We performed a systematic multi-omics analysis using paired metagenomic and metabolomic profiles-including untargeted serum metabolomics, lipidomics, and short-chain fatty acids (SCFAs)-with body mass index (BMI) from a cohort of 495 US men. Single omics analysis identified 52 gut bacteria species and 31 serum metabolites for potential associations with BMI. Among the identified bacteria, Collinsella stercoris (C. stercoris) (Coef.=-0.147, P = 0.015) was negatively associated, whereas Bacteroides fragilis (B. fragilis) (Coef.=0.294, P = 1.22E-04) and Veillonella dispar (V. dispar) (Coef.=0.135, P = 0.001) were positively associated, these results were further validated by an independent Chinese cohort. Several of the identified metabolites, including gamma-glutamylglycine (Coef.=-0.713, P = 4.53E-06), asparagine (Coef.=-0.629, P = 3.53E-05), glycine (Coef.=-0.952, P = 5.28E-09), and serotonin (Coef.=0.566, P = 1.78E-04) were associated with these significant bacteria (P&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: This multi-omics study identifies key gut bacteria and serum metabolites that interact to associate with host obesity, providing systemic insight into microbiome-host metabolic interactions.}, }
@article {pmid42429609, year = {2026}, author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA}, title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.}, journal = {mSphere}, volume = {11}, number = {7}, pages = {e0002726}, pmid = {42429609}, issn = {2379-5042}, support = {AI173448//National Institute of Allergy and Infectious Diseases/ ; HD117458//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; F31 DK138748/DK/NIDDK NIH HHS/United States ; R21 AI173448/AI/NIAID NIH HHS/United States ; F31 HD117458/HD/NICHD NIH HHS/United States ; T32 AI055449/AI/NIAID NIH HHS/United States ; DK138748/DK/NIDDK NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; F31 DK136201/DK/NIDDK NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; DK136201/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; AI167538//National Institute of Allergy and Infectious Diseases/ ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; AI167547//National Institute of Allergy and Infectious Diseases/ ; S10 RR024574/RR/NCRR NIH HHS/United States ; HD111236//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, mesh = {Animals ; Female ; *Vagina/microbiology/immunology ; *Cytokines/immunology ; Mice ; *Streptococcus agalactiae/growth &amp; development/immunology ; *Streptococcal Infections/immunology/microbiology ; *Diabetes Mellitus, Type 2/immunology/complications/microbiology ; *Mucous Membrane/immunology/microbiology ; Mice, Inbred C57BL ; *Immunity, Mucosal ; Microbiota ; Disease Models, Animal ; }, abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS vaginal carriage is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokines at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences, with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to eight pro-inflammatory cytokines post-GBS infection. Diabetic mice exhibited decreased proportions of uterine neutrophils and, following GBS exposure, also displayed an expanded vaginal γδ T cell compartment compared with controls. Pairing cytokine observations with GBS colonization revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS phenotypes. Intravaginal supplementation with rIL-1α resolved GBS burden differences between diabetic mice and controls, confirming that deficient vaginal cytokines contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention.IMPORTANCEPeople with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances the colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes in the vaginal microbiome but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.}, }
@article {pmid42429677, year = {2026}, author = {Sarkar, M and Maddheshiya, A and Tailor, P and Nath, S and Makkar, N and ,  and Misra, S and Desiraju, BK and Wadhwa, N and Bhatnagar, S and Kshetrapal, P and Mukherjee, S}, title = {Longitudinal shifts in oral microbiome composition and metabolic pathways associated with preterm birth.}, journal = {mSystems}, volume = {11}, number = {8}, pages = {e0018426}, pmid = {42429677}, issn = {2379-5077}, support = {BT/PR34219/MED/97/463/2019//Department of Biotechnology, Ministry of Science and Technology, India/ ; 60108//BRIC-NIBMG Intramural funding/ ; }, mesh = {Humans ; Female ; *Premature Birth/microbiology/metabolism ; *Microbiota/genetics ; Pregnancy ; *Metabolic Networks and Pathways ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Adult ; Longitudinal Studies ; Saliva/microbiology ; }, abstract = {Oral dysbiosis in pregnant women with oral diseases has been associated with adverse pregnancy outcomes. However, the inter-individual variability in oral microbiome composition of pregnant women without any oral disease, and its role in preterm birth, has not been studied yet. Here, we have collected saliva from 20 term birth (TB) and 20 preterm birth (PTB) delivering women without any self-reported oral disease at three trimesters (n = 120). Microbial DNA was subjected to 16S rRNA gene sequencing for taxonomic classification, and microbial pathways were investigated by PICRUSt2. In a subset of samples, shotgun metagenomic sequencing was done to identify microbial species, their gene families, and their pathways. TB and PTB women were distributed into three distinct oral community types (OCTs). Haemophilus parainfluenzae and Rothia mucilaginosa were associated with TB and PTB, respectively. The chorismate biosynthesis pathway, essential for folic acid biosynthesis, was significantly enriched in TB, whereas the enterobactin biosynthesis pathway that produces iron chelators (siderophores) was significantly enriched in PTB. The heterolactic fermentation pathway that reduces oral pH was enriched in PTB. Our data suggest that oral microbiome changes might have an impact on birth outcomes in women even without any history of self-reported oral disease during the pregnancy period.IMPORTANCEThe importance of this study lies in demonstrating that compositional and functional shifts in the oral microbiome are associated with pregnancy outcomes. Using a longitudinal design across three trimesters in an Indian cohort, we show that pregnant women segregate into distinct oral community types with consistent associations to term birth (TB) and preterm birth (PTB). Importantly, the TB-associated microbiome was enriched in taxa and pathways linked to vitamin and amino acid biosynthesis, including chorismate and threonine metabolism, which are critical for fetal growth. In contrast, PTB was associated with pathways related to iron scavenging and acidification of the oral environment, suggesting a metabolically stressed and dysbiotic state. These findings highlight the oral microbiome as a previously underappreciated, modifiable factor in pregnancy outcomes and underscore its potential relevance for early risk stratification and preventive strategies against PTB.}, }
@article {pmid42429762, year = {2026}, author = {Putman, T and Abdel-Hamid, AM and Galbraith, E and Schimmel, P and Kim, H and Yasuma, T and Alhawsawi, MAB and Boateng, KA and Holmes, J and Duersteler, M and D'Alessandro-Gabazza, CN and Fujimoto, H and Kobayashi, T and Walden, KKO and Rendon, G and Fields, CJ and Zuckermann, FA and Mackie, RI and Son, S and Leistikow, KR and Gabazza, EC and King, MR and Cann, I}, title = {A Bacillus-based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella-infected pigs.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {8}, pages = {e0097226}, pmid = {42429762}, issn = {1098-5336}, support = {MDG Project fund 547965//Microbial Discovery Group/ ; 2017-67015-26629//U.S. Department of Agriculture/ ; }, mesh = {Animals ; Swine ; *Salmonella Infections, Animal/microbiology/therapy ; *Bacillus/physiology ; *Gastrointestinal Microbiome/drug effects ; *Porcine Reproductive and Respiratory Syndrome/microbiology ; Lung/pathology/microbiology ; Animal Feed/analysis ; *Swine Diseases/microbiology ; Porcine respiratory and reproductive syndrome virus/physiology ; *Probiotics/administration &amp; dosage ; }, abstract = {Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus-based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella-infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella-only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella-only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health.IMPORTANCEAntibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus, as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella-infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus-based DFM could improve outcomes along the gut-lung axis under realistic co-infection conditions.}, }
@article {pmid42430408, year = {2026}, author = {Khan, N and Nasir, MM and Aziz, U and Manzoor, H and Raziq, MF and Hussain, Z and Jabeen, I and Kayani, MUR}, title = {Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0340748}, pmid = {42430408}, issn = {1932-6203}, mesh = {*Crohn Disease/microbiology/genetics ; Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; Molecular Dynamics Simulation ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/chemistry/metabolism ; Colitis, Ulcerative/microbiology/genetics ; }, abstract = {Metagenomics has revealed disease-associated shifts in microbial taxa and functions in inflammatory bowel disease (IBD) patients. However, the role of genomic variation in gut commensals remains poorly understood. Here, we integrated metagenomic profiling, variant calling, and structural bioinformatics to identify disease-associated variants in the gut microbes. Crohn's disease (CD) and ulcerative colitis (UC) showed significant negative associations with Bacteroides uniformis, Bacteroides vulgatus, and Eubacterium rectale. These bacteria exhibited 190,712 single-nucleotide polymorphisms, including 479 CD-specific and 235 UC-specific variants. Variant prioritization identified a CD-specific Val170Leu substitution in the conserved starch-binding domain of the Starch Utilization System D (SusD) protein in B. uniformis. Structural modeling and cyclodextrin docking indicated reduced binding affinity in the mutant, while 200-ns molecular dynamics simulations showed stable ligand retention only in the wild type. These findings suggest that impaired starch metabolism driven by SusD variation may contribute to B. uniformis depletion in CD and demonstrate the value of integrating metagenomics with structural analyses to identify functionally relevant microbial variants.}, }
@article {pmid42437546, year = {2026}, author = {Fregolente, LG and Roth, FN and Warncke, JD and Macpherson, AJ and Yilmaz, B and Bassetti, CLA}, title = {The gut-sleep connection: a scoping review into microbiome alterations in sleep-wake and circadian disorders.}, journal = {Sleep medicine}, volume = {147}, number = {}, pages = {109136}, doi = {10.1016/j.sleep.2026.109136}, pmid = {42437546}, issn = {1878-5506}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sleep/physiology ; Sleep Duration ; *Sleep Wake Disorders/microbiology/physiopathology ; *Chronobiology Disorders/microbiology ; Circadian Rhythm/physiology ; }, abstract = {Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.}, }
@article {pmid42437837, year = {2026}, author = {Devi, U and Ramadass, B and Pullattayil, AK and Vishnu Bhat, B}, title = {Gut Microbiome in Neonatal Necrotizing Enterocolitis - A Comprehensive Review of Evidence.}, journal = {Indian journal of pediatrics}, volume = {93}, number = {9}, pages = {968-975}, pmid = {42437837}, issn = {0973-7693}, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/physiology ; Infant, Premature ; }, abstract = {Necrotizing enterocolitis (NEC) is one of the most catastrophic gastrointestinal emergency occurring predominantly in preterm neonates. It contributes to substantial neonatal morbidity and mortality. Disturbances in the intestinal microbiome are crucial to disease pathogenesis. In preterm infants, an immature intestinal barrier, dysregulated immune responses, and environmental exposures altogether predispose to alteration in microbial colonization and intestinal inflammation. This review was done to present the current evidence on gut microbiome alterations associated with NEC in preterm infants. A systematic search of the MEDLINE and EMBASE databases was performed using search strategy related to prematurity, intestinal microbiota, and necrotizing enterocolitis. A total of 42 studies assessing microbial composition, microbial progression, or microbial functional patterns in relation to NEC were included. Across the included studies, NEC was commonly preceded by reduced microbial diversity, delayed maturation of anerobic communities, and expansion of Proteobacteria, particularly Enterobacteriaceae family such as Klebsiella and Escherichia. Longitudinal studies further showed that these microbial changes may become evident days to weeks before clinical disease, suggesting a potential window for early risk identification. Functional analyses also showed alterations in microbial metabolic pathways, including short-chain fatty acids, tricarboxylic acid intermediates, volatile compounds, and viral signatures that may lead to epithelial injury and inflammatory signaling. Clinical and environmental factors including antibiotic exposure, mode of delivery, feeding practices, and NICU microbial ecosystem are important determinants of neonatal gut microbiome development. Thus, the current evidence supports a reproducible pattern of intestinal dysbiosis preceding NEC. Better understanding of microbiome dynamics may aid early risk stratification and support microbiome-targeted preventive strategies in vulnerable preterm populations.}, }
@article {pmid42439510, year = {2026}, author = {Hertramph, TL and Dorda, M and Pallenberg, ST and Sauer-Heilborn, A and Ringshausen, FC and Steglich, M and Hansen, G and Tümmler, B and Wiehlmann, L and Rosenboom, I and Dittrich, A-M}, title = {Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0060126}, pmid = {42439510}, issn = {2165-0497}, support = {82DZL002C1//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 2020_EKPK.20//Else Kr&#xf6;ner-Fresenius-Stiftung/ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Aminophenols/therapeutic use/pharmacology ; *Indoles/therapeutic use/pharmacology/administration &amp; dosage ; *Quinolones/therapeutic use/pharmacology ; *Metagenome/drug effects ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; *Pyridines/therapeutic use/pharmacology ; *Pyrazoles/therapeutic use ; *Pyrroles/therapeutic use/pharmacology ; Prospective Studies ; *Microbiota/drug effects ; Female ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; *Benzodioxoles/therapeutic use ; Male ; Child ; Whole Genome Sequencing ; Pyrrolidines ; }, abstract = {Mutation-specific cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved clinical outcomes for people with CF (pwCF), yet its impact on the nasal microbial metagenome remains insufficiently understood. This prospective, post-approval study investigated the impact of 15-week ETI therapy on sinonasal microbiota of pwCF aged 12 years and older. Whole-genome shotgun sequencing was performed on total DNA from 24 paired nasal lavage samples, with synthetic spike-in controls enabling absolute abundance normalization. Taxonomic profiling was conducted using the Wochenende pipeline. ETI did not induce major shifts in alpha or beta diversity. Instead, the overall microbial community became further dominated by the skin commensals Staphylococcus epidermidis and Cutibacterium acnes, accompanied by a more than twofold increase in total bacterial load. Classical CF pathogens showed divergent trajectories: Pseudomonas aeruginosa tended to decrease, whereas Staphylococcus aureus exhibited a tendency toward increased abundance. Co-occurrence network analysis revealed a transition from a dense, multicomponent baseline network to a single, fully connected, but less densely integrated network following treatment initiation.IMPORTANCEThe nasal cavity represents the primary entry point of microorganisms into the respiratory tract and a potential reservoir for lower airway infection, the major cause of CF disease progression. Using shotgun metagenomics with spike-in controls, this study provides the first genome-wide characterization of how ETI alters microbial load and pathogen dynamics in CF nasal airways. Treatment with ETI strengthened the dominance of skin commensals in the nares while reducing P. aeruginosa. Given the observed increase in S. aureus, further work is needed to determine whether this represents expansion of a typical nasal colonizer or a clinically relevant rise of a key CF pathogen that could act as a reservoir for future lower airway infection.}, }
@article {pmid42442277, year = {2026}, author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J}, title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120488}, doi = {10.1016/j.ecoenv.2026.120488}, pmid = {42442277}, issn = {1090-2414}, mesh = {*Pyrethrins/toxicity ; Animals ; *Rumen/microbiology/drug effects ; *Insecticides/toxicity ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Dietary Exposure/adverse effects ; *Gastrointestinal Microbiome/drug effects ; }, abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.}, }
@article {pmid42442320, year = {2026}, author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A}, title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111939}, doi = {10.1016/j.ijfoodmicro.2026.111939}, pmid = {42442320}, issn = {1879-3460}, mesh = {*Cheese/microbiology/analysis ; Spain ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; Food Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Multiomics ; Machine Learning ; Microbiota ; }, abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.}, }
@article {pmid42446470, year = {2026}, author = {Almulhim, F and Narayanasamy, S and Wang, C and Mandal, P and Bensaddek, D and Amad, M and Hong, PY}, title = {Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70372}, pmid = {42446470}, issn = {1462-2920}, support = {BAS/1/1033-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Wastewater/microbiology/chemistry ; Proteomics ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Biofilms ; Metagenomics ; Nitrogen/metabolism ; Denitrification ; }, abstract = {Reclaimed wastewater is increasingly reused for irrigation and other non-potable applications; however, inadequately treated effluent has raised concerns regarding environmental and public health impacts. Water quality in reclaimed distribution systems is shaped by multiple factors, particularly hydraulic stagnation in pipes and storage reservoirs. Stagnation can alter microbial community stability and facilitate persistence of pathogenic taxa. To investigate how prolonged stagnation affects microbial community structure and function, we integrated metagenomics and metaproteomics analyses of biofilms under flow and stagnant conditions over 3, 5 and 7 months. Prolonged stagnation caused pronounced compositional shifts, including strong reductions in nitrogen-removing taxa such as Nitrospira and Nitrosomonas. Correspondingly, key nitrification and denitrification proteins were depleted ≥ twofold under stagnation, indicating impaired nitrogen conversion processes. Stagnation also enriched motility- and transport-related functions and promoted Acidovorax persistence, a genus including phytopathogenic species. In contrast, flow conditions sustained nitrogen-cycling activity, contaminant-degrading enzymes, and quorum-quenching proteins, supporting greater biostability. Overall, our findings show that prolonged stagnation disrupts microbial community balance, suppresses essential nitrogen-cycling and detoxification pathways, and reduces the functional robustness of treated wastewater. Maintaining hydraulic flow within reclaimed water systems is therefore critical for preserving microbial functionality and ensuring safe and reliable reuse in irrigation and other non-potable applications.}, }
@article {pmid42447082, year = {2026}, author = {Rodríguez, JA and Santos-Bay, L and Narechania, A and Carøe, C and Sirén, K and Mak, SST and Broman Nielsen, I and Ramsøe, M and Pontén, TS and Lillevang, S and Andersen, LT and Gilbert, MTP}, title = {The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0350187}, pmid = {42447082}, issn = {1932-6203}, mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota/genetics ; Metagenome ; Food Microbiology ; Pasteurization ; Lactococcus lactis/genetics/isolation &amp; purification ; Clostridium tyrobutyricum/genetics/isolation &amp; purification ; }, abstract = {One of the biggest challenges for dairy producers is the substantial variability in final product properties caused by changes in the production environment. In cheese production, this variation is influenced by several factors, particularly the milk base and its pretreatment, which shape the microbiome throughout the process and ultimately affect the cheese's organoleptic characteristics. To examine the impact of three different pretreatments for pasteurised milk- microfiltration, protein fortification, and pasteurisation only (control)- on microbiome dynamics, we generated metagenome sequencing data from 14 cheese production steps across these three production trials at a Danish dairy factory. We constructed three metagenomic co-assemblies, identifying nine high-quality metagenome-assembled genomes. Our analysis revealed that a specific strain of Lactococcus lactis dominates the process, while other minor bacterial species persist at very low abundances (<1%), contributing non-negligibly to product properties. Notably, we detected DNA from Clostridium tyrobutyricum, a known bacterium whose heat-resistant spores may cause dairy spoilage, in pasteurised only and protein-fortified milk trials but was nearly absent in microfiltered milk. To enhance our analyses, we implemented KHILL, a novel k-mer based method, which facilitates metagenomic co-assembly and enables early detection of unwanted microorganisms. Our findings provide industrial dairy producers with a comprehensive view of microbial dynamics during cheese production, offering insights to improve process consistency and product quality.}, }
@article {pmid42447623, year = {2026}, author = {Su, K and Tian, S and Xia, Y and Zhao, X and Huang, J and Hu, S and Ye, J}, title = {Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study.}, journal = {Journal of forensic and legal medicine}, volume = {122}, number = {}, pages = {103213}, doi = {10.1016/j.jflm.2026.103213}, pmid = {42447623}, issn = {1878-7487}, mesh = {Humans ; Female ; *Microbiota/genetics ; Postmortem Changes ; Male ; Metagenomics ; Mouth/microbiology ; Lung/microbiology ; Middle Aged ; Aged ; Anal Canal/microbiology ; Trachea/microbiology ; Colon/microbiology ; Adult ; Nasal Cavity/microbiology ; Shotgun Sequencing ; Aged, 80 and over ; Forensic Microbiology ; *Metagenome ; }, abstract = {Postmortem microbial communities may provide useful information for forensic microbiology, but species-level and functional profiles across multiple cadaveric anatomical sites remain poorly characterized. Here, shotgun metagenomic sequencing was performed on 144 samples from six anatomical sites, including the oral cavity, nasal cavity, trachea, lung, colon, and anus, collected from 24 human cadavers. A total of 15,301,799,968 raw reads were obtained, and 6565 species were identified, and KEGG pathways were annotated at the L1, L2, and L3 levels. Species-level microbial composition differed significantly among anatomical sites. PERMANOVA with permutations blocked by individual identity showed that anatomical site was the dominant factor explaining microbial community variation (R[2] = 0.3778, p = 0.001, q = 0.001), whereas postmortem interval did not show a significant independent effect within the 1-38-day interval. KEGG functional profiles also differed significantly among anatomical sites at the L2 and L3 levels, and 182 of 214 L3 pathways showed significant site-associated differences after false-discovery-rate correction. Pathway-level mixed-effect models further indicated that anatomical site remained significantly associated with most L3 pathways after accounting for postmortem interval, age, sex, cause of death, and repeated sampling from the same individual. Species-pathway correlation analysis identified significant taxon-function associations, but these were interpreted as correlative rather than direct evidence of species-specific functional contribution. Low-biomass sensitivity analyses indicated that respiratory-site results, especially lung and tracheal findings, should be interpreted cautiously because of high host DNA proportions and low non-host read counts. Inter-site shared occurrence and intra-site co-occurrence analyses further described distributional associations across anatomical sites. This study establishes a multi-site postmortem metagenomic reference framework for characterizing anatomical-site-specific microbial and functional patterns, offering insights into forensic microbiology and postmortem microbial ecology.}, }
@article {pmid42448379, year = {2026}, author = {Feng, Y and Lin, G and Jiang, Z and Shi, W and Deng, L and Dong, J}, title = {A Phenotype-Embedded Mapper Framework Links Microbiome-Metabolome Interaction Modules to Colorectal Cancer.}, journal = {Journal of proteome research}, volume = {25}, number = {8}, pages = {4177-4188}, doi = {10.1021/acs.jproteome.6c00192}, pmid = {42448379}, issn = {1535-3907}, support = {82360363//National Natural Science Foundation of China/ ; 82372087//National Natural Science Foundation of China/ ; 2026Y0004//Natural Science Foundation of Fujian Province/ ; 20232BAB206136//Natural Science Foundation of Jiangxi Province/ ; }, mesh = {*Colorectal Neoplasms/microbiology/metabolism/genetics ; Humans ; *Metabolome ; Phenotype ; Algorithms ; Multiomics ; Metabolomics/methods ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {Integrative analysis of the gut microbiome and metabolome can help characterize colorectal cancer (CRC)-associated molecular changes that are difficult to resolve from either omics layer alone. However, microbiome-metabolome data are high-dimensional, heterogeneous, and often contain nonlinear or locally confined associations that may be obscured by global linear models. Here, we propose a phenotype-guided topological framework that extends the Mapper algorithm for local interpretation of paired microbiome and metabolome profiles. Disease-associated variation from each omics block was summarized by partial least-squares regression and used to construct a two-dimensional filter space for Mapper graph construction. We further developed an Extended Spatial Analysis of Functional Enrichment strategy (eSAFE) to evaluate the spatial enrichment of phenotypes, individual features, and feature-pair associations on the resulting graph. Applied to paired fecal metagenomic and metabolomic profiles from a CRC cohort, the framework organized samples into phenotype-aligned neighborhoods and identified localized microbial, metabolic, and cross-omics association patterns linked to CRC. Coenrichment analysis further prioritized disease-associated features and interaction modules that were partly distinct from those obtained by univariate differential analysis or supervised sparse multiblock integration. One disease-localized microbiome-metabolome module showed moderate CRC discrimination in internal cross-validation and was enriched for metabolites involved in butanoate and amino acid-related pathways. These results suggest that phenotype-guided topological analysis can provide a complementary, interpretable view of localized multiomics organization in CRC-associated gut ecosystems.}, }
@article {pmid42448967, year = {2026}, author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK}, title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.}, journal = {Experimental &amp; molecular medicine}, volume = {58}, number = {7}, pages = {2339-2355}, pmid = {42448967}, issn = {2092-6413}, support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/metabolism/microbiology/etiology/pathology/immunology ; Humans ; Mice ; *Gastrointestinal Microbiome ; Female ; Disease Models, Animal ; Microglia/metabolism/immunology ; Phosphatidylethanolamines/metabolism ; Multiple Sclerosis ; }, abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.}, }
@article {pmid42449941, year = {2026}, author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S}, title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, pmid = {42449941}, issn = {1422-0067}, support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; }, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.}, }
@article {pmid42450074, year = {2026}, author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S}, title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, pmid = {42450074}, issn = {1422-0067}, support = {CARS-12//China Agriculture Research System/ ; }, mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; }, abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.}, }
@article {pmid42450138, year = {2026}, author = {Getsina, M and Tsyba, N and Chernevskaya, E}, title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, pmid = {42450138}, issn = {1422-0067}, mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; }, abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.}, }
@article {pmid42451140, year = {2026}, author = {Ibor-Miguel, M and Pérez-Sánchez, D and Marques-Martínez, L and Aura-Tormos, JI and Guinot-Barona, C and Miralles, EG}, title = {Influence of Early Feeding Practices on Oral Microbiota Composition During Infancy and Potential Implications for Early Childhood Caries: A Systematic Review.}, journal = {Nutrients}, volume = {18}, number = {13}, pages = {}, pmid = {42451140}, issn = {2072-6643}, mesh = {Humans ; Infant ; *Dental Caries/microbiology/epidemiology ; *Microbiota ; *Mouth/microbiology ; Breast Feeding ; Child, Preschool ; Infant, Newborn ; Female ; *Feeding Behavior ; Child ; Infant Nutritional Physiological Phenomena ; Milk, Human ; Infant Formula ; }, abstract = {BACKGROUND: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components-immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria-that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk.<br><br>OBJECTIVES: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes.<br><br>METHODS: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity.<br><br>RESULTS: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12-448 participants; age range at microbiota assessment: 2 days-14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (&#x2265;12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated.<br><br>CONCLUSIONS: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies.}, }
@article {pmid42451600, year = {2026}, author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I}, title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {13}, pages = {}, pmid = {42451600}, issn = {1420-3049}, mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; }, abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.}, }
@article {pmid42451744, year = {2026}, author = {Yan, S and Li, J and Chen, K and Ren, C and Zhang, S and Chen, Q and Gao, Y and Liu, B}, title = {Metagenomic and Metabolomic Insights into Volatile Flavor Changes and Microbial Community Shifts in Physalis pubescens L. Fermentation by Lactiplantibacillus plantarum.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {13}, pages = {}, pmid = {42451744}, issn = {1420-3049}, support = {CZKYF2025-1-B013//Provincial Research Institutes Scientific Research Operating Funds Project of Heilongjiang Province/ ; }, mesh = {*Fermentation ; *Metagenomics/methods ; *Metabolomics/methods ; *Volatile Organic Compounds/metabolism/analysis ; *Physalis/microbiology/metabolism/chemistry ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metabolome ; Fruit/microbiology/chemistry ; *Flavoring Agents/metabolism ; Metagenome ; }, abstract = {Physalis pubescens L. is a seasonal fruit with high nutritional value but a short shelf life that limits its processing and utilization. This study integrated metagenomics and metabolomics to investigate the comparative effects of Lactiplantibacillus plantarum fermentation on volatile flavor metabolites and microbial community composition of P. pubescens by comparing initial (0 h) and post-fermentation (24 h) states. After 24 h of fermentation, 1316 volatile compounds were putatively identified by GC-MS, with 592 metabolites significantly changed and 501 upregulated and 91 downregulated. Key flavor compounds that impart citrus, floral, fruity, and rose notes including D-limonene, geraniol, D-carvone, and phenylethyl alcohol were markedly increased. Metagenomic analysis revealed that L. plantarum rapidly dominated the microbial community (relative abundance surged from <0.05% to ~72%) while effectively suppressing potential spoilage bacteria such as Escherichia coli. Functional gene annotation demonstrated significant enrichment of amino acid, carbohydrate, and fatty acid metabolism pathways, with key enzyme genes (L-lactate dehydrogenase, pyruvate oxidase, acetyl-CoA carboxylase) predominantly assigned to L. plantarum, suggesting their potential contribution to the generation of organic acids, ethanol, and esters. Spearman correlation analysis indicated that Lactobacillaceae genera were significantly positively correlated with terpenoids, phenols, alcohols, and aldehydes. This study provides the first metagenomics-metabolomics insight into the microbial and molecular mechanisms associated with flavor formation in LAB-fermented P. pubescens, offering a theoretical foundation for developing stable and controllable fermented fruit products.}, }
@article {pmid42453369, year = {2026}, author = {Cui, Y and Li, Q and Liu, Z and Yu, Y}, title = {Induced Sputum Microbial Diversity and Function Changes in Patients with Acute Exacerbations of Chronic Obstructive Pulmonary Disease by Metagenomic Sequencing: A Cross-Sectional Study.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {21}, number = {}, pages = {600218}, pmid = {42453369}, issn = {1178-2005}, mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Female ; Aged ; Cross-Sectional Studies ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Disease Progression ; *Microbiota ; Middle Aged ; *Lung/microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; China ; Phenotype ; Ribotyping ; }, abstract = {PURPOSE: The underlying pathogenesis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is closely related to airway microbiota dysregulation. Currently, there is a lack of systematic elaboration based on deep metagenomic sequencing regarding the species-level and functional characteristics of the microbiota during AECOPD, as well as its correlation with clinical phenotypes of the host. This study aims to systematically analyze the taxonomic composition and functional profile changes of the microbiota in induced sputum samples from COPD patients during the stable and acute exacerbation periods using metagenomic next-generation sequencing and to explore their correlations with clinical indicators through metagenomic methods.<br><br>PATIENTS AND METHODS: A total of 66 patients with COPD were recruited from the Department of Respiratory and Critical Care Medicine at Jiading District Central Hospital in Shanghai, China. Of these, 49 induced sputum samples were obtained from 47 patients (17 in the stable group; 30 in the acute exacerbation group) after the quality control with DNA extraction and deep metagenomic sequencing. The species annotation and functional analysis were conducted using bioinformatics procedures, and microbial &#x3b1;-diversity analysis, LEfSe analysis was performed to identify differentially expressed markers. Spearman correlation analysis was used to evaluate the correlation between microbial/functional characteristics and a series of clinical indicators.<br><br>RESULTS: The &#x3b1;-diversity of the sputum microbiota in AECOPD patients was significantly lower at the species level compared to the stable stage (p < 0.01), and the community structure also underwent significant changes. Functional annotation and comparative analysis further identified 9 KEGG pathways (ko00970, ko04112, ko03420, ko03440, ko03060/ko03070, ko03410, ko04930, and ko00680) and 1 eggNOG functional category (M: Cell wall/membrane/envelope biogenesis) that differed significantly between the two groups. Among them, pathways such as methane metabolism were downregulated in the exacerbation period.<br><br>CONCLUSION: This study revealed significant dysregulation of the airway microbiome in AECOPD patients at species-level diversity, community structure, and functional metabolism, providing a molecular basis for the discovery of functional biomarkers and therapeutic targets in the microbiome.}, }
@article {pmid42454401, year = {2026}, author = {Pettinga, D and Fonseca-García, C and Krause, G and Ploemacher, H and Wheeler, T and Clendinen, CS and Handakumbura, P and Egbert, R and Coleman-Derr, D}, title = {Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.}, journal = {The New phytologist}, volume = {251}, number = {6}, pages = {3507-3521}, pmid = {42454401}, issn = {1469-8137}, support = {2019-67019-29306//National Institute of Food and Agriculture/ ; DE-AC05-76RL01830//Pacific Northwest National Laboratory/ ; CRIS 2030-12210-003-000D//Agricultural Research Service/ ; DE-AC05-76RL0183//Biological and Environmental Research/ ; }, mesh = {*Sorghum/microbiology/growth &amp; development/genetics ; *Flavonoids/metabolism ; Plant Roots/microbiology ; Gene Expression Regulation, Plant ; *Microbiota ; Plant Shoots/microbiology ; Rhizosphere ; }, abstract = {Plant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes present a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. We designed four distinct, reduced-complexity variants of SynCom Sorghum Root Consortium 1 and assessed their capacities for colonization, stability, and plant growth promotion (PGP). To understand the impact on plant performance of our highest performing SynCom variant, we characterized the host's longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. The top-performing SynCom stably colonized Sorghum bicolor roots and rhizospheres, elicited PGP, and induced dynamic spatiotemporal gene transcription in S. bicolor roots and shoots defined by modulation of growth-defense trade-off machinery and enhanced flavonoid production. The resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization.}, }
@article {pmid42454926, year = {2026}, author = {Davies, J and Ireland-Hughes, J and Stronati, S and Smith, RP and Oastler, C and Nunez-Garcia, J and Anjum, MF and AbuOun, M}, title = {Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0147626}, pmid = {42454926}, issn = {2165-0497}, support = {APHARDOZ0514//Department for Environment, Food and Rural Affairs, UK Government/ ; }, mesh = {Animals ; *Livestock/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Microbiota/genetics/drug effects ; *Manure/microbiology ; Metagenomics ; Anaerobiosis ; Pilot Projects ; }, abstract = {UNLABELLED: The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (AD) and on-farm slurry lagoon treatment affect microbial community composition and relative AMR gene abundance in livestock waste. Samples were collected before and after treatment from three AD sites and two on-farm slurry lagoon sites. Taxonomic profiles and diversity metrics were generated from short-read Illumina sequencing, and AMR gene presence and relative abundance were assessed using APHA SeqFinder, an in-house analysis pipeline. AD treatment led to decreased microbial richness and evenness, and reduced the relative abundance of several high-prevalence taxa, including members of the Enterobacteriaceae. On-farm slurry lagoon treatment had a comparatively minor effect on microbial composition. AD was also associated with significant reductions in the relative abundance of genes conferring resistance to macrolides, aminoglycosides, fusidic acid, and beta-lactams. These findings suggest that AD and on-farm slurry lagoon treatment exert distinct effects on microbial communities and AMR gene profiles. The results provide preliminary evidence that AD may contribute to reducing AMR gene burden in agricultural waste, although further investigation across broader temporal scales and treatment methods is needed.<br><br>IMPORTANCE: Antimicrobial resistance is a major global health challenge, and agricultural waste is a key environmental reservoir of resistance genes. This study examined how two livestock waste treatments (anaerobic digestion and on-farm slurry lagoon storage) affect microbial communities and relative antimicrobial resistance gene (ARG) abundance. The findings show that anaerobic digestion reduces both microbial diversity and the relative abundance of several resistance genes, while on-farm slurry lagoon treatment has a limited impact. These results highlight the potential for treatment strategies to reduce the environmental spread of resistance.}, }
@article {pmid42454945, year = {2026}, author = {Oworae, KO and Rabacal, W and Hu, A and Wychrij, DA and Rayens, E and Chapman, TI and Bahl, J and Norris, KA}, title = {Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0104726}, pmid = {42454945}, issn = {2165-0497}, support = {R01 AI148365/AI/NIAID NIH HHS/United States ; Charles H. Wheatley Endowment//Georgia Research Alliance/ ; //University of Georgia Research Foundation/ ; 1R01A1148365//National Institute of Allergy and Infectious Diseases/ ; Office of Research Faculty and Graduate Affairs Competitive Research Grant//College of Veterinary Medicine, University of Georgia/ ; }, mesh = {Animals ; *Fungal Vaccines/immunology/administration &amp; dosage ; *Mycobiome/immunology ; Macaca mulatta ; *Gastrointestinal Microbiome/immunology/drug effects ; Female ; *Mycoses/prevention &amp; control/immunology/microbiology ; *Fungi/immunology/genetics/classification ; Antigens, Fungal/immunology ; Antibodies, Fungal/immunology ; Immunization ; Vaccination ; }, abstract = {Fungal infections remain a significant public health concern with high mortality, morbidity, and increasing associated health costs. This burden is projected to rise due to expansion of at-risk populations, limited therapeutics, increasing drug resistance, and the emergence of new fungal pathogens. Even with these challenges, there are currently no approved vaccines. We previously developed a "pan-fungal" vaccine candidate, NXT-2, that confers protection against multiple invasive fungal infections such as pulmonary aspergillosis, pneumocystosis, and invasive candidiasis, as well as non-invasive vulvovaginal candidiasis. NXT-2 is a 90 amino acid consensus peptide designed from a conserved region of the fungal antigen (KEX1). We assessed the effect of NXT-2 immunization on gut microbial diversity, composition, and functional capacity in non-human primates. To do this, we monitored changes in the gut mycobiome and microbiome pre- and post-vaccination using ITS2 and metagenomic sequencing, respectively, in Japanese and rhesus macaque cohorts. NXT-2 elicited a robust antibody response without disrupting the gut microbial communities in both macaque species. The mycobiome exhibited stability with no significant changes in alpha and beta diversity, taxonomic composition, or functional guild distributions. The relative abundance of gut resident Candida and Aspergillus species remained stable and was not significantly altered following vaccination. The microbiome showed stability with preserved alpha and beta diversities, taxonomic composition, and functional capacity. Results from this study show the first cross-kingdom analysis demonstrating that antifungal vaccination can achieve protective immunity without perturbing gut microbial communities. This establishes a framework for microbiome-informed vaccine assessment beyond conventional immunogenicity and adverse effect monitoring.IMPORTANCEFungal infections cause millions of deaths annually, yet no vaccines are approved despite growing drug resistance and limited treatment options. NXT-2 is a pan-fungal vaccine that protects against multiple fungal infections such as pneumocystosis, candidiasis, and aspergillosis. Here, we demonstrate in NHPs that NXT-2 elicits robust protective antibody responses without altering gut bacterial or fungal communities. This is the first study to assess antifungal vaccination across both microbial kingdoms and establish that protective antifungal immunity can be achieved while preserving resident microbiota. This work provides a framework for incorporating microbiome assessment into vaccine development beyond conventional immunogenicity and adverse event monitoring.}, }
@article {pmid42455624, year = {2026}, author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC}, title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001738}, pmid = {42455624}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation &amp; purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation &amp; purification ; }, abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.}, }
@article {pmid42456442, year = {2026}, author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y}, title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.}, journal = {Multiple sclerosis and related disorders}, volume = {113}, number = {}, pages = {107383}, doi = {10.1016/j.msard.2026.107383}, pmid = {42456442}, issn = {2211-0356}, mesh = {Humans ; Female ; Pilot Projects ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; *Microbiota ; Case-Control Studies ; Adult ; *Mouth/microbiology ; Australia ; Cross-Sectional Studies ; Middle Aged ; }, abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.<br><br>METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.<br><br>RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for &#x223c;6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.<br><br>CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.}, }
@article {pmid42456685, year = {2026}, author = {Steriade, C and Segata, N and Saxena, D}, title = {The role of the gut microbiome in mediating neuroinflammation in immune-based neurological disorders.}, journal = {The Lancet. Neurology}, volume = {25}, number = {8}, pages = {764-780}, doi = {10.1016/S1474-4422(26)00193-6}, pmid = {42456685}, issn = {1474-4465}, mesh = {Humans ; *Neuroinflammatory Diseases/immunology/microbiology ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; *Nervous System Diseases/immunology/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The gut microbiome can influence brain health by modulating neuroinflammation through various mechanisms, including immune regulation, the production of metabolites that affect neural function, gut and blood-brain barrier integrity, upstream effects via the vagus nerve, upstream migration of gut-resident lymphocytes to the brain, bile acid signalling, and endocrine activity. Changes in gut microbiota have been observed in demyelinating conditions, autoimmune encephalitis, and epilepsy. Gut microbiota composition changes can affect neuroinflammation, disease progression, and treatment outcomes. Advances in microbiome research have improved the potential for clinical translation of findings; but limitations persist, driven by the largely correlational nature of clinical studies and the complexity of microbiome sequencing and interpretation. At present, only the ketogenic diet is routinely recommended by clinicians, whereas other microbiome-based interventions remain investigational. Multiple strategies for manipulating the gut microbiome, including dietary changes, prebiotics, probiotics, postbiotics, and faecal microbiota transplantation, might be used as disease-modifying therapies in the future.}, }
@article {pmid42461036, year = {2026}, author = {Munford, KE and Grégoire, DS and Hug, LA}, title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {8}, pages = {e0031126}, pmid = {42461036}, issn = {1098-5336}, support = {Tier II//Canada Research Chairs/ ; ER19-15-228//Ontario Early Research Award/ ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Waste Disposal Facilities ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Solid Waste/analysis ; *Microbiota ; Metals/metabolism/analysis ; Water Pollutants, Chemical/analysis ; Metagenome ; }, abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.}, }
@article {pmid42463489, year = {2026}, author = {Gao, Z and Wu, J and Lucaci, AG and Ouyang, J and Wang, L and Ryon, KA and Elhaik, E and Probst, AJ and Rodó, X and Velavan, TP and Chasapi, A and Ouzounis, CA and Oliveira, M and Dias-Neto, E and Osuolale, O and Poulsen, M and Meleshko, D and Bhattacharyya, M and Ugalde, JA and Tull, A and Rubins, KH and Sierra, MA and Tierney, BT and Prithiviraj, B and Sharma, NK and Munteanu, V and Mangul, S and Kurt, KC and Ushio, M and Mazur-Panasiuk, N and Kopera, K and Marszałek, K and Kowalski, M and Toscan, RB and Branicki, W and Pyrć, K and Łabaj, PP and Subramanian, B and Frolova, A and Burkhart, JG and Deng, Y and Udekwu, KI and Schriml, LM and Hazrin-Chong, NH and Suzuki, H and Lee, PKH and Camargo, AP and Kyrpides, NC and Liu, D and Wang, LF and Mason, CE and Shi, T and , }, title = {Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42463489}, issn = {2041-1723}, support = {32370720//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; RNA, Viral/genetics ; Cities ; Animals ; }, abstract = {RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban &amp; Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.}, }
@article {pmid42464944, year = {2026}, author = {Hazan, S and Bao, G and Goudzwaard, A and Ichim, T and Martin, L and Vidal, AC}, title = {Gut Microbiome Alterations in Cancer and Non-cancer Adults: A Cross-Sectional Metagenomic Study.}, journal = {Technology in cancer research &amp; treatment}, volume = {25}, number = {}, pages = {15330338261470516}, pmid = {42464944}, issn = {1533-0338}, mesh = {Humans ; Female ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Neoplasms/microbiology/pathology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; *Bacteria/classification/genetics ; Metagenome ; Retrospective Studies ; }, abstract = {IntroductionPrevious studies found associations between cancer and the gut microbiome. Thus, we aimed to investigate the gut microbiome composition in adults with and without cancer to try to identify specific microbes that may be associated with cancer in a cross-sectional, observational, and retrospective study.MethodsStool samples from sixty participants, n=20 controls, n=25 with aggressive cancer, and n=15 with non-aggressive cancer were analyzed using Metagenomic Next Generation Sequencing. Mann-Whitney U test tests were used to examine differences in the relative abundances of bacterial genera.ResultsCompared to controls, aggressive cancer patients had statistically significantly lower levels of gut Bifidobacterium, Faecalibacterium, and Collinsella, (all p≤0.05), while they had higher levels of gut Bacteroides (p=0.015). Non-aggressive cancer patients had lower levels of gut Bifidobacterium compared to controls, an association that was approaching statistical significance (p=0.054).ConclusionAggressive-cancer patients showed significantly altered levels of key gut microbes compared to controls. These are preliminary associations, and thus further larger studies are needed to confirm these findings.}, }
@article {pmid42466871, year = {2026}, author = {Jin, C and Chen, Q and Liu, X and Liu, H and Wang, Y}, title = {The functional structure of foxtail millet rhizoplane microbiome and its association with yield.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0070726}, pmid = {42466871}, issn = {2165-0497}, support = {32300265//National Natural Science Foundation of China/ ; }, mesh = {Rhizosphere ; *Setaria Plant/microbiology/growth &amp; development ; *Microbiota/genetics ; *Plant Roots/microbiology/growth &amp; development ; Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenome ; Metagenomics ; }, abstract = {UNLABELLED: Root-associated microbial communities profoundly influence plant growth and productivity. Although the rhizosphere microbiome has been extensively studied, the functional distinctiveness and host-specific role of the closely adhering rhizoplane microbiota remain unclear. In this study, we performed deep metagenomic sequencing of both the rhizosphere and rhizoplane microbiomes in foxtail millet (Setaria italica). We constructed a comprehensive non-redundant gene catalog, reconstructed 595 metagenome-assembled genomes (MAGs), and analyzed the co-occurrence networks. Our results revealed that the rhizoplane sustains a core microbial network with greater complexity and connectivity than rhizospheres. Metabolically, the rhizoplane microbiome is enriched in the functions underlying host adaptation, including ammonium production and polysaccharide decomposition. Our results showed that the associations between microbial features (taxonomic and functional) and yield were significantly stronger in the rhizoplane than in the rhizosphere. We identified 22 yield-positive MAGs, primarily from Bacillales, harboring genes for plant growth-promoting traits, such as nutrient solubilization and phytohormone synthesis. Collectively, our findings illustrate that the rhizoplane is not only a subset of the rhizosphere but also a critical host-microbe interface and functional hotspot where specialized microbial processes are directly coordinated to enhance plant performance and yield.<br><br>IMPORTANCE: Plant roots selectively recruit diverse and beneficial microorganisms from the surrounding soil, assembling a distinctive rhizosphere microbiome. Substantial research, primarily utilizing amplicon sequencing, has elucidated the taxonomic composition of these rhizosphere communities across a wide range of plant species. The functional architecture, assembly processes, and coexistence mechanisms of the rhizoplane microbiome remain poorly understood, and their link to host plant traits is unclear. We elucidate the taxonomic and functional structural disparities between the rhizosphere and rhizoplane microbiomes, thereby clarifying the composition and functional roles of the rhizoplane microbiome, and further examine the association between the rhizoplane microbiome and millet yield. A deeper understanding of root-associated microbial communities may inform the development of effective agricultural probiotics, thereby enhancing sustainable farming practices. Additionally, the candidate biomarkers identified in this work offer potential targets for improving cultivation practices and supporting the long-term agricultural sustainability of foxtail millet.}, }
@article {pmid42466883, year = {2026}, author = {Han, H and Qian, Q and Wu, W and Yang, J and Zhou, J and Sun, W}, title = {Diabetes-associated Parvimonas enrichment and altered lung microbiota profiles in lower respiratory tract infection: an analysis of 632 metagenomes.}, journal = {Microbiology spectrum}, volume = {14}, number = {8}, pages = {e0404825}, pmid = {42466883}, issn = {2165-0497}, mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; Metagenome ; *Lung/microbiology ; Retrospective Studies ; *Respiratory Tract Infections/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; *Diabetes Mellitus/microbiology ; Aged ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/genetics/isolation &amp; purification ; *Diabetes Complications/microbiology ; Metagenomics ; Pneumonia/microbiology ; }, abstract = {The homeostasis of pulmonary microbiota is crucial in maintaining human health and modulating disease progression. The stability of pulmonary microbial flora may be associated with diabetes, yet the specific alterations remain poorly characterized. This retrospective observational study aims to analyze the profiles in pulmonary microbiota between individuals with and without diabetes, using metagenomic next-generation sequencing (mNGS). A total of 632 patients were sequentially enrolled, including 77 patients with both pneumonia and diabetes, 46 patients without either pneumonia or diabetes, 499 patients with pneumonia but without diabetes, and 10 diabetic patients without pneumonia. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA). The lung microbiota of diabetic individuals significantly differs from that of non-diabetic individuals in the non-lower respiratory tract infection (non-LRTI) cohort. Parvimonas was more abundant in the diabetic group. Compared to non-diabetic patients with LRTI, those with diabetes and LRTI showed an increased relative abundance of Parvimonas, but decreased relative abundances of Prevotella and Malassezia. Our analysis revealed a negative correlation between Parvimonas and Malassezia, alongside a positive association of Parvimonas with the expression of antimicrobial resistance genes ICR-Mc and RbpA. This suggests a potential association between Parvimonas enrichment and microbial dysbiosis during infection, although the underlying host-microbe interactions require further validation. Interestingly, Parvimonas abundance showed no significant association with HbA1c levels. Our findings suggest that Parvimonas enrichment is associated with diabetes-related alterations in lower respiratory tract microbiota. Whether microbiota-associated alterations represent clinically actionable targets in diabetic patients with pulmonary infections remains to be determined in prospective and interventional studies.IMPORTANCEThis study reveals significant differences in lung microbiota between diabetic and non-diabetic individuals. Parvimonas was enriched in the diabetic lung, and its abundance correlated with the expression of antimicrobial resistance genes, such as ICR-Mc and RbpA. Surprisingly, microbial dysbiosis was independent of HbA1c levels, indicating that mechanisms other than glycemic control contribute to infection progression. This study suggests that Parvimonas enrichment may be a diabetes-associated microbial feature in bronchoalveolar lavage fluid (BALF) microbiota, but its potential diagnostic or clinical relevance requires validation in future studies. Our work provides a scientific foundation for optimizing infection prevention and advancing precision anti-Parvimonas therapies.}, }
@article {pmid42468189, year = {2026}, author = {Wan, S and Huang, W and Zhang, Z and Liu, X and Dong, W and Chen, Y and Ke, L and Yang, Q and Chen, S and Hu, Y and Zhang, Y}, title = {Microbial succession and flavor-related metabolic potential during industrial eight-round mechanized stacking fermentation of Maotai-flavor Baijiu.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111975}, doi = {10.1016/j.ijfoodmicro.2026.111975}, pmid = {42468189}, issn = {1879-3460}, mesh = {Fermentation ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Flavoring Agents/metabolism ; Volatile Organic Compounds/analysis/metabolism ; Taste ; *Wine/microbiology/analysis ; Fungi/metabolism/genetics/classification/isolation &amp; purification ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Food Microbiology ; }, abstract = {Mechanized production of Maotai-flavor Baijiu (MFB) is increasingly adopted in the Baijiu industry; however, microbial succession and flavor-related metabolic potential throughout the complete eight-round mechanized stacking fermentation (SF) process remain insufficiently understood. In this study, microbial communities, functional genes, physicochemical properties, and volatile compounds during SF were investigated using metagenomic sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC/MS). A total of 168 volatile compounds were detected, of which 41 representative compounds were selected for further analysis. Among them, 15 differential volatiles were identified by PLS-DA, with furfural showing the highest abundance. Microbial profiling revealed pronounced community differentiation and continuous succession across fermentation rounds. Acidity, starch, and reducing sugars were significantly associated with microbial community variation, with acidity and starch exhibiting the strongest associations. In the initial round (R1), microbial communities were mainly derived from raw materials and Daqu. Bacterial communities shifted from lactic-acid-bacteria-enriched communities to those characterized by Kroppenstedtia and Bacillus, whereas fungal communities transitioned from yeast-enriched stages to mold-enriched and mold-yeast coexistence stages. Metagenome-inferred functional annotation, co-occurrence network, and correlation analyses suggested potential links between microbial succession and flavor-related metabolic pathways. Yeasts were mainly associated with ethanol- and organic-acid-related metabolism during the early stage, whereas Bacillus and Kroppenstedtia were linked to predicted starch-degradation and organic-acid-related pathways during the middle and late stages. Overall, this study provides a comprehensive characterization of microbial succession and metagenome-inferred flavor-related metabolic potential during mechanized SF and offers reference data for process monitoring and quality management in MFB production.}, }
@article {pmid42470960, year = {2026}, author = {Chen, Y and Han, D and Hu, Q and Xiong, Y and Zhou, X and Wang, Y and Li, D and Yan, J and Yang, J and Zhang, F and Cao, H and Wu, P and Liu, Y and Xia, Y and Sun, J}, title = {Gut-liver axis through microbiota-metabolite interplay driving age-dependent susceptibility to arsenite-induced liver injury in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120522}, doi = {10.1016/j.ecoenv.2026.120522}, pmid = {42470960}, issn = {1090-2414}, mesh = {Animals ; *Arsenites/toxicity ; *Liver/drug effects/metabolism/pathology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Chemical and Drug Induced Liver Injury/metabolism/etiology ; Male ; Aging ; Intestinal Barrier Function ; Mice, Inbred C57BL ; Age Factors ; Signal Transduction/drug effects ; }, abstract = {Arsenic is a highly toxic metalloid that contributes to many chronic diseases. The liver is a primary target organ because it mediates detoxification and metabolism. However, the differences in susceptibility to age-related arsenic-induced liver injury and their underlying mechanisms remain unclear, particularly regarding the involvement of the gut-liver axis. Young, adult, and old mice ingested arsenic via drinking water. We assessed glucose metabolism, liver injury, and intestinal barrier integrity. To investigate the role of the gut microbiota, we performed metagenomic sequencing on fecal samples. Liver metabolic changes and signaling pathways were analyzed using non-targeted metabolomics and transcriptomics technologies, respectively. This study reveals that aged mice exhibit heightened susceptibility to arsenite-induced liver injury and metabolic disorders. Histological examination and reduced occludin expression confirm this is associated with impaired intestinal barrier function. Metagenomic analysis indicated that arsenite exposure was associated with gut microbiota remodeling in aged mice, characterized primarily by genus-level alterations, including reduced Muribaculaceae-related genera and relative enrichment of genera associated with altered mucosal homeostasis and inflammatory signaling. Metagenomic pathway analysis further suggested shifts in microbial metabolic and inflammatory signaling-related pathways, including changes in insulin/glucagon signaling, glycerolipid metabolism, and NOD-like receptor signaling. Metabolomics detection revealed significant accumulation of uridine diphosphate glucose (UDPG) in the livers of arsenite-exposed aged mice. Transcriptomic analysis revealed upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway, while western blotting confirmed its activation in the liver. These findings suggest that aging is associated with increased susceptibility to arsenite-induced liver injury, potentially involving gut microbiota remodeling, intestinal barrier dysfunction, and hepatic UDPG accumulation. UDPG may function as a metabolic stress-associated factor or potential amplifier of MAPK-related inflammatory signaling, thereby potentially contributing to liver injury. Consequently, a novel gut-liver axis mechanism is revealed, elucidating the intrinsic link between aging and susceptibility to environmentally induced toxic diseases.}, }
@article {pmid42474201, year = {2026}, author = {Palmer, B and Couradeau, EM and Johansen, JR and Kurbessoian, T and Carranza, JO and Stajich, JE and Ward, R and Pietrasiak, N}, title = {Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {8}, pages = {e0104326}, pmid = {42474201}, issn = {1098-5336}, support = {DEB-0842702//National Science Foundation/ ; DEB-841734//National Science Foundation/ ; DEB-9870201//National Science Foundation/ ; CA-R-PPA-5062-H//USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; JOTR-2006-SCI-0018//National Park Service and Bureau of Land Management/ ; MOJA-2008-SCI-0024//National Park Service and Bureau of Land Management/ ; MOJA-2009-SCI-0039//National Park Service and Bureau of Land Management/ ; PEN04949//USDA National Institute of Food and Agriculture and Hatch Appropriations/ ; UT-06-032-12-P//National Park Service and Bureau of Land Management/ ; }, mesh = {*Cyanobacteria/genetics/classification/physiology/metabolism ; *Microbiota ; Metagenome ; *Soil Microbiology ; Phylogeny ; Metagenomics ; }, abstract = {The cyanosphere is composed of non-cyanobacterial microorganisms living within the exopolysaccharide sheath of cyanobacteria, interacting with the cyanobacterial hosts and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres can help predict the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity and functions within the cyanosphere remains limited. Here, we used metagenomic sequencing to reconstruct 415 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 terrestrial cyanobacteria cultures, representing 12 cyanobacterial orders. Our findings showed that the composition of cyanosphere microbial communities was significantly shaped by environmental factors such as habitat of host origin, including precipitation and temperature. Three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, suggesting a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, an anaerobic process that retains nitrogen in the host-cyanosphere system in contrast to denitrification. While nitrogen fixation was more common in the cyanobacteria, 15 cyanospheres also contained nitrogen fixation genes, including in hosts that were nitrogen fixation capable themselves. The cyanosphere also contained genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities.IMPORTANCEOur study identifies members of an understudied and under-valued microbial community, the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a novel approach to studying the cyanosphere, providing insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.}, }
@article {pmid42475242, year = {2026}, author = {Shi, W and Cen, L and Huang, J and Lei, X and Wang, Y and Wang, S and Ying, J and Li, Y and Ma, Y and Fang, Y and Liu, A and Lu, C and Dai, M}, title = {LECT2 deficiency contributes to bile acid metabolic reprogramming and cholestatic liver injury.}, journal = {Hepatology communications}, volume = {10}, number = {8}, pages = {}, doi = {10.1097/HC9.0000000000001007}, pmid = {42475242}, issn = {2471-254X}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Knockout ; Mice ; *Intercellular Signaling Peptides and Proteins/deficiency/genetics/metabolism ; Liver/metabolism/pathology ; Disease Models, Animal ; Receptor, Farnesoid X-Activated ; Gastrointestinal Microbiome ; Male ; Receptors, Cytoplasmic and Nuclear/metabolism ; Metabolic Reprogramming ; Fibroblast Growth Factors/metabolism ; *Cholestasis, Intrahepatic/metabolism ; *Cholestasis/metabolism ; Signal Transduction ; Mice, Inbred C57BL ; Humans ; }, abstract = {BACKGROUND: Cholestatic liver injury involves impaired bile acid (BA) formation or flow, leading to toxic hepatic BA accumulation, yet the underlying mechanisms remain poorly understood. Leukocyte cell-derived chemotaxin 2 (LECT2) has been implicated in liver metabolic disorders; however, its specific role in cholestasis remains incompletely understood.<br><br>METHODS: ANIT was administered to wild-type (WT) and LECT2 knockout (KO) mice to establish an intrahepatic cholestasis model. Metabolomics and metagenomics were performed to discover the role of BA metabolism and the gut-liver axis in cholestatic liver injury. Clinical samples were analyzed to assess the relationship between LECT2 and cholestatic liver injury.<br><br>RESULTS: LECT2 deletion was associated with altered BA synthesis, characterized by a shift toward the classical pathway with upregulation of CYP7A1 and CYP8B1. Under cholestatic conditions, LECT2 deficiency was associated with aggravated liver injury, accompanied by alterations in gut microbiota composition, changes in intestinal FXR-FGF15 signaling, and increased hepatic JNK activation. In KO mice, HDCA supplementation restored the alternative synthesis pathway, FMT reshaped gut microbiota, and antibiotic cocktail treatment suppressed intestinal FXR signaling, each of which was associated with improved cholestatic liver injury. In clinical samples, LECT2 levels were negatively correlated with markers of cholestasis, supporting its potential relevance to disease severity.<br><br>CONCLUSION: LECT2 deficiency is associated with aggravated cholestatic liver injury, which may involve altered BA synthesis, gut microbiota dysbiosis, and modulation of intestinal FXR-hepatic JNK signaling. These findings offer new insights into the role of LECT2 in regulating metabolism and identify potential therapeutic targets for managing cholestatic liver injury.}, }
@article {pmid42476135, year = {2026}, author = {Zhao, W and Wang, J and Chen, C and Jiang, A and Wang, Y and Hu, A and Qi, Q and Chen, Y and Sui, W and Dong, L and Zhang, Y and Xiao, X}, title = {Hadal topography incubates hidden microbial hotspots in the deepest ocean.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {8}, pages = {1523-1539.e7}, doi = {10.1016/j.chom.2026.06.015}, pmid = {42476135}, issn = {1934-6069}, mesh = {Oceans and Seas ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; Carbon Cycle ; Ecosystem ; Metagenomics ; *Microbiota ; Water Microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Biomass ; }, abstract = {Plate subduction creates unique topographic features in hadal trenches, yet their influence on microbial ecosystems and the global ocean remains unclear. Here, we conducted a topography-targeted investigation across 6-11 km of water depth within the Mariana Trench, integrating metagenomic, metaproteomic, and geochemical analyses. Coupled with high-resolution topographic mapping, our analyses reveal topography as an overlooked determinant of hadal geochemical and microbial heterogeneity. Convex areas exhibit classical sediment-depth-decay patterns with sparse, cooperative microbial communities. Conversely, concave features maintain higher biomass and activity as well as dense microbial interactions. Critically, slope concave sites incubate previously unrecognized microbial hotspots and may serve as interchange hubs, potentially facilitating genetic exchange and upward dispersal of microorganisms from Earth's deepest regions to the broader ocean. Our findings demonstrate that topographic features, rather than water depth, significantly correlate with organic carbon influx and its microbial turnover rates, enabling predictive modeling of hadal carbon cycling with global implications.}, }
@article {pmid42476199, year = {2026}, author = {Hoepers, PG and Figueiredo Nunes, PL and Oliveira Almeida-Souza, H and Martins, MM and Bastos, LM and Dias de Oliveira Carvalho, R and Figueira Aburjaile, F and de Jesus E Silva, B and Sommerfeld, S and Aguiar de Souza Penha, V and Rodrigues Alves, LB and Azevedo, V and Fonseca, BB}, title = {Enhancing poultry health and food safety with probiotics: A study on Bacillus velezensis against Salmonella Heidelberg in broilers.}, journal = {Microbial pathogenesis}, volume = {219}, number = {}, pages = {108717}, doi = {10.1016/j.micpath.2026.108717}, pmid = {42476199}, issn = {1096-1208}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; *Bacillus/physiology ; Chickens/microbiology ; Feces/microbiology/chemistry ; Cecum/microbiology ; *Food Safety ; *Poultry Diseases/prevention &amp; control/microbiology ; *Salmonella Infections, Animal/prevention &amp; control/microbiology ; *Salmonella/growth &amp; development/drug effects ; Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; Animal Feed ; }, abstract = {The growing concern over antibiotic use and foodborne pathogens such as Salmonella Heidelberg (SH) highlights the need for effective alternative strategies in poultry production. This study evaluated the probiotic potential of Bacillus velezensis (BV) to control SH colonization and modulate gut microbiota and metabolism in broilers. In vitro, BV exhibited inhibitory activity against SH. In vivo, a total of 100 one-day-old broiler chicks were randomly assigned to four treatments (n = 25/group): NC (negative control), PC (positive control, challenged with SH), BV-Neg (BV supplementation without SH challenge), and BV-SH (BV supplementation with SH challenge). Birds were orally challenged at 4 days of age with 0.2 mL of SH (6 × 10[9] CFU/mL). Cecal SH counts, microbial diversity, and fecal metabolomic profiles were evaluated at 7, 14, 21, and 28 days. Data were analyzed using ANOVA, chi-square tests, and multivariate approaches, including principal component analysis (PCA) and multivariate analysis of variance (MANOVA), with significance set at P < 0.05. BV supplementation significantly reduced SH colonization in the cecum at 28 days, with a reduction of 3.53 log CFU/g (∼99.9%) compared to the positive control (P < 0.01), indicating a time-dependent probiotic effect. Microbial diversity was influenced by treatment and age, with BV-supplemented and SH-challenged groups showing higher diversity than NC (P < 0.05). Metabolomic analysis identified 60 analytes across multiple metabolic classes, with BV increasing beneficial compounds such as fatty acyl glucosides, lignin, artemisinin, and taurodeoxycholic acid, while reducing metabolites associated with SH infection. Overall, BV demonstrated a cumulative effect in reducing SH colonization and modulating gut microbiota and metabolism, supporting its potential as a probiotic strategy to improve poultry health and food safety.}, }
@article {pmid42476406, year = {2026}, author = {Li, N and Yi, J and Zhu, L and Chen, D and Wang, M and Huang, D}, title = {Nanoconfined humic acid-supported nZVI enhances imidacloprid remediation without compromising soil microbiome or exacerbating ARG health risks.}, journal = {Environmental research}, volume = {306}, number = {Pt 3}, pages = {125277}, doi = {10.1016/j.envres.2026.125277}, pmid = {42476406}, issn = {1096-0953}, mesh = {*Neonicotinoids/chemistry ; *Humic Substances/analysis ; *Nitro Compounds/chemistry ; *Soil Pollutants/chemistry ; *Microbiota/drug effects ; *Soil Microbiology ; *Environmental Restoration and Remediation/methods ; }, abstract = {Pesticide contamination of agricultural soils poses persistent risks to ecosystem function and agricultural sustainability, yet the application of reactive nanomaterials for remediation remains constrained by physicochemical instability and uncertain ecological consequences. Here, we synthesized a nanoconfined humic acid-supported nZVI composite (HA-nZVI) and evaluated its performance in imidacloprid (IMI)-contaminated soil through kinetic analysis, interfacial characterization, metagenomic sequencing, and dual-framework ARG risk assessment. HA nanoconfinement improved particle dispersion, increased active-site accessibility, and facilitated interfacial electron shuttling. These effects accelerated predominantly abiotic IMI dissipation, raising the degradation rate by 3.8-fold relative to the unamended control and shortening the half-life to 18.56 d. Despite the accelerated removal, dominant phylum-level abundances fluctuated by less than 3%, suppression of plant-beneficial bacteria (PBB) observed with pristine nZVI was alleviated, and no measurable increase in human- or livestock-associated ARG risk was detected among the 525 identified ARG subtypes. Collectively, these findings show that HA nanoconfinement can couple improved pesticide dissipation with phylum-level microbiome compatibility and no detectable increase in resistome-associated health risk, supporting the design of iron-based nanomaterials for sustainable agricultural remediation.}, }
@article {pmid42476558, year = {2026}, author = {D'Agostino, GD and Kim, CH and Park, J and Zhang, Y and Amer, B and Franzosa, EA and Bird, SS and Huttenhower, C and Huh, JR and Devlin, AS}, title = {Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.}, journal = {Journal of the American Chemical Society}, volume = {148}, number = {30}, pages = {31759-31773}, pmid = {42476558}, issn = {1520-5126}, support = {R01 DK140810/DK/NIDDK NIH HHS/United States ; R35 GM128618/GM/NIGMS NIH HHS/United States ; R01 DK140810//National Institutes of Health (NIH)/ ; R35 GM128618//National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Sulfates/metabolism/chemistry ; *Metabolomics ; *Gastrointestinal Microbiome ; Sulfotransferases/metabolism ; Phosphoadenosine Phosphosulfate/metabolism ; }, abstract = {The sulfated metabolome─the collection of sulfate-containing metabolites─is an emerging source of structurally unique bioactive compounds that influence metabolism, immune responses, and neurological function. Recent studies have shown that, in addition to host enzymes, gut bacteria also encode sulfotransferase enzymes (SULTs) that generate sulfated metabolites. However, the substrate scope of characterized gut bacterial SULTs remains narrow, and comprehensive discovery is limited by a lack of methods to detect and assign sulfated metabolites in complex samples. Here, we develop a comparative metabolomics workflow that leverages the universal SULT cofactor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to incorporate heavy (34S) or light (32S) sulfur into sulfated metabolites, enabling discovery of microbiome-dependent sulfated compounds. By applying this approach in both "bottom-up" bacterial culture and "top-down" in vivo studies, we find that gut bacteria sulfonate hydroxy fatty acids. We identify a gut commensal microbe, Eubacterium ramulus, that performs this transformation, as well as an enzyme in this bacterium that performs this sulfonation, ErSULT. Metagenomic analyses reveal that ErSULT is prevalent across diverse human gut microbiomes. Together, this workflow and its application demonstrate that sulfated metabolite production by gut bacteria is more widespread than previously appreciated and provide a platform for future studies investigating the biosynthesis and biological functions of microbiome-derived sulfated small molecules.}, }
@article {pmid42476661, year = {2026}, author = {Zhang, F and Hu, W and Zhao, X and Fu, B and Lin, Y and Xie, C and Yang, R and Fu, Y and Tan, W and Ye, L}, title = {Comorbid depression exacerbates Gelsemium elegans toxicity via disruption of the Clostridium-LCA-PXR-CYP3A11 metabolic axis.}, journal = {Chinese journal of natural medicines}, volume = {24}, number = {8}, pages = {987-998}, doi = {10.1016/S1875-5364(26)61197-1}, pmid = {42476661}, issn = {1875-5364}, mesh = {Animals ; *Gelsemium/toxicity/chemistry ; Mice ; *Clostridium/metabolism ; Gastrointestinal Microbiome/drug effects ; *Pregnane X Receptor/metabolism/genetics ; Male ; *Depression/metabolism/microbiology/complications ; *Cytochrome P-450 CYP3A/metabolism/genetics ; *Plant Extracts/toxicity ; Indole Alkaloids/toxicity ; Alkaloids ; }, abstract = {Gelsemium elegans (G. elegans) is a toxic medicinal plant traditionally used to treat chronic pain, with its toxicity linked to indole alkaloids such as gelsemine and humantenmine (HMT). Chronic pain often co-occurs with depression, a condition known to disrupt host-microbiota interactions, potentially affecting drug metabolism and toxicity. However, the impact of comorbid depression on the toxicity of G. elegans remains unclear. This study investigates how depression exacerbates the neurotoxicity of G. elegans and explores the role of the gut microbiota-host metabolic axis in this process. Depression-model mice were treated with G. elegans aqueous extract, gelsemine and HMT. Multi-omics approaches, including 16S rRNA sequencing and shotgun metagenomics, were used to analyze microbiota changes under depressive conditions. Functional validation was performed using pseudo-germ-free mice, fecal microbiota transplantation, and supplementation with Clostridium species and lithocholic acid (LCA), as well as pregnane X receptor (Pxr) knockout models. The results showed that depression significantly heightened the neurotoxicity of G. elegans, gelsemine and HMT. Mechanistically, depression reduced Clostridium abundance and LCA levels, impairing PXR activation and downregulating hepatic CYP3A11 expression. This disruption of the Clostridium-LCA-PXR-CYP3A11 axis hindered the detoxification of indole alkaloids, leading to increased systemic exposure and exacerbated neurotoxicity. Restoration of this pathway through Clostridium or LCA supplementation alleviated the toxicity. These findings highlight the role of the Clostridium-LCA-PXR-CYP3A11 axis in the altered toxicity of G. elegans in a depressive state, and suggest that Clostridium species and their metabolites may serve as a potential strategy for mitigating toxicity.}, }
@article {pmid42476978, year = {2026}, author = {Xu, Z and Xing, J and Zeng, X and Wu, Y and Wang, Y and He, Y and Lin, X and Huang, H and Zhao, Z and Wu, H and Guo, Z and Chen, T}, title = {Citywide metagenomics reveals microbial community and resistome dynamics in urban wastewater.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42476978}, issn = {2041-1723}, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; China ; Cities ; *Microbiota/genetics ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Urban wastewater systems connect hospitals, residential communities, transport hubs, and wastewater treatment plants, creating opportunities for the dissemination of microorganisms and antibiotic resistance genes (ARGs). Here, we conduct a three-month, citywide metagenomic survey of wastewater in Xiamen, China, comprising 252 samples from seven hospital sites (n = 16), 27 residential sites (n = 55), 16 wastewater treatment plant sites (n = 159), and individual international flights (n = 22). Genome-resolved analyses reveal source-specific microbial community structures, resistome profiles, lineage-sharing patterns, and associations between ARGs and mobile genetic elements across wastewater sources. Hospital wastewater harbors the most diverse resistome, while international flight wastewater introduces microbial taxa and ARGs absent from local wastewater networks. Wastewater treatment plants accumulate ARGs from multiple upstream sources, exhibiting frequent lineage sharing and signals of potential horizontal gene transfer. Compared with within-environment sharing, cross-environment lineage sharing is associated with lower nucleotide diversity, consistent with possible genetic bottlenecks. Among potential correlates, pH shows strong non-linear associations with microbial diversity and resistome composition. These findings indicate that urban wastewater systems function as interconnected networks for microbial and ARG dissemination and identify potential hotspots for targeted antimicrobial resistance surveillance.}, }
@article {pmid42477864, year = {2026}, author = {Lakamp, AD and Adams, S and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML}, title = {Influence of host genetics on the functional composition of the rumen metagenome in beef cattle.}, journal = {Journal of animal science}, volume = {104}, number = {}, pages = {}, pmid = {42477864}, issn = {1525-3163}, support = {2022-33522-38219//USDA-National Institute of Food and Agriculture/ ; 2023-68015-40015//USDA-National Institute of Food and Agriculture/ ; 2024-33522-43699//USDA-National Institute of Food and Agriculture/ ; 2018-67015-27496//USDA-National Institute of Food and Agriculture/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/genetics/microbiology ; *Metagenome ; Diet/veterinary ; Genotype ; *Gastrointestinal Microbiome/genetics ; Male ; }, abstract = {Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.}, }
@article {pmid42478129, year = {2026}, author = {Zhou, Y and Xu, J and Zhou, W and Wu, P and Yang, S and Ji, L and Shen, Q and Wang, X and Liu, Y and Zhou, C and Zhang, W and Xu, M}, title = {Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.}, journal = {Journal of medical virology}, volume = {98}, number = {7}, pages = {e71063}, pmid = {42478129}, issn = {1096-9071}, support = {2023YFD1801300//National Key Research and Development Programs of China/ ; 82550118//National Natural Science Foundation of China/ ; 82341106//National Natural Science Foundation of China/ ; BK20241926//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Humans ; *Genetic Variation ; *Virome/genetics ; *Genome, Viral ; *Respiratory Tract Infections/virology/microbiology ; Sputum/virology ; Metagenomics ; Phylogeny ; *Mycoses/virology/microbiology ; *Viruses/genetics/classification/isolation &amp; purification ; Female ; Male ; Middle Aged ; Adult ; Sequence Analysis, DNA ; }, abstract = {Respiratory tract infections represent a leading cause of morbidity and mortality globally, with viral pathogens accounting for a substantial proportion of these cases. However, research on the human respiratory virome is still in its infancy, and our understanding of this field remains relatively limited. In the present study, viral metagenomic sequencing was conducted on 65 sputum samples obtained from patients with severe fungal infections. We successfully assembled viral genome sequences belonging to four distinct viral families: Anelloviridae, Genomoviridae, Microviridae, and Inoviridae. Through systematic analysis of the virome composition, this study characterized the structural features of the respiratory virome in patients with severe fungal infections. The findings provide a foundational description of viral diversity in this specific clinical context. These findings lay a theoretical foundation for clinical pathogen detection, targeted interventions, and the development of future prevention strategies.}, }
@article {pmid42480452, year = {2026}, author = {Shan, X and Shi, L and Zhu, T and Liang, X and Yang, J and Zhou, G and He, L and Mei, B and Wang, S and Li, F}, title = {Microbial tryptophan-IPA axis mediates 6:2 chlorinated polyfluorinated ether sulfonate (6:2Cl-PFESA)-induced gut-brain dysfunction and neurobehavioral impairments.}, journal = {Environment international}, volume = {214}, number = {}, pages = {110422}, doi = {10.1016/j.envint.2026.110422}, pmid = {42480452}, issn = {1873-6750}, mesh = {Animals ; Mice ; Male ; Mice, Inbred C57BL ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Fluorocarbons/toxicity ; *Alkanesulfonic Acids/toxicity ; *Indoles/metabolism ; *Brain/drug effects ; Intestinal Barrier Function ; }, abstract = {Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are widely used substitutes for perfluorooctane sulfonate (PFOS) and are increasingly detected in environmental and human matrices, yet their neurobehavioral risks during early life remain poorly defined. Here, male C57BL/6J mice were orally exposed to F-53B (6:2Cl-PFESA; 0.1 or 1 mg/kg/day) during juvenility for four weeks. F-53B selectively impaired recognition memory and social novelty preference, whereas locomotor activity, anxiety-like behavior, and Y-maze working memory were largely preserved. Mechanistically, F-53B compromised intestinal barrier integrity, as evidenced by reduced occludin expression and disrupted ZO-1 continuity, accompanied by elevated circulating lipopolysaccharide (LPS) and a systemic pro-inflammatory cytokine shift. In parallel, the hippocampus exhibited microglial activation, enhanced inflammatory signaling, and reduced PSD95 expression, consistent with neuroinflammatory stress and synaptic vulnerability. Shotgun metagenomics revealed pronounced microbiome restructuring and network rewiring, while widely targeted metabolomics converged on a marked disruption of tryptophan metabolism, characterized by depletion of microbiota-derived indole metabolites, including indole-3-propionic acid (IPA), together with altered serotonin-related signatures. Notably, oral IPA supplementation rescued behavioral deficits and attenuated gut-brain inflammatory alterations, restoring intestinal aryl hydrocarbon receptor (AhR) nuclear translocation, reducing LPS and cytokine levels, and ameliorating hippocampal inflammatory phenotypes. Collectively, these findings provide mechanistic evidence that a microbiota-tryptophan metabolite-gut barrier-inflammation axis links exposure to substitute PFAS with selective neurobehavioral dysfunction, highlighting microbiota-derived metabolites as potential modulators of PFAS-associated neurotoxicity.}, }
@article {pmid42480622, year = {2026}, author = {Ren, X and Ma, J and Zhao, Y and Yang, M and Li, Y and Song, W and Wang, N}, title = {Microbiome remodeling during aging: Integrative multi-omics and spatiotemporal perspectives on immune and metabolic regulation.}, journal = {Ageing research reviews}, volume = {121}, number = {}, pages = {103269}, doi = {10.1016/j.arr.2026.103269}, pmid = {42480622}, issn = {1872-9649}, mesh = {Humans ; *Aging/immunology/metabolism ; Multiomics ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Homeostasis ; }, abstract = {Changes in the gut microbiota occur throughout the human lifespan, and maintaining microbial homeostasis plays a critical role in promoting healthy aging. In recent years, substantial progress has been made in elucidating the mechanistic links between aging and microbiota remodeling, highlighting the central role of microbiota-host interactions in regulating immune responses and maintaining metabolic homeostasis. These findings provide new potential targets for the precision prevention and treatment of age-related diseases. This review systematically summarizes the patterns of gut microbiota succession across different stages of the human life cycle, including infancy, adolescence, adulthood, and old age, as well as the mechanisms through which the microbiota regulates immune and metabolic functions. Furthermore, the role of the gut microbiota as a key mediator linking aging with an increased risk of chronic inflammation, cardiovascular disease, cognitive impairment, neurodegenerative disorders, and cancer was explored. In addition, this review evaluates the therapeutic potential of microbiota-targeted interventions, such as dietary modification, probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), and lifestyle interventions-in maintaining microbiome homeostasis and mitigating age-related diseases. The feasibility of personalized microbiota-based intervention strategies is also discussed. Finally, we highlight the current challenges and limitations in this field and outline future research directions. In particular, integrating multi-omics approaches with metagenomic sequencing, including emerging spatial and spatiotemporal multi-omics technologies, is crucial for advancing our understanding of the complex interactions within the gut microbiome. These insights provide a theoretical framework for optimizing anti-aging therapeutic strategies and promoting healthy lifespan extension.}, }
@article {pmid42481656, year = {2026}, author = {Stallhofer, J and Leonhardt, J and Semmler, J and Neugebauer, S and Kiehntopf, M and Löhden, W and Homeister, L and Ungelenk, M and Hübner, CA and Steube, A and Waschina, S and Stallmach, A}, title = {Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42481656}, issn = {2045-2322}, mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Bile Acids and Salts/metabolism/blood ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology ; Female ; Feces/chemistry/microbiology ; Male ; Gastrointestinal Microbiome ; Adult ; Middle Aged ; }, abstract = {The gut microbiota communicates extensively with its host through small metabolites, such as bile acids. Primary bile acids are synthesized by the host and secreted into the intestine, where they are actively converted by the microbiota into secondary bile acids. Depending on the resulting bile acid composition, the host's bile acid receptor, Takeda G protein-coupled receptor 5 (TGR5), is activated and mediates immune tolerance. It has been suggested that a disturbed bile acid profile in inflammatory bowel disease (IBD) might lead to inflammation via reduced activation of TGR5. Our study is the first to investigate whether bile acid-induced TGR5 activation differs between healthy individuals and patients with IBD. Bile acid profiles in stool and plasma were quantified by mass spectrometry, and TGR5 bioactivity was assessed from these profiles. In parallel, metagenomic sequencing was performed on fecal samples. We demonstrate that reduced alpha diversity in IBD is associated with a loss of microbial capacity for bile acid transformation, resulting in a significantly decreased secondary-to-primary bile acid ratio (sBA/pBA) in both stool and circulation. TGR5 bioactivity induced by bile acid profiles was substantially reduced in IBD patients, and a lower TGR5 bioactivity correlated with increased inflammatory activity.}, }
@article {pmid42484632, year = {2026}, author = {Vernon, JJ and Lynch, J and Yu, X and Do, T}, title = {Clostridioides difficile in the oral microbiome: an in silico analysis.}, journal = {Journal of medical microbiology}, volume = {75}, number = {7}, pages = {}, doi = {10.1099/jmm.0.002188}, pmid = {42484632}, issn = {1473-5644}, mesh = {Humans ; *Clostridioides difficile/genetics/isolation &amp; purification/classification ; Saliva/microbiology ; *Dental Plaque/microbiology ; *Microbiota ; *Clostridium Infections/microbiology/epidemiology ; Periodontitis/microbiology ; *Mouth/microbiology ; Computer Simulation ; Computational Biology ; Metagenomics ; Female ; Male ; }, abstract = {Introduction. High rates of recurrent Clostridioides difficile infection (CDI) and environmental contamination are attributed to its ability to form spores. Periodontal diseases are characterized by gingival inflammation, caused by dental plaque accumulation.Hypothesis. Periodontal plaque could harbour C. difficile spores, acting as a reservoir for reinfection.Aim. Compare the prevalence and abundance of C. difficile in metagenomic sequences of saliva and dental plaque from healthy and periodontal disease patients.Methodology. Publicly available metagenomic reads from oral samples of healthy (n=80) and periodontitis (n=204) patients were analysed for C. difficile presence through an in-house bioinformatic pipeline. Briefly, reads underwent quality control (cutadapt/fastQC) prior to subsampling of 3 million reads (seqtk). Reads and MEGAHIT-assembled contigs were aligned to a C. difficile reference genome (ASM1888508v1) or a full non-redundant protein DIAMOND database. Outputs were filtered, annotated (Entrez Direct) and top hits identified via National Center for Biotechnology Information blast. Abundance and prevalence were compared between cohorts.Results. Low levels of C. difficile sequences were observed, with significantly higher prevalence in periodontitis (7.4%, n=15/204) vs. healthy cohorts (5.0%, n=4/80) (P=0.0087) with reference genome alignment. Using the full non-redundant database, prevalence was also higher in periodontitis (14.2% vs. 3.8%; P=0.012), along with significantly greater average C. difficile sequence counts (0.608 vs. 0.075; P=0.018) and relative abundance (0.00029% vs. 0.0000003%; P=0.009).Conclusion. Sequences pertaining to C. difficile were detected in oral samples, with significantly more observed in periodontal disease compared to healthy cohorts. This highlights the possibility for dental plaque to act as a reservoir, potentially contributing to reinfection in CDI patients.}, }
@article {pmid42485562, year = {2026}, author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K}, title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.}, journal = {Journal of basic microbiology}, volume = {66}, number = {7}, pages = {e70185}, pmid = {42485562}, issn = {1521-4028}, support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation &amp; purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; Shotgun Sequencing ; Phylogeny ; }, abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.}, }
@article {pmid42486576, year = {2026}, author = {Venugopal, DC and Srinivas, KS}, title = {Challenges and future directions in head and neck microbiome research.}, journal = {Advances in immunology}, volume = {170}, number = {}, pages = {189-227}, doi = {10.1016/bs.ai.2026.03.010}, pmid = {42486576}, issn = {1557-8445}, mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.}, }
@article {pmid42486580, year = {2026}, author = {Perera, ML and Perera, IR}, title = {Microbiome based diagnostic approaches.}, journal = {Advances in immunology}, volume = {170}, number = {}, pages = {93-125}, doi = {10.1016/bs.ai.2026.03.004}, pmid = {42486580}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; }, abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.}, }
@article {pmid42487113, year = {2026}, author = {Ma, Y and Sun, J and Guo, C and Cao, J and Zhang, L and Zhu, F and Yu, X and Yang, L and Fang, J}, title = {Exploring brain-gut interaction mechanisms in Transcutaneous auricular Vagus Nerve stimulation for Major Depressive Disorder.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {}, pmid = {42487113}, issn = {1471-244X}, support = {82474663//National Natural Science Foundation of China/ ; HLCMHPP2023072//High Level Chinese Medical Hospital Promotion Projec/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Brain/physiopathology/diagnostic imaging ; *Brain-Gut Axis/physiology ; *Gastrointestinal Microbiome/physiology ; Magnetic Resonance Imaging ; *Major Depressive Disorder/therapy/physiopathology/diagnostic imaging ; Randomized Controlled Trials as Topic ; *Transcutaneous Electric Nerve Stimulation/methods ; Treatment Outcome ; *Vagus Nerve Stimulation/methods ; }, abstract = {BACKGROUND: The gut microbiota is intricately implicated in the pathogenesis of Major Depressive Disorder (MDD), with the vagus nerve serving as a key regulatory bridge. Transcutaneous Auricular Vagus Nerve Stimulation (taVNS) has emerged as a promising non-invasive therapeutic strategy for MDD by modulating the gut-brain axis, yet the precise brain-gut interaction mechanisms underlying its antidepressant effects remain poorly characterized. This study is a registered clinical trial (ChiCTR2200059591; Registered 4 May 2022; https://www.chictr.org.cn).<br><br>OBJECTIVE/HYPOTHESIS: This study aimed to verify the clinical efficacy of taVNS for MDD and elucidate the underlying brain-gut crosstalk mechanisms, by integrating comprehensive clinical assessments, resting-state functional magnetic resonance imaging (rs-fMRI) neuroimaging data and gut metagenomic profiling.<br><br>METHODS: Ninety-five patients diagnosed with MDD were randomly allocated at a 1:1 ratio to either the active taVNS group (auricular concha stimulation) or the sham taVNS group (superior concha of mid-helix stimulation). Eighty patients (40 per group) completed the entire intervention course and were included in the final statistical analysis. All participants underwent 30-minute stimulation twice daily (4/20 Hz, 3-8&#xa0;mA) for 8 consecutive weeks (5 days per week). Standardized clinical assessments were administered at baseline and post-intervention, including the 17-item Hamilton Depression Rating Scale (HAMD-17), 14-item Hamilton Anxiety Rating Scale (HAMA-14), and Gastrointestinal Symptom Rating Scale (GSRS). Rs-fMRI was performed to quantify core neural activity metrics, including amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo), and degree centrality (DC); fecal samples were collected for high-throughput metagenomic analysis. Spearman correlation analysis and mediation analysis were further conducted to dissect the interactive relationships between brain neural activity and gut microbiota.<br><br>RESULTS: The active taVNS group achieved significantly superior clinical efficacy relative to the sham group, with a HAMD-17 response rate of 62.50% and remission rate of 35.00%, versus 30.00% and 2.50% in the sham group (all P&#x2009;<&#x2009;0.05). Rs-fMRI analyses revealed significant group&#xd7;time interaction effects on neural activity: decreased ALFF in the right calcarine sulcus; altered fALFF in the right inferior temporal gyrus, left cuneus, right superior frontal gyrus (SFG) and right angular gyrus; reduced ReHo in the right calcarine sulcus and bilateral insula; and increased DC in the right caudate nucleus and left anterior cingulate gyrus. Gut microbiota profiling identified anaerobic butyrate-producing bacteria and Faecalibacterium prausnitzii as potential biomarkers linked to taVNS therapeutic effects. HAMD-17 scores were negatively correlated with Faecalibacterium prausnitzii abundance (r=-0.566, P&#x2009;<&#x2009;0.01) and positively correlated with anaerobic butyrate-producing bacteria abundance (r&#x2009;=&#x2009;0.406, P&#x2009;<&#x2009;0.01). Mediation analysis suggested that fALFF values in the right SFG may indirectly modulate depressive symptoms via regulating Faecalibacterium prausnitzii abundance (indirect effect 95% CI: 0.3039-2.4466), with a significant partial mediation effect observed, though future studies controlling for dietary and other confounding variables are needed to confirm this relationship.<br><br>CONCLUSION: taVNS effectively alleviates depressive symptoms in MDD patients via dual complementary pathways: directly modulating neural activity in the right SFG to regulate depression-related brain function, and indirectly maintaining gut microbiota homeostasis by enriching beneficial taxa such as Faecalibacterium prausnitzii. These findings provide novel mechanistic insights into the brain-gut interaction underlying the antidepressant effects of taVNS, laying a theoretical foundation for its clinical application in MDD management.}, }
@article {pmid42487569, year = {2026}, author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV}, title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.}, journal = {Molecular ecology}, volume = {35}, number = {14}, pages = {e70485}, pmid = {42487569}, issn = {1365-294X}, support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; }, mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; }, abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley &amp; Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.}, }
@article {pmid42489029, year = {2026}, author = {Ma, R and Guo, G and Liu, C and Deng, P and Dong, X and Mu, L and Qu, Q and Hu, X}, title = {Microplastic Pollution Is Associated with Fragmentation and Environmental Sensitivity of Marine Planktonic Microbial Communities.}, journal = {Environmental science &amp; technology}, volume = {60}, number = {30}, pages = {21051-21060}, doi = {10.1021/acs.est.6c06158}, pmid = {42489029}, issn = {1520-5851}, support = {2025D01E63//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 22576112//National Natural Science Foundation of China/ ; 25JCYBJC00100//Natural Science Foundation of Tianjin Municipality/ ; NA//Fundamental Research Funds for the Central Universities/ ; B17025//Higher Education Discipline Innovation Project/ ; 1102021600110070049//Central Public Research Institutes Basic Funds for Research and Development/ ; 25FV0CWZ02//Fujian Ocean Innovation Center/ ; }, mesh = {*Microplastics ; *Plankton ; *Microbiota ; }, abstract = {The effects of increasing marine microplastic (MP) pollution on the microbial community structure and function remain uncertain, particularly under natural conditions. Specifically, our study focuses on free-living marine microbial communities (0.8-5 μm) rather than plastisphere biofilms. Here, we systematically evaluated differences in microbial community responses to environmental gradients across MP concentration regimes on the basis of a response modulation analysis framework (RMAF). In this framework, co-occurrence network analysis, random forest modeling, and SHapley Additive exPlanations (SHAP) and partial dependence-based interpretation methods are integrated to quantify changes in microbial sensitivity and ecological interactions. Through the use of Tara Oceans metagenomic data, we analyzed seven functional gene categories and species diversity across MP concentration gradients. High-MP environments (with concentrations exceeding 5,500 items·km-2) were characterized by a notable decrease in nondominant taxa (from 17-21% to 6.53-9.45%) alongside increased dominance of abundant species. The functional profiles showed higher abundance levels of genes involved in carbon, nitrogen, and sulfur cycling. The results of network analysis indicated reduced connectivity and increased fragmentation, suggesting weakened ecological interactions and decreased system stability. Microbial communities in high-MP environments exhibited increased sensitivity to environmental drivers, characterized by response centralization and niche compression, suggesting a narrower range of environmental responses. MPs were associated with high microbial functional activity and potential indications of low ecosystem resilience.}, }
@article {pmid42489979, year = {2026}, author = {Zhao, Z and Zhao, Y and Sun, Y and Bao, Y and Feng, J and Jiang, T and Lin, A}, title = {Metagenomic screening of antimicrobial peptide candidates and isolation of two active peptides from bat gut bacteria.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42489979}, issn = {1573-0972}, support = {32430066, 32271558, 32571749//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Antimicrobial Peptides/pharmacology/isolation &amp; purification/genetics/chemistry ; Microbial Sensitivity Tests ; Metagenomics/methods ; *Chiroptera/microbiology ; Anti-Bacterial Agents/pharmacology/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Bacteriocins/pharmacology/isolation &amp; purification/genetics ; Amino Acid Sequence ; Tandem Mass Spectrometry ; Metagenome ; }, abstract = {Bacterial antibiotic resistance has intensified the need to identify new antimicrobial molecules from underexplored microbial systems. Wild mammalian gut microbiota may harbor antimicrobial peptide (AMP) candidates and candidate bacteriocins, but these systems remain poorly investigated as sources for antimicrobial discovery. Here, we used parallel metagenomic and culture-dependent approaches to explore candidate AMP sequences and candidate bacteriocins from the gut bacteria of the Asian particolored bat Vespertilio sinensis. Machine-learning screening of 553,401 short non-redundant ORF protein sequences identified 12,907 candidate AMP sequences. Of these, 31 were prioritized after in silico safety and structural filtering. In parallel, culture-dependent screening yielded two antagonistic bacterial isolates, CQJ and LYS. Activity-guided purification followed by LC-MS/MS identified two active peptides, CQJ01 and LYS01, with no exact matches in public databases. Both peptides exhibited broad in vitro antibacterial activity against 16 pathogenic strains, with minimum inhibitory concentration (MIC) values as low as 8 µg/mL against selected Gram-positive and Gram-negative bacteria. CQJ01 retained activity across pH 2-9 and after heat treatment up to 80 °C, whereas LYS01 retained activity from - 20 °C to 100 °C. Both peptides remained active after catalase, trypsin, papain, and proteinase K treatments but were sensitive to pepsin. They showed low hemolytic activity and limited cytotoxicity in preliminary assays. These findings support bat gut bacteria as an underexplored source of AMP candidates and candidate bacteriocins.}, }
@article {pmid42491728, year = {2026}, author = {Suzuki, D and Yang, J and Obana, N and Yachida, S and Shiba, S and Mizutani, S and Takamaru, H and Saito, Y and Fukuda, S and Yamada, T}, title = {Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21488}, pmid = {42491728}, issn = {2167-8359}, mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Animals ; Mice ; *Carcinogenesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenome ; Male ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is prevalent worldwide and is associated with gut commensals. Recent studies have highlighted the effects of gut microbes on CRC development driven by their strain diversity. Nevertheless, the impact of the gut microbial community on tumorigenesis in early-stage (ES) CRC remains unexplored.<br><br>METHODS: To assess the potential gut microbial community, which is critical to tumorigenesis in early-stage CRC, we collected publicly available shotgun metagenomes from CRC patient faecal samples from a Japanese population. Correlation analysis of the microbial profiles derived from the metagenomes revealed an ES CRC-associated community. To elucidate the strain diversity of the targeted community, we isolated strains from ES CRC patient faecal samples and employed comparative genomics. To evaluate the strain-specific effects of the community on tumorigenesis, we introduced an isolated strain cocktail into a CRC mouse model.<br><br>RESULTS: Among the most significant ES CRC-associated species, we identified Lancefieldella parvula (Lp), as reported in a previous study. The 20 species were identified as positively correlated with Lp. Seven of the 20 species were associated with ES CRC, including Actinomyces and Solobacterium. Schaalia odontolytica (So) (formerly known as Actinomyces odontolyticus) and Solobacterium moorei (Sm) were previously reported as potential species that promote CRC. Thus, we isolated clinical strains of Lp, So, and Sm from faecal samples as potential members of the ES CRC-associated community. Comparative genomics revealed that iron-related genes were shared among clinical strains. In the oral challenge with clinical strains, namely, Lp, So, and Sm, the mice exhibited shorter survival and significantly increased tumorigenesis, suggesting that the cocktail of clinical strains is more pathogenic to the CRC mouse model than the type strain is. In summary, we inferred that the ES CRC-associated community could promote CRC, and the effects depend on the strains involved.}, }
@article {pmid42493771, year = {2026}, author = {Yi, Y and Xie, F and Xia, C and Li, J and Zhao, P and Liu, M and Ma, X and Chen, J}, title = {Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology.}, journal = {Medical gas research}, volume = {16}, number = {4}, pages = {352-358}, pmid = {42493771}, issn = {2045-9912}, mesh = {*Hydrogenase/metabolism/genetics ; *Hydrogen/metabolism ; *Hypertension/microbiology/etiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; }, abstract = {JOURNAL/mgres/04.03/01612956-202612000-00006/figure1/v/2026-07-23T200825Z/r/image-tiff Hypertension is a prevalent chronic condition and serves as a significant risk factor for numerous cardiovascular and cerebrovascular disorders. Gut microbiota dysbiosis has been considered to contribute to the pathogenesis of hypertension. It has been reported that a large majority of gut microbiota possess genes encoding hydrogenases. These hydrogenases are involved in the alteration of gut microbiota in non-infectious colitis, suggesting a potential link between microbial hydrogen metabolism and disease onset. This study aims to explore the relationship between hydrogenase expression patterns in the gut microbiome and the incidence of hypertension. In this study, publicly available gut microbiome metagenomic data were used to comprehensively analyze the expression patterns of hydrogenases in the gut microbiota of hypertensive patients. Compared with the control group, a 2.3-fold increase in electron bifurcating [FeFe] group A3 hydrogenases (P = 0.0299), a 55.6% decrease in [NiFe] group 1d hydrogenases (P = 0.0097), increased hydrogen-sensing hydrogenases and decreased hydrogen-uptake hydrogenases in the hypertension group. The main difference between the two groups is reflected in the abundance of [NiFe] hydrogenase subtypes. After eliminating the effects of factors such as age, sex, and lifestyle, significant differences in the abundance of [FeFe] group A3, [NiFe] group 1d, and [NiFe] group 1c were observed between the two groups, suggesting that these three indicators could serve as potential biomarkers for diagnosing the onset of hypertension. Additionally, Mendelian randomization analysis showed a protective effect of hydrogen metabolism against hypertension (odds ratio = 0.72, 95% confidence interval: 0.61-0.85, P < 0.001). Our study advances the understanding of microbiome-mediated mechanisms in hypertension by demonstrating an association between hydrogenase expression dynamics and blood pressure regulation, providing a foundation for future microbiome-based diagnostic and therapeutic strategies.}, }
@article {pmid42493801, year = {2026}, author = {Van Den Bossche, T and Grenga, L and Alves, G and Arntzen, M&#xd8; and Benndorf, D and Brauer, M and Figeys, D and Henry, C and Hettich, RL and Heyer, R and Jagtap, PD and Jehmlich, N and Kleiner, M and Li, L and Mesuere, B and Pabst, M and Pandhal, J and Pope, PB and Seifert, J and Trautwein-Schult, A and Verschaffelt, P and Wilmes, P and Armengaud, J and Kunath, BJ}, title = {The Metaproteomics Initiative: five years of community-driven progress.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42493801}, issn = {2049-2618}, mesh = {Humans ; Metagenomics ; *Microbiota ; *Proteomics/methods ; }, abstract = {The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.}, }
@article {pmid42496154, year = {2026}, author = {Zhang, J and Cai, L and Wang, L and Zhang, L and Meng, N and Chen, A and Ma, Q}, title = {Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {8}, pages = {e0081926}, pmid = {42496154}, issn = {1098-5336}, support = {2025-MSLH-076//Liaoning Provincial Science and Technology Joint Program Project/ ; KF2026005//Key Laboratory of Biotechnology and Bioresources Utilization/ ; }, mesh = {*Geologic Sediments/microbiology ; *Disinfectants/pharmacology ; *Thiazoles/pharmacology/toxicity ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/analysis/genetics ; *Bacteria/drug effects/enzymology/genetics/classification ; }, abstract = {The organic booster biocide DCOIT (4,5-dichloro-2-n-octyl-4-isothiazolin-3-one) is widely used in marine antifouling systems, yet its ecological impacts on sediment microbiomes remain poorly understood. Here, we integrated absolute quantitative 16S rRNA gene sequencing, metagenomics, and enzyme activity assays to examine microbial responses to DCOIT exposure (0-50 μg/g sediment) over 30 days. DCOIT induced oxidative stress and bioenergetic impairment, accompanied by reduced microbial activity and inhibition of key enzyme-mediated processes involved in organic matter turnover and nitrogen transformation. Absolute quantification revealed a compensatory increase in total microbial abundance by Day 30, despite persistent diversity loss and community restructuring. Metagenomic analysis showed that DCOIT disturbed functional potentials related to carbon and nitrogen cycling. Kordiimonas, Aliikangiella, and Neptuniibacter emerged as potential contributors to nitrogen transformation, whereas Marinobacter was more closely associated with potential DCOIT transformation. DCOIT exposure also enriched adaptive traits, including chemotaxis, motility, quorum sensing, and biofilm regulation, and was accompanied by increased multidrug efflux systems and heavy metal resistance determinants. Our findings provide novel insights into the ecotoxicological risks of isothiazolinone biocides and highlight the potential for DCOIT to undermine sediment ecosystem functions and microbial habitat health. Given its extensive application, this study emphasizes the need to consider the microbial ecological consequences of DCOIT accumulation in seafloor environments.IMPORTANCEDCOIT is widely used in marine antifouling coatings and can accumulate in benthic sediments, yet its effects on sediment microbiomes remain poorly defined. This study shows that DCOIT disrupts microbial energy status, enzyme activities, community structure, and nitrogen-cycling functions while selecting for adaptive traits and resistance-related determinants. By integrating absolute quantification, metagenomics, and enzyme assays, our work demonstrates that DCOIT poses microbial ecological risks beyond toxicity to macroorganisms and should be considered in assessments of antifouling biocides.}, }
@article {pmid42497724, year = {2026}, author = {Jiang, G and Yin, Y and Tian, L and Lu, JN and Cai, X and Deng, T and Cao, Y and Wang, S and Tang, YT and Morel, JL and Qiu, R and Ruan, Z and Chao, Y}, title = {Keystone and potentiator taxa in hyperaccumulator rhizospheres: A new perspective for microbiome-assisted phytoremediation.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143053}, doi = {10.1016/j.jhazmat.2026.143053}, pmid = {42497724}, issn = {1873-3336}, mesh = {*Rhizosphere ; Biodegradation, Environmental ; *Microbiota ; *Nickel/metabolism ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; }, abstract = {Soil heavy-metal contamination threatens agroecosystem functioning, and hyperaccumulators, together with their rhizosphere microbiomes, offer promise for the phytoremediation of contaminated soils. Most rhizosphere microbiome studies have emphasized keystone taxa, but abundant and stable non-keystone members may also contribute to community functioning. Here, we examined the rhizosphere microbiome of the Ni hyperaccumulator Odontarrhena chalcidica using a combination of amplicon and metagenomic sequencing. Keystone taxa were identified as taxa supported by multiple ecological inference approaches, whereas potentiator taxa were defined as abundant and stable taxa that were not identified as keystones. We then compared their taxonomic composition, functional potential, and model-predicted metabolic interactions. Keystone and potentiator taxa were taxonomically distinct. Potentiator taxa showed broader functional potential than keystone taxa, suggesting that these stable non-keystone members may contribute functions that are overlooked by keystone-focused analyses alone. Genome-scale metabolic modeling further predicted greater metabolite exchange in mixed keystone-potentiator assemblages than in single-role assemblages, with model-predicted metabolic support directed mainly from potentiator taxa to keystone taxa. These findings indicate that abundant and stable non-keystone taxa can complement keystone taxa in the rhizosphere microbiome of a Ni hyperaccumulator. More broadly, this study provides an analytical strategy for identifying candidate microbial combinations that may support microbiome-assisted phytoremediation of metal-contaminated soils.}, }
@article {pmid42498043, year = {2026}, author = {Kaki, D and Kore, U and Talari, A and Komati, A and Garlapati, C and Dondra, T and De, S and Mandava, K}, title = {Modern approaches to gut microbiome investigation: Sequencing, culturomics, metabolomics, and beyond.}, journal = {Journal of microbiological methods}, volume = {248}, number = {}, pages = {107636}, doi = {10.1016/j.mimet.2026.107636}, pmid = {42498043}, issn = {1872-8359}, mesh = {Humans ; *Metabolomics/methods ; Multiomics ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Host Microbial Interactions ; Bacteria/genetics/classification/isolation &amp; purification ; Proteomics/methods ; }, abstract = {The human gut microbiome is a complex and constantly evolving community of trillions of microorganisms that are crucial to various aspects of health and disease. It impacts digestion, metabolism, immune function, neurological processes, and vulnerability to illnesses. Recent technological advancements in biology and engineering have transformed microbiome research, allowing for more detailed analysis of microbial composition, functions, and interactions with the host. This review offers a thorough overview of both current and emerging methods for studying the gut microbiome, including sample collection techniques, culture-based approaches like culturomics and microfluidics, as well as culture-independent methods such as 16S rRNA sequencing, shotgun metagenomics, and the integration of multi-omics approaches like metabolomics, proteomics, and transcriptomics. It also discusses innovative tools including single-cell genomics, spatial transcriptomics, and microbiome-on-a-chip platforms, which hold promise for revealing host-microbe interactions at unprecedented levels of detail. The review underscores the importance of combining biological insights with engineering innovations particularly microfluidics and organ-on-a-chip models to recreate gut environments that mimic physiological conditions. Additionally, it explores the potential of artificial intelligence and machine learning in analyzing data and developing predictive models for personalized microbiome-based diagnostics and therapies. Acknowledging challenges such as microbial diversity, environmental sensitivity, and technical hurdles, this review aims to guide researchers in choosing optimal tools to study the gut microbiota, deepen mechanistic understanding, and translate findings into clinical applications that enhance human health.}, }
@article {pmid42499546, year = {2026}, author = {Jiang, Z and Li, L and Long, Q and Guo, W and Wang, M and Li, X and Li, J and Yi, Y}, title = {Cross-sectional gut microbiota and serum metabolite differences across clinically defined groups in colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1815707}, pmid = {42499546}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/blood/microbiology/pathology ; Cross-Sectional Studies ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Aged ; Metabolomics ; *Serum/chemistry ; *Metabolome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Colorectal cancer (CRC) is a prevalent malignancy associated with alterations in the gut microbiota and host metabolic profiles. This cross-sectional study aimed to characterize gut microbiota and serum metabolite differences among healthy controls (HC), patients with non-metastatic colorectal cancer (CRC-nm), and patients with metastatic colorectal cancer (CRC-m). Stool metagenomic sequencing and untargeted serum metabolomics were performed in 107 participants, followed by exploratory differential analyses and internally cross-validated modeling to identify candidate microbial and metabolic features and evaluate their discriminatory performance. Differential analyses identified two CRC-m-enriched species-level features (Enterocloster clostridioformis and Lactobacillus crispatus) and two CRC-m-depleted features (Megamonas rupellensis and Phocaeicola plebeius) across comparisons with both CRC-nm and HC groups. Metabolomic analysis identified eight pathway-mapped metabolites, mainly involved in amino acid-related metabolic pathways. In modeling analyses, metabolite-only models provided the primary discriminatory signal, whereas adding bacterial features did not improve predictive performance. Integrated microbiota-metabolite models showed lower internal performance than metabolite-only models in some comparisons, including CRC-m versus CRC-nm. Overall, these findings suggest that observed discriminatory performance was primarily driven by serum metabolite features rather than additional bacterial features, and highlight candidate microbial and metabolic markers for future validation. Because all CRC-m cases were stage IV and all CRC-nm cases were stages I-III, these results should be interpreted as exploratory cross-sectional group differences that may reflect disease stage, tumor burden, or broader progression-related changes rather than metastasis-specific biology.}, }
@article {pmid42501556, year = {2026}, author = {Bhuyan, B}, title = {Enhancing crop productivity under stress through plant growth-promoting bacterial consortia: Relevance to sustainable development goals.}, journal = {Microbiological research}, volume = {312}, number = {}, pages = {128641}, doi = {10.1016/j.micres.2026.128641}, pmid = {42501556}, issn = {1618-0623}, mesh = {*Stress, Physiological ; *Sustainable Development ; *Crops, Agricultural/microbiology/growth &amp; development ; *Plant Development ; *Microbial Consortia/physiology ; *Bacteria/metabolism ; Soil Microbiology ; Rhizosphere ; Plant Growth Regulators/metabolism ; *Crop Production/methods ; }, abstract = {Abiotic and biotic stresses significantly threaten global food security and agricultural sustainability. Achieving the United Nations Sustainable Development Goals (SDGs), particularly SDG 2 (Zero Hunger), SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), SDG 13 (Climate Action), and SDG 15 (Life on Land), requires sustainable agricultural approaches. Recently, plant growth-promoting bacterial (PGPB) consortia have emerged as an effective strategy for enhancing crop productivity under stress conditions. These microbial communities improve plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, phytohormone production, siderophore secretion, ACC deaminase activity, induction of systemic resistance, while enhancing nutrient uptake, antioxidant activity, osmotic regulation, and stress-responsive signalling pathways, thus improving plant health and productivity. Compared with single-strain inoculants, consortia provide synergistic effects that enhance rhizosphere colonization, microbial survival, and plant-microbe interactions, thus contributing to the achievement of the SDGs. Recent advances in modern tools such as metagenomics, metatranscriptomics, metabolomics, and machine learning for predictive microbiome modelling, as well as field-level engineering approaches such as encapsulation technologies, biochar-based carriers, seed coating, and root microbiome editing, have accelerated the development of efficient microbial formulations for sustainable agriculture. This review discusses the potential of PGPB consortia as a sustainable solution for boosting crop productivity under stress. The integration of consortia into modern agricultural practices can play a crucial role in supporting resilient farming systems and advancing the global SDG agenda. This review highlights the key limitations, challenges, and research gaps associated with PGPB consortia, as well as future prospects for enhancing crop productivity.}, }
@article {pmid42502975, year = {2026}, author = {Taldaev, A and Smutin, D and Danilov, L and Kashchenko, G and Ryabova, A and Adonin, L}, title = {Brain Transcriptomic Reprogramming and Comb-Associated Microbiome Variation During the Larva-To-Pupa Transition in Apis Mellifera.}, journal = {Archives of insect biochemistry and physiology}, volume = {122}, number = {4}, pages = {e70196}, pmid = {42502975}, issn = {1520-6327}, support = {25-26-00381//Russian Science Foundation/ ; }, mesh = {Animals ; Bees/microbiology/growth &amp; development/genetics/metabolism ; *Brain/metabolism/growth &amp; development ; Larva/growth &amp; development/microbiology/genetics/metabolism ; *Transcriptome ; *Microbiota ; Pupa/growth &amp; development/microbiology/genetics/metabolism ; Metamorphosis, Biological ; }, abstract = {The larva-to-pupa transition in honey bees (Apis mellifera) involves extensive neural remodeling, yet the molecular dynamics of brain development and their relationship with the surrounding microbial environment remain poorly characterized. This study integrated brain transcriptomic profiling with comb-associated metagenomic analysis to characterize stage-specific molecular signatures during metamorphosis. RNA sequencing of larval and pupal brains was combined with honeycomb shotgun metagenomics from the same sample. Brain transcriptomes exhibited marked stage-specific divergence. Pupae displayed downregulation of transcriptional regulators, ecdysone and insulin signaling, and growth-related pathways, alongside upregulation of cuticular proteins, glutathione metabolism, and odorant-binding proteins. Notably, numerous poorly annotated, lineage-specific loci showed extreme stage-specific regulation. In contrast, comb-associated microbial communities remained globally stable across developmental stages, though supervised ordination identified stage-discriminatory taxa, including core symbionts and opportunistic pathogens. Integrative network analysis revealed significant correlations between comb potential bee pathogens' abundances and brain transcripts involved in translation, stress response, and metabolic regulation. Our data suggest that honey bee neural maturation is primarily driven by intrinsic transcriptional reprogramming, while structured variation in the external microbial milieu correlates with host neural gene expression. Honeycomb microbiome shift should be the consequence of the environmental conditions changes and host developmental shifts. Their roles in that process, as well as the brood immune system-comb microbiome interactions, may be part of future research.}, }
@article {pmid42505983, year = {2026}, author = {Li, D and Wu, X and Yuan, F and Zhou, F and Cai, B and Wei, K and Huang, W}, title = {Microbial Community Differentiation and Predicted Chemical-Defense-Related Functional Potential Across Distinct Microhabitats of Cultured Hemicentrotus pulcherrimus.}, journal = {Marine drugs}, volume = {24}, number = {7}, pages = {}, pmid = {42505983}, issn = {1660-3397}, support = {2025Y01//Ningde Normal University/ ; }, mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Sea Urchins/microbiology ; Aquaculture ; Quorum Sensing ; Ecosystem ; }, abstract = {Sea urchins harbor diverse microbial communities that may contribute to host-associated ecological interactions, microbial competition, and chemical defense. However, the compartment-specific organization of sea urchin-associated microbiota and their predicted chemical-defense-related functional potential remain poorly understood under aquaculture conditions. In this study, 16S rRNA gene amplicon sequencing was used to characterize microbial communities in rearing water, coelomic fluid, intestine, stomach contents, and surface mucus of Hemicentrotus pulcherrimus (H. pulcherrimus). KEGG Orthology (KO)-based functional prediction was further performed to evaluate predicted chemical-defense-related functional potential, including predicted chemical-defense-related pathways, siderophore-related functions, quorum sensing-related functions, and bacterial competition- and secretion system-related functions. Rarefaction curves and Coverage values indicated sufficient sequencing depth. Alpha diversity and Nonmetric multidimensional scaling (NMDS) analyses revealed clear microbial differentiation among the five sample types, with rearing water showing higher microbial richness. Taxonomic analysis identified Pseudomonadota, Bacteroidota, Campylobacterota, Bacillota, Planctomycetota, and Spirochaetota as dominant phyla, with several discriminative taxa across compartments. KO prediction showed that total predicted abundance of predicted chemical-defense-related KOs differed significantly among sample types. Among host-associated compartments, surface mucus showed relatively higher predicted siderophore-related KO potential, whereas stomach contents showed higher predicted quorum sensing-related KO potential among host-associated compartments. These findings suggest compartment-specific microbial communities and predicted chemical-defense-related functional potential in cultured H. pulcherrimus under aquaculture conditions. Because these functions were inferred from 16S-based KO prediction, they should be interpreted as preliminary hypotheses for future metagenomic, metabolomic, and culture-dependent validation.}, }
@article {pmid42508331, year = {2026}, author = {Zhang, J and Cao, W and Xiong, W and Yao, Y and Jiang, D and Liang, W and Wang, L}, title = {Revealing the correlation between microbial community and flavor compounds in traditional Chinese sourdough by integrating flavoromics and metagenomics.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111927}, doi = {10.1016/j.ijfoodmicro.2026.111927}, pmid = {42508331}, issn = {1879-3460}, mesh = {Volatile Organic Compounds/analysis ; *Bread/microbiology/analysis ; Fermentation ; China ; Metagenomics ; Taste ; *Flavoring Agents/analysis/chemistry ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Saccharomyces cerevisiae/isolation &amp; purification/genetics/metabolism ; Odorants/analysis ; }, abstract = {Traditional Chinese sourdough (CTS) is mainly used for the fermentation of steamed pastries, providing a unique natural fluffiness and distinctive flavor, and thus holds important culinary value. However, the microbial mechanisms underlying the diversity of its regional characteristic flavors remain poorly understood. In this study, we integrated metagenomic sequencing with multi-platform flavor profiling-including high-performance liquid chromatography (HPLC), electronic nose, gas chromatography-mass spectrometry (GC-MS), and gas chromatography-ion mobility spectrometry (GC-IMS)-to characterize the physicochemical properties, microbial composition, and flavor compounds of 10 CTS samples collected from five provinces across China. A total of 1231 genera and 3358 species were identified, with Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Lactiplantibacillus plantarum being the dominant species. Flavor profiling analysis revealed 109 volatile organic compounds (VOCs), of which 11 key aroma-active compounds (e.g., 1-nonanol, phenethyl alcohol) were identified based on odor activity values (OAV ≥ 1). Using orthogonal partial least squares (O2PLS) modeling, we established associations between 25 potential flavor-producing microorganisms and specific metabolites. Notably, S. cerevisiae exhibited a significant positive correlation with acetic acid, 1-nonanol and glutamic acid, while L. plantarum showed a strong positive correlation with phenethyl alcohol. This study reveals the correlation patterns between microbial communities and flavor compounds in CTS, offering foundational insights for starter culture design, flavor standardization, and industrial application of traditional fermented doughs.}, }
@article {pmid42511774, year = {2026}, author = {Nappo, A and Abbasi, AM and Berno, G and Rueca, M and Smoquina, F and Gruber, CEM and Fabeni, L and Spezia, PG and Carletti, F and Pietrucci, D and Petricciuolo, M and Carnevali, A and Sanna, N and Talarico, C and Federici, E and Chillemi, G and Maggi, F}, title = {Comparative Analysis of Viral Communities in Hospital, University and Urban Wastewater by Shotgun Metagenomic Sequencing.}, journal = {International journal of molecular sciences}, volume = {27}, number = {14}, pages = {}, pmid = {42511774}, issn = {1422-0067}, support = {CUP F53C24001620001//European Union Next-GenerationEU/ ; Ricerca Corrente-Linea 1 on emerging and re-emerging infections//Ministry of Health/ ; }, mesh = {*Wastewater/virology ; *Metagenomics/methods ; Humans ; Shotgun Sequencing ; *Viruses/genetics/classification/isolation &amp; purification ; Universities ; Hospitals ; *Virome ; Metagenome ; Phylogeny ; }, abstract = {Wastewater-based surveillance has emerged as a powerful approach for population-level monitoring of pathogen circulation in a timely and non-invasive manner. In this study, shotgun metagenomic sequencing was applied to wastewater samples collected from a hospital (HP), a university campus (UN), and a wastewater treatment plant (WTP). Viral sequences were taxonomically classified using Kraken2. Specifically, HP samples showed the highest viral richness, followed by WTP and UN samples (HP vs. UN, p = 0.0003; WTP vs. UN, p = 0.0018). Using Jaccard distance, significant differences were observed between WTP and UN (R[2] = 0.181, p < 0.001), WTP and HP (R[2] = 0.159, p < 0.001), and UN and HP (R[2] = 0.223, p < 0.001), and similarly, for Sørensen-Dice dissimilarity: WTP vs. UN (R[2] = 0.238, p < 0.001), WTP vs. HP (R[2] = 0.212, p < 0.001), and UN vs. HP (R[2] = 0.307, p < 0.001). Human-associated viral families were detected across all sources, predominantly Poxviridae, Orthoherpesviridae, Polyomaviridae and Circoviridae. Furthermore, the taxonomic composition of indirectly associated viruses, mainly Anelloviridae and Crassvirales, was examined. Overall, these findings support the potential of wastewater metagenomics as a reliable tool for monitoring viral diversity within environmental and public health contexts, although further research is needed to establish its operational utility for routine surveillance applications within a One Health framework.}, }
@article {pmid42515020, year = {2026}, author = {Dalle Carbonare, L and Vareschi, A and Dervishi, K and Deiana, M and Locatelli, E and Minoia, A and Piritore, FC and Ruggiero, A and Barbu, IC and Zipeto, D and Piubelli, C and Valenti, MT}, title = {High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {42515020}, issn = {2076-0817}, support = {FUR LDC//University of Verona/ ; FUR MTV//University of Verona/ ; Fondi Ricerca Corrente" - L3P6//Ministry of Health/ ; }, mesh = {Humans ; *Microbiota ; *Wheelchairs/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Equipment Contamination ; Pilot Projects ; DNA, Bacterial/genetics ; }, abstract = {In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10[5] cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98-100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies.}, }
@article {pmid42515556, year = {2026}, author = {Martino, F and Panmei, K and Duchen, D and Thomas, DL and Kandathil, AJ and Clipman, SJ}, title = {Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, pmid = {42515556}, issn = {1999-4915}, support = {DP2 DA056130/DA/NIDA NIH HHS/United States ; R01 DA058567/DA/NIDA NIH HHS/United States ; 1DP2DA056130-01/NH/NIH HHS/United States ; R01DA058567/NH/NIH HHS/United States ; }, mesh = {*DNA, Circular/genetics ; *Nanopore Sequencing/methods ; *DNA, Viral/genetics ; *Nucleic Acid Amplification Techniques/methods ; *Virome/genetics ; Metagenomics/methods ; Genome, Viral ; Anelloviridae/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; }, abstract = {Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log10 copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log10 input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds.}, }
@article {pmid42515641, year = {2026}, author = {Liu, W and Wang, Y and Ma, J and Liang, X and Yang, L}, title = {Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, pmid = {42515641}, issn = {1999-4915}, support = {42407182//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Manure/virology/microbiology ; *Metagenome ; Chickens/virology ; *Composting ; *Drug Resistance, Microbial/genetics ; *Virome ; *Viruses/genetics/classification/isolation &amp; purification/drug effects ; Metagenomics ; Genome, Viral ; }, abstract = {Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.}, }
@article {pmid42515825, year = {2026}, author = {Kean, K and Mayne, RM and Reid, K and Secret, S and Singleton, BK and Rockett, R and Rajendra, P and Harvala, H and Breuer, J and Azim Ansari, M and Lythgoe, K and Simmonds, P and Golubchik, T}, title = {A Snapshot of the UK Blood Donor Plasma Virome: A Retrospective Cross-Sectional Cohort Study.}, journal = {Journal of medical virology}, volume = {98}, number = {8}, pages = {e71081}, pmid = {42515825}, issn = {1096-9071}, support = {/WT_/Wellcome Trust/United Kingdom ; NIHR203338//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Blood Donors ; *Virome ; Cross-Sectional Studies ; United Kingdom/epidemiology ; *Plasma/virology ; Retrospective Studies ; Female ; Male ; Viral Load ; Metagenomics ; Blood Donation ; Adult ; *Viruses/classification/isolation &amp; purification/genetics ; Prevalence ; Sequence Analysis, DNA ; Phylogeny ; Middle Aged ; }, abstract = {Estimates of population prevalence and genetic diversity of bloodborne viruses in healthy humans are essential to support population-scale monitoring for transfusion transmission risk. In the UK and globally, blood donations are routinely screened for a limited number of high-consequence pathogens, but the full composition of the plasma virome remains to be characterized. Using a novel quantitative targeted metagenomics sequencing approach, we analyzed previously unscreened plasma donations collected by NHS Blood and Transplant in England for all major pathogenic and known commensal human bloodborne viruses, and quantified their viral burden. Here we show that in a representative sample of 5064 UK blood donors in pools of 24 collected over a 1-month period, the virome was dominated by a small number of largely persistent species, representing < 10% (10/106) of previously identified human bloodborne viruses. The principal genera of human anelloviruses (TTV, TTMV and TTMDV) were detected in 89% of pools, albeit at low read count, inconsistent with measured anellovirus viral loads. In contrast, human pegivirus type 1 (HPgV-1), had an estimated population prevalence of 3.7% (95% CI 3.0%-4.4%), with high read count and complete genome recovery in around one half of positive pools, consistent with high titer in plasma. Less common detections included one species of gemykibovirus in five separate plasma pools, one hepatitis C virus (genotype 1a), and polyomaviruses and herpesviruses with prevalences between 0.04% (parvovirus 4, BK polyomavirus) to 0.41% (human herpesvirus 6). Phylogenetic analyses revealed mixed TTV, TTMV, and TTMDV populations and almost exclusively genotype 2 HPgV-1, consistent with known genotype distributions in Europe. Our results provide a baseline for describing the healthy plasma virome in UK blood donors.}, }
@article {pmid42516368, year = {2026}, author = {Zhang, Y and Wang, S and Chang, S and Li, Y and Dang, Y and Wang, Z}, title = {Navigating the gut-metabolite-immune axis: enhancing efficacy and mitigating toxicity of immune checkpoint inhibitors.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1803970}, pmid = {42516368}, issn = {1664-3224}, mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/immunology/drug effects ; Animals ; *Neoplasms/immunology/drug therapy/microbiology/metabolism ; Tumor Microenvironment/immunology/drug effects ; Fecal Microbiota Transplantation ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the oncological landscape by disrupting inhibitory pathways, notably programmed cell death protein-1/programmed death-ligand 1 (PD-1/PD-L1) and cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) pathways, thereby reinvigorating host antitumor immunity. Although these agents have emerged as frontline standard therapies for malignancies, their clinical utility remains limited. Interpatient therapeutic variability is inextricably linked to the composition and functional capacity of the gut microbiome. The underlying mechanisms appear to involve a complex dialogue between the microbiota and host immune system, where microbial metabolites serve as critical mediators in remodeling the tumor microenvironment. Despite these insights, progression in the field remains constrained due to heterogeneity in study cohorts and sample-processing methodologies, hindering the establishment of reproducible individualized predictive models and clinical intervention strategies. Consequently, there is an urgent need to systematically delineate the microbiome-metabolite-immune axis to optimize the balance between ICI efficacy and systemic toxicity. By synthesizing the latest evidence, this review aimed to highlight the pivotal roles of specific taxa, including Bacteroides, Bifidobacterium, and Akkermansia muciniphila, in ICI efficacy. These microbes and their metabolic byproducts potentiate therapeutic responses by enhancing dendritic cell cross-presentation and promoting CD[8+] T-cell infiltration, often via activation of the cyclic GMP-AMP synthase-stimulator of interferon genes or nucleotide-binding oligomerization domain-containing protein 2 signaling pathways. Furthermore, these microbial components demonstrate the ability to protect the heart and colon against inflammation and barrier disruption, thereby mitigating immune-related adverse events. Although the feasibility and safety of interventions such as fecal microbiota transplantation and supplementation with next-generation encapsulated probiotics, postbiotics, or dietary fiber have been demonstrated in preclinical and Phase I trials, substantial hurdles remain. Future progress requires large-scale, multicenter, standardized, longitudinal studies integrating metagenomics and metabolomics to construct robust cross-cancer and cross-population predictive models. Such rigorous validation would enable the development of precise microbial interventions that maximize therapeutic gains while minimizing the incidence of adverse reactions.}, }
@article {pmid42520232, year = {2026}, author = {Bhuta, R and Kuntz, T and DeNardo, B and Morgan, X and Shapiro, J}, title = {Shotgun Metagenomics Identify Unique Changes of the Intestinal Microbiome in Pediatric Survivors of Acute Lymphoblastic Leukemia.}, journal = {Rhode Island medical journal (2013)}, volume = {109}, number = {8}, pages = {32-37}, pmid = {42520232}, issn = {2327-2228}, mesh = {Humans ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/drug therapy ; Metagenomics ; Child ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Child, Preschool ; Adolescent ; Survivors ; *Dysbiosis/microbiology ; Feces/microbiology ; Shotgun Sequencing ; Case-Control Studies ; *Cancer Survivors ; }, abstract = {BACKGROUND: Intestinal microbiota plays an important role in human health and metabolism. Microbial dysbiosis has been observed in various chronic conditions, many of which are late effects of leukemia treatment. We previously observed significant differences in the gut microbiome of pediatric ALL survivors compared to healthy sibling controls. Shotgun metagenomic analyses were completed to better characterize the durability and metabolic implication of these changes.<br><br>PROCEDURE: Shotgun metagenomic sequencing was completed on DNA extracted from stool samples obtained from nine survivors of childhood acute lymphoblastic leukemia (ALL) and 10 healthy sibling controls.<br><br>RESULTS: Beta diversity (dissimilarity between samples) was significant with survivors' microbiomes becoming more similar to siblings further from treatment. The functional potential of gluconate-5-dehydrogenase enzyme (Ga5DH) decreased significantly with time from treatment. Relative abundance of Faecalibacterium prausnitzii was identified as the major contributor to differential Ga5DH expression within subjects.<br><br>CONCLUSIONS: Time from treatment has a significant effect on functional microbial recovery in ALL. Increased time from chemotherapy corresponds to microbiomes becoming more similar to sibling controls in select dyads. More significant differences were noted in patients closer to treatment. Additional, prospective studies will focus on deeper characterization of these findings and further investigate the functional role of Ga5DH in ALL survivors.}, }
@article {pmid42520350, year = {2026}, author = {Chen, Q and Niu, X and Wu, W and Shi, H and Liu, G and Chen, L and Wang, H and Zhang, Y}, title = {Composted cattle manure enhances microbial nitrogen retention and increased seed watermelon yield in saline-alkali soil.}, journal = {Microbiological research}, volume = {312}, number = {}, pages = {128647}, doi = {10.1016/j.micres.2026.128647}, pmid = {42520350}, issn = {1618-0623}, mesh = {*Manure/microbiology/analysis ; Animals ; *Soil Microbiology ; *Soil/chemistry ; Cattle ; *Nitrogen/metabolism/analysis ; *Composting/methods ; Salinity ; Alkalies ; Bacteria/metabolism/classification/genetics ; Nitrogen Cycle ; Nitrification ; Microbiota ; }, abstract = {Soil salinity and alkalinity represent a global environmental challenge that severely hampers agricultural productivity. While composted manure amendment represents a sustainable strategy relates to nutrient supplementation and soil health improvement. However, the influence of composted manure on microbial nitrogen cycles in a saline-alkali soil remains obscure. Saline-alkali soil amendment with cattle manure (CM) and composted CM (CCM) were conducted to systematically evaluate their efficacy in ameliorating soil physicochemical properties and enhancing crop productivity under saline-alkaline stress conditions. Physicochemical properties of saline-alkali soils under different amendments were investigated. The changes in microbial communities and nitrogen metabolism were analyzed using metagenomic sequencing and qPCR. Furthermore, the correlations between microbial nitrogen cycle and soil physicochemical factors were assessed. Compared to control (CK), soil salinity was significantly mitigated by 43.0%% and 51.9% in CM and CCM treatments. The organic matter, humus and nitrogen contents were also significantly increased in CM and CCM treatments. CCM significantly improved abundance of nrf in dissimilatory nitrate reduction to ammonium (DNRA), while reducing amoA abundance in nitrification. These findings suggest a potential redirection of microbial nitrogen fluxes toward retention rather than loss pathways, thereby enhances soil fertility. And the seed yield in CCM treatment was significantly higher than those of CM and CK. Our results provided mechanistic evidence for the use of composted manure as a sustainable strategy for enhancing soil fertility, mitigating salinization, and increasing crop yield of saline-alkali soils.}, }
@article {pmid42520798, year = {2026}, author = {Zhang, WJ and Hu, A and Wu, Z and Liu, L and Li, C and Wang, Y and Wei, Z and Lu, R and Li, J and He, Y and Zhang, T and Liu, S and Wang, J and Meng, L and Xiao, X and Zhao, W}, title = {Unveiling active microbial processes in Earth's deepest seawater.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {8}, pages = {1540-1559.e10}, doi = {10.1016/j.chom.2026.07.001}, pmid = {42520798}, issn = {1934-6069}, mesh = {*Seawater/microbiology ; *Microbiota/genetics ; Metagenome ; Ecosystem ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Oceans and Seas ; Earth, Planet ; Proteome ; Proteomics ; }, abstract = {Microorganisms dominate life in the hadal zone, yet extreme sampling difficulty and low biomass have precluded characterization of their in situ activities. Here, we analyze microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives. DNA-protein co-extraction and metagenome-guided metaproteomic analysis identify 135,073 non-redundant active proteins, with over 95% being hadal-specific. Metaproteomic quantification distinguishes highly active and less active taxa that differ in biogeographic origins and genomic traits. Hadal microorganisms operate a metabolic regime fundamentally distinct from the upper ocean, preferentially utilizing refractory organic matter (aromatics, halogenated compounds, and D-amino acids) and expanded electron acceptors (thiosulfate and heavy metals), collectively shaping hadal element cycling. Active viruses extend beyond "Piggyback-the-Winner" dynamics, enhancing host adaptation through auxiliary metabolic genes. These findings provide proteome-level evidence of hadal microbial activities and reveal biogeochemical cycling distinct from that of the upper ocean, highlighting the underappreciated significance of hadal microbiomes within global ocean ecosystems.}, }
@article {pmid42520901, year = {2026}, author = {Zhang, L and Zhao, B and Zhang, X and Li, Y and Li, H and Yuan, S and Ning, H and Lv, B and Li, L and Fan, X and Yue, X}, title = {Fe[2+] alters carbon and nitrogen metabolic networks in a composite microbial consortium: Metagenomic insights into the shift from denitrification to DNRA.}, journal = {Environmental research}, volume = {306}, number = {Pt 3}, pages = {125349}, doi = {10.1016/j.envres.2026.125349}, pmid = {42520901}, issn = {1096-0953}, mesh = {*Denitrification ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Microbial Consortia/drug effects ; Metabolic Networks and Pathways/drug effects ; Metagenomics ; *Iron/metabolism ; Metagenome ; Bacteria/metabolism/genetics ; }, abstract = {Conventional biological nitrogen removal processes are constrained by lengthy treatment trains and dependence on organic carbon sources, necessitating the development of novel enhanced nitrogen removal strategies that integrate multiple functions and ensure operational stability. In this study, a synthetic bacterial consortium was constructed, comprising the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. The effects of five iron species as well as their combined effects with polyacrylamide (PAM), on nitrogen removal performance and oxidative stress responses of the consortium were investigated, and metagenomic sequencing was employed to elucidate the regulatory mechanisms of Fe[2+] on metabolic processes. The results showed that, compared with the other iron species, the Fe[2+] group achieved a 20-30% increase in nitrate-N removal efficiency. The addition of PAM attenuated the specific regulatory effects of different iron species through physical mass-transfer limitation. Metagenomic analysis revealed that Fe[2+] modulated the carbon and nitrogen metabolic networks: in the carbon metabolic network, enrichment of the por gene in the glycolytic pathway generated substantial reducing power in the form of reduced ferredoxin; concomitantly, the transcript abundance of the dissimilatory nitrate reduction to ammonium pathway increased from 775 to 802, whereas that of the denitrification pathway decreased from 1259 to 1222. This study elucidates the intrinsic mechanism by which Fe[2+] promotes synergistic carbon and nitrogen removal, providing a theoretical foundation for the development of a multi-process coupled deep nitrogen removal system integrating bioaugmentation, chemical regulation, and physical sedimentation.}, }
@article {pmid42521693, year = {2026}, author = {Rodríguez-Ramos, JA and Zimmerman, AE and Wu, R and Bell, SL and Alfaro, TD and Reichart, NJ and Hofmockel, KS and Nelson, WC}, title = {Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42521693}, issn = {2041-1723}, support = {FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC05-76RL01830//DOE/ ; DE-AC02-05CH11231//DOE/ ; }, mesh = {*Soil Microbiology ; Metagenomics/methods ; *RNA, Viral/isolation &amp; purification/genetics ; *RNA Viruses/genetics/isolation &amp; purification ; *DNA, Viral/isolation &amp; purification/genetics ; Soil/chemistry ; *DNA Viruses/genetics/isolation &amp; purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; Bacteria/genetics ; }, abstract = {Deciphering viral ecology in soils is challenging due to soil's high physicochemical and microbial community complexity. To enhance detection of DNA and RNA viruses, we applied different preparation methods to soils collected from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses, total soil metagenomics and metatranscriptomics, total soil metatranscriptomics with polyadenylation enrichment, and metagenomics of bacteria/archaea as well as eukaryote-enriched samples. DNA viromes outperformed total soil metagenomes in viral detection and quality. Contrastingly, RNA viromes and total soil metatranscriptomes performed similarly for viral recovery, though RNA viromes yielded higher-quality genomes. Together, our results highlight how different preparation methods can influence the recovery and quality of DNA and RNA vOTUs. Further, we demonstrate the power of different methods in identifying distinct viral communities with unique host predictions, which in turn can have significant implications for ecological investigations related to interkingdom interactions.}, }
@article {pmid42523106, year = {2026}, author = {Xu, S and Yang, L and Gao, J and Shi, Y and Tang, X and Cai, H and Yang, L and Han, Y and Lin, L and Meng, R and Sun, J and Guan, W-j and Tang, T and Shu, W and Cao, C and Zheng, X-y and Wang, Z and Yi, X}, title = {The associations of human genetic variations with airway microbiome, environmental exposures, and respiratory health.}, journal = {mSystems}, volume = {11}, number = {8}, pages = {e0044226}, pmid = {42523106}, issn = {2379-5077}, support = {2022YFA1304300//National Key Research and Development Program of China/ ; 82495200, 82495201, 32170109, 32470094, 82404335, 32400372//National Natural Science Foundation of China/ ; 2024ZD0528400, 2025ZD0549003//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; GZNL2023A02001//Major Project of Guangzhou National Laboratory/ ; 2023A1515012367, 2023A1515012328//GuangDong Basic and Applied Basic Research Foundation/ ; 0820250237//Guangdong Special Support Program/ ; SKLRD-OP-202507//Open Project of Sate Key Laboratory of Respiratory Disease/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Environmental Exposure/adverse effects ; *Genetic Variation ; Female ; Male ; *Respiratory System/microbiology ; Air Pollutants/adverse effects ; Polymorphism, Single Nucleotide ; Middle Aged ; Sputum/microbiology ; Pulmonary Disease, Chronic Obstructive/genetics/microbiology ; }, abstract = {UNLABELLED: The intricate interactions between environmental exposures, the respiratory microbiome, and host genetic variations remain inadequately understood in the context of respiratory health. This study utilized sputum metagenomic data from 1,651 individuals in our previous cohort to elucidate these associations. Mendelian randomization indicated that air pollutants (e.g., SO2, CO, and PM2.5) were associated with lung function, which is potentially mediated by microbes, such as Actinomyces, Haemophilus influenzae, and Veillonella spp. Several genetic loci associated with respiratory microbiome variation were found to be linked to genotype-dependent associations between environmental exposures and lung function. For bacteria, the MEOX1 locus (rs1973191819) was associated with lower Filifactor alocis abundance under air pollutant exposure. The FAM110D (1:26157175) and USP36 (rs1343834070) loci showed associations with higher levels of certain pathogenic taxa (e.g., Ralstonia pickettii, Neisseria) and lower levels of the commensal Oribacterium, increasing chronic obstructive pulmonary disease (COPD) risk. For fungi, DNAJC18 and CCDC57 loci exhibited associations with Candida and Penicillium abundance, respectively. These genotype-dependent associations between the microbiome and environmental exposures provide insights into airway dysbiosis and susceptibility to respiratory diseases.<br><br>IMPORTANCE: This study reveals why individuals exposed to identical air pollution exhibit varying degrees of respiratory severity, pointing to a critical missing link: our genetics. While pollution is a known disease trigger, our findings demonstrate that host genetic variation actively regulates and shapes the respiratory microbiome under environmental stress. By mapping specific genetic loci to pollutant-driven bacterial shifts, this work elucidates how host genetics filters environmental risks to govern microbial homeostasis. These results underscore the necessity of incorporating host-microbiome genetic regulation into environmental health research. Ultimately, this study shifts the paradigm toward personalized medicine, enabling the early identification of at-risk individuals and the development of targeted, microbiome-informed interventions.}, }
@article {pmid42524914, year = {2026}, author = {Calixto, SL and Macedo, ACLP and Aguiar, JAK}, title = {GUT MICROBIOTA ALTERATIONS IN RODENT MODELS OF CHOLESTASIS INDUCED BY BILE DUCT LIGATION: A SYSTEMATIC REVIEW.}, journal = {Arquivos de gastroenterologia}, volume = {63}, number = {}, pages = {e25159}, pmid = {42524914}, issn = {1678-4219}, mesh = {Animals ; *Cholestasis/microbiology ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Ligation ; Bile Ducts/surgery ; Mice ; *Dysbiosis/microbiology ; Rats ; }, abstract = {BACKGROUND AND OBJECTIVE: Cholestatic liver diseases are a major public health issue, marked by impaired bile flow and significant disruptions in liver and systemic physiology. Growing evidence points to the gut microbiota as a key player in cholestasis pathogenesis through gut-liver axis interactions. This systematic review aimed to synthesize and evaluate current findings on intestinal microbiota changes in rodents (rats and mice) subjected to bile duct ligation (BDL)-induced cholestasis, focusing on microbial diversity, taxonomic shifts, and potential pathophysiological implications.<br><br>METHODS: A comprehensive literature search was conducted in PubMed, Scopus, and Embase for studies published from January 2020 to February 2025, following PRISMA guidelines. Eligible studies included original research using BDL in rodents without therapeutic intervention and reporting gut microbiota profiles. Data were qualitatively analyzed, emphasizing experimental conditions and microbiome outcomes.<br><br>RESULTS: Twenty-two studies met inclusion criteria. Most used 16S rRNA sequencing; two used shotgun metagenomics. BDL consistently induced gut dysbiosis, with reductions in alpha diversity (in most studies), altered beta diversity, and shifts in dominant phyla such as Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobiota. At finer taxonomic levels, increases in Prevotella, Enterococcus, Escherichia coli, and Alistipes were common, while Lactobacillus and Ruminococcus often decreased. Elevated levels of Akkermansia muciniphila and Bifidobacterium pseudolongum may represent compensatory microbial responses.<br><br>CONCLUSION: Bile duct ligation (BDL)-induced cholestasis leads to complex changes in the microbiota that can worsen intestinal barrier integrity, increase bacterial translocation, and intensify liver inflammation. These findings reinforce the central role of the gut-liver axis and corroborate the potential of microbiota-targeted therapies in the management of cholestatic liver diseases. However, as most of the available evidence derives from experimental models, further well-designed clinical studies are needed to validate the safety, efficacy, and translational applicability of these strategies in human diseases.}, }
@article {pmid42528818, year = {2026}, author = {Chen, M and Wang, X and Peng, G and Jiang, L and Liang, H and Cui, P}, title = {Gut microbiota induces immune-related alterations in gene expression, RNA methylation, and metabolism in glioblastoma revealed by single-cell and spatial multi-omics.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1899954}, pmid = {42528818}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; RNA Methylation ; *Brain Neoplasms/metabolism/genetics/immunology/microbiology ; Mice ; Multiomics ; *Glioblastoma/metabolism/genetics/immunology/microbiology ; Humans ; *Gene Expression Regulation, Neoplastic ; Epitranscriptome ; Single-Cell Analysis ; Spatial Transcriptomics ; Epigenesis, Genetic ; Tumor Microenvironment/immunology ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling ; }, abstract = {Glioblastoma (GBM) is a highly malignant tumor with poor prognosis and limited effective treatment options. Emerging studies have suggested that gut microbiota may influence glioma progression through the gut-brain axis, though the precise mechanisms remain largely unclear. In this study, we employed a comprehensive multi-omics approach-encompassing single-cell transcriptomics, spatial transcriptomics, metagenomics, metabolomics, and m6A-seq-to investigate how antibiotic-induced gut microbiota disruption impacts glioma progression in a mouse model. Gene expression analysis revealed significant alterations in antibiotics-treated mice (ABX-treated mice), including reduced expression of Epha6 and upregulated expression of Tead1, key genes associated with glioma progression and immune modulation. Spatial transcriptomics and metabolomic profiling identified reduced methionine levels in gliomas of ABX-treated mice, linking gut-derived metabolite changes to epigenetic regulation via m6A methylation. Single-cell RNA sequencing further demonstrated an increased proportion of AC-like cells, disrupted intercellular communication, and aberrations in the EPHA and NRXN signaling pathways. These findings highlight the interplay between gut microbiota, immune signaling, and epigenetic modifications in shaping the glioma microenvironment. This study advances our understanding of the gut-brain axis in glioma biology and proposes the EPHA pathway as a promising biomarker for the immune-mediated modulation of tumor progression, thereby providing new insights into the role of the gut-brain axis in glioma regulation.}, }
@article {pmid42530375, year = {2026}, author = {Wang, Z and Gao, Q and Li, S and Fang, Z and Hu, L and Li, R and Zeng, Z and Liu, Y and Li, C and Chen, H}, title = {Epigallocatechin gallate inhibits high-fat/choline diet-induced trimethylamine production via regulation of intestinal Serratia and Lactobacillus communities.}, journal = {Food &amp; function}, volume = {17}, number = {16}, pages = {7400-7414}, doi = {10.1039/d6fo02528e}, pmid = {42530375}, issn = {2042-650X}, mesh = {Animals ; *Catechin/analogs &amp; derivatives/pharmacology ; *Methylamines/metabolism ; *Choline/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Male ; *Lactobacillus/drug effects/metabolism ; Intestines/microbiology ; Mice, Inbred C57BL ; }, abstract = {High-fat/choline diets can induce the production of the enterogenous metabolite trimethylamine-N-oxide (TMAO). TMAO is synthesized from its precursor trimethylamine (TMA), which is generated via choline cleavage catalyzed by choline trimethylamine-lyase/choline TMA-lyase-activating enzyme (CutC/D) expressed by gut microbes; subsequently, TMA is oxidized to TMAO by flavin-containing monooxygenase 3 (FMO3) in the liver. While epigallocatechin gallate (EGCG) is well recognized for its gut microbiota-remodeling capacity, how it modulates TMA/TMAO metabolism through this pathway, along with the time-dependent effectiveness of EGCG intervention, remains to be elucidated. We conducted animal experiments to evaluate the inhibitory effect of time-dependent EGCG intervention on TMA/TMAO production induced by high-fat/choline diets in mice. We further identified gut bacterial strains associated with TMA levels using metagenomics and machine learning techniques, and verified the underlying mechanisms through in vitro anaerobic culture and molecular simulations. Results demonstrated EGCG significantly reduced TMA/TMAO levels in mice by regulating the choline-CutC/D-FMO3 axis. Specifically, Serratia exhibited a positive correlation with CutC enzyme activity, while Lactobacillus showed a negative correlation with TMA levels. Mechanistically, EGCG exerted a direct bacteriostatic effect on Serratia marcescens by disrupting its cell membrane structure and inhibiting its CutC enzyme activity. Meanwhile, EGCG significantly enriched Lactobacillus johnsonii, with the abundance of this strain peaking after long-term intervention. Although Lactobacillus johnsonii does not directly degrade TMA, it indirectly reduces TMA levels by inhibiting the growth of Serratia marcescens. Long-term continuous supplementation with EGCG yielded the optimal inhibitory effect on TMA/TMAO production. Hence, EGCG exerts its function primarily through a dual mechanism: directly inhibiting the growth and CutC enzyme activity of the TMA-producing bacterium Serratia marcescens, and indirectly antagonizing Serratia marcescens by promoting the proliferation of the beneficial bacterium Lactobacillus johnsonii. This study provides novel theoretical insights into the mechanism by which EGCG alleviates TMA/TMAO metabolic disorders induced by high-fat/choline diets via gut microbiota modulation.}, }
@article {pmid42531353, year = {2026}, author = {Riddell V, J and Shatadru, RN and Smith, GJ and McGivern, BB and Ellenbogen, JB and Jurgensen, SK and Fofana, A and Tfaily, MM and Wrighton, KC and Sullivan, MB}, title = {Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.}, journal = {PLoS biology}, volume = {24}, number = {7}, pages = {e3003925}, pmid = {42531353}, issn = {1545-7885}, mesh = {*Methane/metabolism ; *Microbiota/drug effects/physiology/genetics ; *Soil Microbiology ; *Polyphenols/metabolism ; Soil/chemistry ; }, abstract = {Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus eco-genomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.}, }
@article {pmid42531833, year = {2026}, author = {Wang, Y and Liu, Z and Hou, Q and Xu, Y and Chen, W and Chen, M and Liu, J and Tang, J and Wang, Y and Zhou, M and Wu, X and Wang, X}, title = {Poricoic acid a ameliorates ulcerative colitis via AMPK/PPARγ pathway-dependent cellular senescence inhibition and concomitant gut microbiota-metabolome modulation.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {160}, number = {}, pages = {158628}, doi = {10.1016/j.phymed.2026.158628}, pmid = {42531833}, issn = {1618-095X}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; *PPAR gamma/metabolism ; *Cellular Senescence/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; *AMP-Activated Protein Kinases/metabolism ; Metabolome/drug effects ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Disease Models, Animal ; Male ; Dextran Sulfate ; Intestinal Mucosa/drug effects ; Epithelial Cells/drug effects ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is an intractable inflammatory bowel disorder characterized by persistent intestinal inflammation and impaired gut barrier integrity. Its pathogenesis is multifactorial, involving gut microbiota dysbiosis, metabolic dysfunction, and cellular senescence. Current therapeutic regimens remain limited, underscoring an urgent need for innovative agents that target these interrelated pathological cascades.<br><br>PURPOSE: This study aimed to evaluate the pharmacological effects of poricoic acid A (PAA) on DSS-induced senescence in intestinal epithelial cells and in a murine model of ulcerative colitis (UC), as well as the underlying molecular mechanisms.<br><br>METHODS: We established a DSS-stimulated senescent intestinal epithelial cell model and a DSS-induced UC mouse model. Multi-omics and bioinformatics strategies, including network pharmacology, transcriptome profiling, gut metagenomics, and intestinal targeted metabolomics, were combined with molecular docking to predict candidate signaling axes. Subsequent pharmacological inhibition and siRNA-mediated silencing assays were performed to validate core pathways functionally.<br><br>RESULTS: PAA robustly suppressed DSS-induced senescence and inflammatory responses in intestinal epithelial cells. In vivo assays verified that PAA alleviated UC-related manifestations, including body weight loss, rectal hemorrhage, and colonic histological injury. Joint network pharmacology and transcriptomic screening identified the AMPK/PPAR&#x3b3; as the core pathway mediating PAA's bioactivity. Mechanistic experiments confirmed that PAA directly bound and activated PPAR, further functionally triggering downstream AMPK/SirT1/PGC1&#x3b1; signaling. Blockade of AMPK via pharmaceutical antagonists or siRNA largely abolished PAA's anti-senescence and anti-inflammatory capacities; PPAR&#x3b3; suppression, in turn, secondary deactivated the AMPK and its downstream functional effectors. In mouse models, AMPK inhibition drastically compromised PAA's protective effects against UC. Moreover, PAA treatment of UC is closely associated with remodeling of the gut microbiome-metabolome axis and restoration of intestinal homeostasis.<br><br>CONCLUSION: PAA exerts potent anti-senescence, anti-inflammatory, and colon-protective effects in UC via activating the AMPK/PPAR&#x3b3; signaling pathway. Such beneficial activity may be associated with the normalization of gut microbiota-metabolome homeostasis. This work identifies novel molecular targets and a promising lead compound for the intervention of ulcerative colitis.}, }
@article {pmid42532286, year = {2026}, author = {Zhang, Y and Hu, L and Ding, X and Liu, L and Xue, L and Miao, L}, title = {Investigating gut microbiota and their metabolites as biomarkers for tacrolimus pharmacokinetic variability.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {225}, number = {}, pages = {107626}, doi = {10.1016/j.ejps.2026.107626}, pmid = {42532286}, issn = {1879-0720}, mesh = {*Tacrolimus/pharmacokinetics ; *Immunosuppressive Agents/pharmacokinetics/pharmacology ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; Fatty Acids, Volatile/metabolism ; Kidney Transplantation ; Humans ; }, abstract = {Tacrolimus (TAC), a cornerstone immunosuppressant in transplantation, presents a clinical challenge due to its narrow therapeutic index and substantial interindividual pharmacokinetic (PK) variability. This exploratory study investigated the association between gut microbiota composition, short-chain fatty acid (SCFA) metabolites, and TAC PK variability during the early post-kidney transplantation period. Based on prediction errors derived from a previously established population PK model, 36 transplant recipients were stratified into positive (n = 17) and negative (n = 19) deviation groups. Metagenomic sequencing and targeted SCFA metabolomic analysis of fecal samples revealed that the negative deviation group exhibited significantly reduced gut microbial diversity and altered community structure. Among 142 differentially abundant taxa, 10 microbial features, including Enterococcaceae - associated taxa, showed discriminative potential between the two PK phenotypes (AUC > 0.7), with three Enterococcus species (E. durans, E. faecium, and E. hirae) showing particularly robust signals (Cohen's d > 1.0 and power > 80%). Functional analysis suggested downregulation of butyrate biosynthesis pathways in the negative deviation group, which was consistent with significantly lower fecal butyrate and total SCFA concentrations. These hypothesis-generating findings suggest that gut microbiota and SCFAs are associated with TAC PK phenotypes, but independent validation in larger cohorts is required before clinical translation.}, }
@article {pmid42533554, year = {2026}, author = {Yang, K and Yang, M and Yu, Q and Liong, MT and Chen, D and Cai, M}, title = {The Effect of a Probiotic on Gut Microbiota Stability and Systemic Well-Being during Short-Term Travel.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510037}, pmid = {42533554}, issn = {1738-8872}, mesh = {Humans ; *Probiotics/administration &amp; dosage ; *Bifidobacterium/physiology ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Adult ; *Travel ; Male ; China ; Female ; Feces/microbiology ; Young Adult ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Short-term travel, particularly to new environments, can disrupt gut microbiota homeostasis and induce a range of physical and psychological symptoms. While probiotics are proposed to mitigate these effects, evidence from well-controlled trials during domestic travel, especially along unique routes like China's Silk Road, remains limited. This study investigated the efficacy of a multi-strain Bifidobacterium probiotic in maintaining gut microbiota stability and alleviating travel-related symptoms. In a randomized, double-blind, placebo-controlled trial, 74 healthy adults traveling to Xinjiang were assigned to receive either a probiotic (n = 39; B. longum subsp. infantis M-63, B. breve M-16V, and B. longum BB536, 1.5 × 10[9] CFU/day) or a placebo (n = 35) for five days during travel. Gut microbiota was profiled via metagenomic sequencing (pre- and post-travel), and symptoms were recorded daily. Primary outcomes were changes in gut microbiota composition and function (KEGG pathways). Secondary outcomes included respiratory, gastrointestinal, and systemic symptom scores. Data were analyzed on an intention-to-treat basis. While alpha and beta diversity remained stable in both groups, the probiotic group exhibited a distinct post-travel microbiota enriched with beneficial taxa, including Bifidobacterium breve and Intestinibacillus at the genus level, and Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and other Lacticaseibacillus species. qPCR confirmed significant increases in administered strains B. longum subsp. infantis (p < 0.001) and B. breve (p < 0.001). KEGG analysis revealed that the probiotic group maintained a metabolically focused profile (e.g., peptidoglycan biosynthesis, histidine metabolism), whereas the placebo group showed increased abundance of microbial pathways associated with host disease-related signaling (e.g., Huntington disease, various cancers) and inflammatory signaling (e.g., PI3K-Akt signaling pathway). Symptomatically, the probiotic group demonstrated a significantly greater reduction than the placebo in irritability (-92% vs. -31%; p = 0.033) and fatigue (-24% vs. +43%; p = 0.024) post-travel, and reported less dizziness (-100% vs. -35%; p = 0.024). Supplementation with a multi-strain Bifidobacterium probiotic during short-term travel promoted the colonization of beneficial bacteria, stabilized gut microbial function against travel-induced dysregulation, and may contribute to supporting systemic well-being during travel.}, }
@article {pmid42548466, year = {2026}, author = {Yang, L and Tao, Y and He, Y and Liu, S and Gan, L and Dai, A and Ni, Q and Wang, Y and Li, F and Liu, Q and Hu, Y and Wang, Y and Lu, W}, title = {Metagenomic and metabolomic profiling in primary aldosteronism with coexisting obstructive sleep apnea.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1858100}, pmid = {42548466}, issn = {1664-2392}, mesh = {Humans ; *Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics ; Female ; *Hyperaldosteronism/metabolism/complications/genetics/microbiology ; Male ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Adult ; Feces/microbiology ; Polysomnography ; }, abstract = {BACKGROUND: Primary aldosteronism (PA) frequently coexists with obstructive sleep apnea (OSA), and this comorbidity is associated with increased cardiometabolic risk. Although both PA and OSA have been individually linked to gut microbiome alterations, it remains unclear which layer of gut microbiome-associated variation best reflects clinical heterogeneity in PA with coexisting OSA.<br><br>METHODS: In this prospective observational study, we performed shotgun metagenomic sequencing and untargeted fecal metabolomic profiling in 29 adults with clinically confirmed PA, who were stratified according to OSA severity (G1-G4) based on overnight polysomnography. Microbial gene richness, taxonomic composition, functional potential based on KEGG annotation, and antibiotic resistance gene profiles were analyzed using standardized bioinformatic workflows. Metabolomic variation was assessed using multivariate analysis, pathway enrichment, and additional exploratory analyses incorporating apnea-hypopnea index (AHI) as a continuous variable. Multiple-testing correction was applied to metabolite-level comparisons.<br><br>RESULTS: Global gut microbial gene richness, alpha diversity, beta diversity, and broad functional profiles did not show strong group-level separation across OSA severity strata. Additional analyses using AHI as a continuous variable similarly showed no significant association between AHI and overall gene richness or alpha diversity indices. Nevertheless, selective genera showed exploratory associations with AHI, suggesting that localized taxonomic signals may occur despite relative stability of global community structure. Antibiotic resistance gene profiles showed marked inter-individual variability without clear group-level separation, although ARO richness showed an exploratory inverse association with AHI. In contrast, fecal metabolomic profiling revealed nominal phenotype-associated differences, including trehalose-related metabolites and FAHFA species that showed inverse exploratory associations with AHI. However, no individual metabolite remained significant after global Benjamini-Hochberg false discovery rate correction.<br><br>CONCLUSIONS: In PA with coexisting OSA, gut microbiome-associated heterogeneity appears to be more readily reflected by selected taxonomic and metabolic signals than by global microbial diversity or broad functional potential. However, given the small sample size, limited control of clinical and lifestyle confounders, and lack of metabolite-level significance after global FDR correction, these findings should be interpreted as exploratory and hypothesis-generating. Larger controlled cohorts incorporating PA subtype, medication exposure, dietary assessment, and longitudinal validation are needed.}, }
@article {pmid42549419, year = {2026}, author = {Li, X and Jiang, J and Li, X and Jian, G and Li, F}, title = {Effects of diarrhea and antibiotic-induced microbial elimination on dynamic changes in fecal microbial communities and antibiotic resistance of Hu sheep lambs (Ovis aries).}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21574}, pmid = {42549419}, issn = {2167-8359}, mesh = {Animals ; *Diarrhea/microbiology/veterinary/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Sheep/microbiology ; *Feces/microbiology ; *Sheep Diseases/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects/genetics ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: As a highly reproductive meat sheep breed in China, Hu sheep is an important economic group in ruminant animal breeding. However, research on its intestinal microbiomes under the background of diarrhea and antibiotic treatment remains relatively limited.<br><br>METHODS: This study investigated the intestinal microbiota of Hu sheep lambs in the preliminary stage of diarrhea (group DM), the late recovery stage of diarrhea (group DL), and the healthy stage (group H). Diseased individuals (groups DM and DL) were treated with a combination of Shuanghuanglian, Cefazolin, Lincomycin, and Dexamethasone (0.2 mL dosage). To characterize the intestinal microbiota, fecal samples were collected from all groups, and metagenomic sequencing was performed. Using metagenomic binning tools and co-assembly methods, we reconstructed 482 high-quality non-redundant metagenome assembled genomes (MAGs).<br><br>RESULTS: Among these MAGs, 70% belong to the phyla Bacillota, Bacteroidota, and Pseudomonadota, highly consistent with the typical structure of intestinal microbiota in ruminants. Functional annotation revealed that the genes encoding carbohydrate-active enzymes (CAZymes) are more abundant in Bacillota and Bacteroidota, which supports the degradation and energy metabolism functions of Hu sheep on fibrous feed. During the preliminary stage of diarrhea, the virulence genes carried by symbiotic bacteria such as Lachnospiraceae, Acutalibacteraceae and Bacteroidaceae were enriched. Although diarrhea symptoms alleviated during the late recovery stage of diarrhea, the combined use of multiple antibiotics led to the continuous enrichment of antibiotic resistance genes (ARGs) related to lincosamides and cephalosporins. The average abundance of cephalosporin-related ARGs in group DL was significantly higher than that in group DM and H, indicating a risk of residual ARGs. Microbial diversity analysis showed that there was no significant overall difference in MAGs between group DM and H, but both groups showed significant differences compared to group DL, suggesting that antibiotic driven clearance of sensitive bacteria is the core driving force. Moreover, our study shows that the abundance of the zoonotic pathogens Barnesiella and Campylobacter significantly increased in the diarrhea group (p&#xa0;<&#xa0;&#xa0;0.05), and they carry 567 and 382 virulence genes, respectively. Their pathogenicity is regulated by the dynamic changes in the host intestinal microbiota.<br><br>CONCLUSIONS: This study not only expands the genomic database of ruminant intestinal microorganisms but also provides a key theoretical basis for formulating intestinal microecological regulation strategies and optimizing diarrhea treatment regimens for Hu sheep.}, }
@article {pmid42551230, year = {2026}, author = {Zhuang, T and Wang, X and Zheng, W and Lu, W and Hao, L and Wang, X and Huang, C and Wang, R and Hu, Y and Wang, Z and Chen, K and Li, T and Yang, Q and Yang, L and Ding, L}, title = {Enrichment of Akkermansia muciniphila by red ginseng promotes GDF15 secretion and suppresses obesity in mice.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {160}, number = {}, pages = {158600}, doi = {10.1016/j.phymed.2026.158600}, pmid = {42551230}, issn = {1618-095X}, mesh = {Animals ; *Growth Differentiation Factor 15/metabolism ; *Panax/chemistry ; *Obesity/drug therapy/metabolism/microbiology ; Male ; Mice ; Diet, High-Fat ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; Akkermansia ; *Plant Extracts/pharmacology ; *Anti-Obesity Agents/pharmacology ; Activating Transcription Factor 4/metabolism ; Transcription Factor CHOP/metabolism ; Weight Loss/drug effects ; Appetite/drug effects ; }, abstract = {BACKGROUND: Obesity is a growing global health burden with rising incidence. Red ginseng (RGS), a traditional processed ginseng product, shows potential for improving metabolic parameters, though its anti-obesity mechanism remains incompletely understood.<br><br>PURPOSE: This study investigated the therapeutic effects of short-term RGS administration on obesity and sought to elucidate the underlying mechanism.<br><br>METHODS: A high-fat diet (HFD)-induced obese mouse model was used to assess short-term RGS effects. Antibiotic treatment and fecal microbiota transplantation were performed to evaluate gut microbiota involvement. 16S rRNA sequencing and metagenomic analysis identified key bacterial species, and mass spectrometry-based proteomics identified A. muciniphila-derived proteins. The growth differentiation factor 15 (GDF15)-GFRAL axis was interrogated using Gfral[&#x2012;/&#x2012;] mice.<br><br>RESULTS: Short-term RGS treatment suppressed appetite, reduced body weight, and elevated circulating GDF15 in diet-induced obese (DIO) mice. RGS enriched A. muciniphila, and its depletion abrogated RGS-mediated weight loss and appetite suppression. The A. muciniphila-derived protein Amuc_1631 was identified as a key effector promoting GDF15 secretion. Mechanistically, RGS upregulated colonic Gdf15 transcription via the PERK-eIF2&#x3b1;-ATF4-CHOP axis and activated the brainstem GDF15-GFRAL pathway. The RGS 50% ethanol eluate (RGS/50) fraction was identified as the potential active component responsible for A. muciniphila enrichment and GDF15 elevation.<br><br>CONCLUSIONS: This study identifies a gut microbiota-dependent mechanism underlying the anti-obesity effects of RGS, centered on A. muciniphila enrichment and its derived protein Amuc_1631, which promotes GDF15 secretion to suppress food intake via the GDF15-GFRAL axis.}, }
@article {pmid42554318, year = {2026}, author = {Lin, H and Wu, W and Fang, H and Chen, Y and Wu, H and Lai, X and Li, L}, title = {Integrated Metabolomic and Metagenomic Profiling Reveals Distinct Microbial-Metabolic Signatures in the Adenoma-Carcinoma Sequence of Colorectal Cancer.}, journal = {Biomedical chromatography : BMC}, volume = {40}, number = {9}, pages = {e70588}, pmid = {42554318}, issn = {1099-0801}, support = {3502Z202374067//Natural Science Foundation of Xiamen, China/ ; }, mesh = {Humans ; *Colorectal Neoplasms/metabolism/microbiology ; *Metabolomics/methods ; *Adenoma/metabolism/microbiology ; *Metabolome/physiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Multiomics ; Middle Aged ; *Gastrointestinal Microbiome/physiology/genetics ; Biomarkers, Tumor/metabolism/analysis ; Aged ; }, abstract = {Colorectal cancer (CRC) arises via the stepwise adenoma-carcinoma sequence (ACS). Gut microbial dysbiosis and host metabolic reprogramming jointly correlate with CRC onset and advancement, yet their stage-specific crosstalk across ACS remains largely unclear. Limited multi-omics research on microbial-metabolic interactions throughout ACS hinders the development of early diagnostic biomarkers and preventive strategies. Here, we combined untargeted mucosal metabolomics and fecal shotgun metagenomic sequencing in 36 participants, covering healthy controls, ACS, and CRC patients. We systematically analyzed microbial composition, functions, differential metabolites, and enriched pathways and integrated multi-omics data to screen stage-specific signatures. Distinct gut microbial profiles and progressive functional shifts toward pathogenicity and abnormal carbohydrate metabolism were observed along ACS. Mucosal metabolism was continuously disrupted, with prominent alterations in taurine-hypotaurine, sphingolipid, and bile acid pathways. Core differential metabolites showed excellent diagnostic performance. Microbe-metabolite interactions were progressively enhanced to form a concerted pro-tumor axis. This study characterizes unique ACS-stage microbial-metabolic features. Dysregulated metabolic pathways and key microbe-metabolite crosstalk are closely associated with CRC progression, offering novel non-invasive biomarkers and premalignant intervention targets.}, }
@article {pmid42555569, year = {2026}, author = {Vitry, G and Angdisen, J and Arriaga, P and Irgen-Gioro, S and Sawant, MA and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Mao, JH and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC}, title = {Monitoring radiation exposure through skin swab multi-omic profiling.}, journal = {PloS one}, volume = {21}, number = {8}, pages = {e0354734}, pmid = {42555569}, issn = {1932-6203}, support = {P30 CA051008/CA/NCI NIH HHS/United States ; U01 AI148307/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Skin/radiation effects/metabolism/microbiology ; Animals ; Multiomics ; Mice ; Metabolomics/methods ; *Radiation Exposure/analysis ; Metabolome/radiation effects ; Lipidomics ; Skin Microbiome ; }, abstract = {Exposure to ionizing radiation poses major health risks across medical, occupational, and spaceflight settings, driving the need for rapid, non-invasive biodosimetry tools. As the body's most accessible organ and the most frequent site of radiation injury, the skin represents a promising interface for monitoring exposure. Using colonized human skin equivalents (coHSE; 0 Gy n = 8, 1 Gy n = 6, 4 Gy n = 6) and mice (n = 6/group) models, we performed multi-omic profiling, integrating metabolomics, lipidomics, and metagenomics, on skin swab samples collected after exposure to 0, 1, or 4 Gy of x-rays. We identified two distinct metabolite panels: one discriminating irradiated from non-irradiated skin, and another distinguishing dose-specific response. These panels included conserved radiation-responsive metabolites (e.g., uric acid, xanthine, taurine) and skin-specific markers associated with barrier integrity (e.g., proline, arginine). Diacylglycerol network enrichment and shifts in radioprotective microbial taxa, including Lachnospiraceae and Lactobacillales, further supported a repair-driven molecular response. These data support the feasibility of skin swab signatures for non-invasive exposure classification, providing a molecular and microbial framework for skin based monitoring measure development and motivating validation in human cohorts for real-world biodosimetry.}, }
@article {pmid42557256, year = {2026}, author = {Gicquel, M and Planillo, A and Heitlinger, E and Forslund-Startceva, SK and Kramer-Schadt, S and Ferreira, SCM and Jarquín-Díaz, VH}, title = {Farming practices exert selection pressures on the resistome of natural populations of house mice.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42557256}, issn = {2041-1723}, support = {FO1279/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HE7320/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KR4266/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; F01KI1909A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01KI2404B//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {Animals ; Mice/microbiology ; *Selection, Genetic ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Livestock/microbiology ; Genes, Bacterial ; *Agriculture ; Germany ; Swine ; }, abstract = {The factors maintaining antimicrobial resistance genes (ARGs) in non-domesticated animal microbiomes remain unclear for species inhabiting human-dominated or less human-impacted landscapes. We analysed 875 gut metagenomes from natural populations of house mice (Mus musculus) on German farms between 2016 and 2022 to identify environmental and host determinants of ARG occurrence. Using joint species distribution models, we quantified the influence of landscape, climate and mouse associated characteristics on the occurrence of individual ARGs and on trait dependence among genes. Environmental variables and livestock farming intensity explained 27% of ARG variation, whereas host characteristics accounted for 8%. Analysis of ARG traits revealed that agricultural land use and exposure to livestock increased the occurrence of potentially mobile ARGs. Pig density was strongly associated with an integron-encoded sulfonamide resistance gene (sul1) and genes conferring tetracycline (tet) and beta-lactam resistance (cblA-1) (posterior probability 0.75). Consistently, mouse resistomes have a distinctive resistome, but share more than 50% of ARGs with livestock manure, including widespread genes and those promoted in livestock. Here, we show that landscape conditions, particularly farming intensity, shape the distribution of specific ARGs and potentially mobile ARGs in house mice microbiomes.}, }
@article {pmid42558149, year = {2026}, author = {Ding, R and Qi, F and Dai, Q and Li, K and Zhang, Y}, title = {Multi-omics analysis identifies a hepatocyte-associated signature in alcohol-related liver injury.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1844110}, pmid = {42558149}, issn = {1664-3224}, mesh = {Animals ; *Hepatocytes/metabolism ; Multiomics ; Humans ; *Liver Diseases, Alcoholic/metabolism/genetics/etiology ; Mice ; Male ; Ethanol/adverse effects ; Metabolomics/methods ; Transcriptome ; Feces/chemistry/microbiology ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Disease Models, Animal ; Liver/metabolism ; Metabolome ; Mice, Inbred C57BL ; Metagenomics ; }, abstract = {Alcohol-related liver disease (ALD) is a major cause of liver-related morbidity and mortality worldwide, yet the associations linking alcohol-induced gut microbial alterations to metabolic remodeling and hepatocyte dysfunction remain incompletely understood. Here, we applied an integrative multi-omics strategy combining untargeted fecal metabolomics, shotgun metagenomics, mouse liver bulk RNA sequencing, and reanalysis of publicly available human hepatic single-cell and bulk transcriptomic datasets to characterize alcohol exposure-associated gut-liver immunometabolic features. In a mouse model of acute ethanol-induced liver injury, fecal metabolomic and metagenomic profiling revealed marked alterations in microbial functional potential and fecal metabolic composition, identifying six convergent metabolic pathways across fecal multi-omics layers, including nucleotide metabolism, the pentose phosphate pathway, histidine metabolism, glycerophospholipid metabolism, glycine/serine/threonine metabolism, and the phosphotransferase system. Reanalysis of human ALD single-cell transcriptomes showed hepatocyte-enriched activity patterns for several corresponding pathways, suggesting potential pathway-level associations between fecal metabolic alterations and hepatic transcriptional responses. Integrative transcriptomic analysis further identified a ten-gene hepatocyte-associated signature, comprising LRG1, ORM1, ORM2, TAT, HP, FGB, FGG, ITIH3, NNMT, and AGT, which was associated with pathway activity and showed consistent upregulation across acute ethanol-induced liver injury and human ALD/AH transcriptomic datasets. In an external human cohort, this signature stratified patients into exploratory molecular subgroups with distinct metabolic pathway activities and clinical outcome distributions. Collectively, these findings provide a hypothesis-generating multi-omics framework for investigating alcohol-related liver injury and support further validation in chronic ethanol exposure models and functional studies.}, }
@article {pmid42558207, year = {2026}, author = {Yang, Y and Ren, L and Zhang, Y and Wang, X and Shang, J and Zhang, L}, title = {Microbiota in cholestatic diseases: crosstalk among bile composition, the biliary microbiome, and host immunity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1884030}, pmid = {42558207}, issn = {1664-3224}, mesh = {Humans ; Animals ; *Microbiota/immunology ; Bile Acids and Salts/metabolism ; *Cholestasis/microbiology/immunology/metabolism ; *Bile/metabolism/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; }, abstract = {Cholestatic liver diseases are a heterogeneous group of hepatobiliary disorders caused by impaired bile formation, secretion, or excretion, leading to hepatocyte injury, biliary inflammation, fibrosis, and eventually cirrhosis. Traditional studies have largely focused on isolated mechanisms, including bile acid toxicity, immune dysregulation, and genetic susceptibility. However, recent advances in metagenomics, metabolomics, and immunology have highlighted the critical role of the gut and biliary microbiota in disease pathogenesis. This review proposes the core concept of a "tripartite interplay among bile composition, biliary microbiome, and host immunity," integrating the dynamic crosstalk among these three axes in cholestatic liver diseases. Bile composition shapes microbial communities and modulates immune responses through receptors such as FXR and TGR5. In turn, the biliary microbiome regulates bile acid metabolism and immune activity through microbial metabolites. Meanwhile, the host immune system senses microbial signals via pattern-recognition receptors, triggering inflammatory pathways and influencing microbial colonization and metabolism. These reciprocal interactions form complex feedback loops that drive disease progression from early inflammation to chronic fibrosis and cirrhosis. Based on this framework, emerging diagnostic approaches combine microbial signatures, bile acid profiles, and immune markers into multidimensional biomarker systems. Therapeutically, integrated strategies targeting the microbiome, bile acid metabolism, and immune pathways may offer synergistic benefits. Despite challenges including sampling difficulty, interindividual variability, and limitations of current models, future technologies such as single-cell sequencing, spatial transcriptomics, and multi-omics integration may enable precision diagnosis and targeted therapy.}, }
@article {pmid42558343, year = {2026}, author = {Liu, L and Lin, J and Sang, K and Lai, J and Huang, N and Zhong, P and Liu, Y and Chen, S}, title = {Bile acid signaling at the gut-vascular interface: a novel modulator of hantavirus endothelial barrier dysfunction.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1883162}, pmid = {42558343}, issn = {2235-2988}, mesh = {Animals ; Humans ; *Orthohantavirus/pathogenicity/physiology ; *Bile Acids and Salts/metabolism ; *Signal Transduction ; Receptor, Farnesoid X-Activated ; Rats ; *Endothelial Cells/virology/metabolism ; Gastrointestinal Microbiome ; *Hantavirus Infections/virology/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; NF-kappa B/metabolism ; Lung/virology/microbiology ; Vascular Cell Adhesion Molecule-1/metabolism/genetics ; }, abstract = {Hantavirus infection triggers life-threatening hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), driven by severe endothelial barrier breakdown and systemic capillary leakage. Clinical severity varies widely with undefined host regulators, and no targeted endothelial-protective treatments exist. Recent data link hantaviruses to gut microbiome remodeling, while bile acid (BA) receptors FXR and TGR5 potently inhibit NF-κB-mediated endothelial inflammation. We synthesize four core lines of evidence. First, metagenomic reports confirm hantavirus reshapes gut/lung microbiota in rodent reservoirs. Second, we re-analyzed three public GEO datasets via standardized RNA-seq/microarray pipelines: (i) GSE245916: SEOV-infected human/rat lung ECs show conserved VCAM1/ICAM1 upregulation (human VCAM1 log2FC=+1.17, P = 0.023; rat Icam1 log2FC=+0.32, padj=0.016) with unaltered FXR; (ii) GSE7271: SEOV-infected rat lung displays sustained Nfkb1 suppression (all timepoints, P<0.05) and day-15 Slc10a2 downregulation (P = 0.028); (iii) GSE270172: PUUV 3D vessel chips feature robust IL6 elevation (log2FC=+1.22, P = 3.1×10[-8]) and disrupted BA transporters (ABCC3 log2FC=-1.44, P = 7.4×10[-][12]). TGR5 (GPBAR1) was undetectable in endothelial cells across all datasets. Third, FXR/TGR5 agonists repress NF-κB inflammation and mitigate lung vascular injury. Fourth, HTNV upregulates CH25H to block HMGCR-dependent cholesterol synthesis, depleting BA precursor substrates. We propose a unified pathogenic model: hantavirus-triggered gut dysbiosis plus virus-impaired cholesterol metabolism deplete circulating FXR/TGR5 agonistic BAs, relieving constitutive inhibition of endothelial NF-κB and monocyte NLRP3 inflammasomes to exacerbate capillary leakage. We define tiered testable predictions covering clinical multi-omics cohorts, in vitro receptor modulation assays and in vivo pharmacological interventions. This gut microbiota-BA-FXR/TGR5 axis represents a repurposable therapeutic target for hantavirus diseases, though direct causal evidence connecting BA signaling to viral vascular damage remains absent; our framework offers a rigorous testable roadmap for subsequent validation.}, }
@article {pmid42560299, year = {2026}, author = {Liang, F and Li, J and Yue, Y and Pan, J and Liu, C and Cheng, D and Zhang, N and Li, K and Chu, F and Wu, H}, title = {Distinct Gut Microbiome and Metabolome Profiles Associate with Differential Responses to Immunotherapy in Colorectal Cancer.}, journal = {Polish journal of microbiology}, volume = {75}, number = {2}, pages = {168-194}, pmid = {42560299}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/metabolism ; *Metabolome ; *Immunotherapy ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; Male ; Middle Aged ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The composition of the intestinal microbiome has been identified as a key factor influencing the efficacy of immune checkpoint inhibitors. This study aimed to systematically evaluate the potential associations among gut microbiota, metabolic profiles, and clinical outcomes in patients with MSI-H advanced colorectal cancer (CRC) treated with immunotherapy. Twenty advanced CRC patients receiving immunotherapy were enrolled and categorized into clinical benefit response (CBR) and non-benefit (NCB) groups based on treatment efficacy. Fecal samples were analyzed using metagenomic sequencing and untargeted metabolomics. The results revealed significant enrichments of s_Clostridium unclassified and metabolites such as guanosine, 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, and quercetin 3-(6"-malonyl-glucoside) in the CBR group, suggesting their potential positive predictive value for immunotherapy response. Conversely, the NCB group showed significant enrichments of s_Roseburia hominis, s_Marseilla massiliensis, and metabolites including pyrophosphate, riboflavin, and PC(22:5(4Z,7Z,10Z,13Z,16Z)/14:0), indicating a possible association with treatment resistance. By integrating fecal metagenomics and metabolomics, this study reveals distinctive "flora-metabolite" interactions linked to therapeutic response in advanced CRC patients undergoing immunotherapy. Specific microbial and metabolic profiles were positively or negatively correlated with immunotherapy outcomes, highlighting their potential not only as predictive biomarkers but also as a theoretical foundation for developing individualized immunotherapy strategies based on microecological modulation.}, }
@article {pmid42562454, year = {2026}, author = {Zheng, X and Sun, P and He, C and Liu, M and Qiu, J and Ding, Z and Zhang, Y and Zhou, S and Zhou, J and Sun, J and Feng, W and Zhang, L and Cheng, N and Xu, Q and Li, X and Yang, L and Liang, A}, title = {Royal jelly enhances ovarian function by modulating taurocholic acid metabolism and attenuating oxidative stress in D-galactose-induced POI mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119500}, doi = {10.1016/j.foodres.2026.119500}, pmid = {42562454}, issn = {1873-7145}, mesh = {Animals ; Female ; *Oxidative Stress/drug effects ; Royal Jelly ; Galactose ; Mice ; *Fatty Acids/pharmacology ; *Ovary/drug effects/metabolism ; *Taurocholic Acid/metabolism ; Disease Models, Animal ; *Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Estradiol/blood ; }, abstract = {Premature ovarian insufficiency (POI) is a complex endocrine and metabolic disorder frequently associated with oxidative stress. Royal jelly (RJ) is a well-recognized natural functional food with multiple health benefits; however, its potential effects on POI remain unexplored. This study aimed to investigate the therapeutic potential and underlying mechanisms of RJ in a D-galactose (D-gal)-induced POI mouse model. The results showed that RJ increased serum estradiol (E2) levels, enhanced ovarian reserve and oocyte maturation, reduced ovarian oxidative stress, and ultimately improved the fertility of D-gal-treated mice. Integrated metagenomic and metabolomic analyses revealed that RJ alleviated D-gal-induced gut microbiota dysbiosis, notably increasing the abundance of Muribaculaceae bacterium, and restored levels of taurocholic acid (TCA), which positively correlated with both Muribaculaceae bacterium abundance and serum E2 levels. Importantly, TCA supplementation alone recapitulated the protective effects of RJ by reversing D-gal-induced reductions in E2 and anti-Müllerian hormone (AMH) levels, restoring follicle numbers, and alleviating oxidative stress. Mechanistically, TCA activated the nuclear factor erythroid 2-related factor 2 (NRF2) antioxidant pathway in ovarian tissue, while simultaneously enhancing intestinal β-glucuronidase activity to modulate systemic E2 metabolism. In conclusion, RJ alleviates D-gal-induced POI in mice by modulating the gut microbiota-bile acid-ovarian axis, providing novel insights into its potential application for POI prevention and treatment.}, }
@article {pmid42562478, year = {2026}, author = {Zhang, HY and Huang, TC and Chai, LJ and Shi, W and He, YX and Lu, ZM and Zhang, XJ and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Integrating ecological networks and metagenomics to decipher core microbial drivers of organic acid metabolism during heaped fermentation of sauce-flavor Baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119702}, doi = {10.1016/j.foodres.2026.119702}, pmid = {42562478}, issn = {1873-7145}, mesh = {*Fermentation ; *Metagenomics/methods ; *Food Microbiology ; *Bacteria/metabolism/genetics/classification ; Volatile Organic Compounds/metabolism/analysis ; Acetic Acid/metabolism/analysis ; Caproates/analysis ; Taste ; Lactic Acid/metabolism/analysis ; *Fermented Foods/microbiology ; *Microbiota ; Pentanoic Acids ; Hemiterpenes ; }, abstract = {Organic acids play crucial roles in both flavor quality and microbial succession of sauce-flavor Baijiu; however, the core microbial drivers responsible for their metabolism remain poorly understood. This study systematically investigated the microbial drivers of organic acid metabolism across six sequential rounds (R1-R6) of heaped fermentation. A total of 24 organic acids were identified, including nine non-volatile organic acids (NVOAs) and 15 volatile organic acids (VOAs). HPLC analysis revealed that the total content of acetic acid and nine NVOAs increased significantly across rounds, rising from 29.35 g/kg in R1 to 66.40 g/kg in R6. Lactic acid was the most abundant NVOA, while acetic acid, isovaleric acid, and hexanoic acid were the primary volatile contributors. Co-occurrence network analysis identified 488 consistently correlated bacterial pairs that clustered into two distinct guilds. Guild 2, mainly comprising Virgibacillus, Kroppenstedtia, Oceanobacillus, and Bacillus, exhibited high abundance (47%-78%) across all rounds and was defined as the core bacterial guild. Spearman correlation analysis revealed that guild 2 was positively correlated with NVOAs (69.41%) but negatively correlated with VOAs (63.02%). Metagenomic analysis reconstructed seven key pathways involved in organic acid biosynthesis. Kroppenstedtia, Lentibacillus, Desmospora, and Oceanobacillus were identified the taxa harboring the genetic potential most frequently detected across multiple pathways, with Kroppenstedtia and Lentibacillus exhibiting the highest gene abundances. These findings provide a theoretical foundation for targeted regulation of organic acid content in sauce-flavor Baijiu production.}, }
@article {pmid42562486, year = {2026}, author = {Sehar, H and Chen, Z and Zhang, J and Wu, K and Li, BS and Yan, H}, title = {Microbial composition, dynamics, and functional roles in jinhua ham fermentation: integrating starter cultures and multi-omics for quality and safety.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119711}, doi = {10.1016/j.foodres.2026.119711}, pmid = {42562486}, issn = {1873-7145}, mesh = {*Fermentation ; *Meat Products/microbiology/analysis ; Multiomics ; *Food Microbiology ; Animals ; Bacteria/metabolism/classification ; *Microbiota ; Food Safety ; Swine ; Fungi/metabolism ; }, abstract = {Jinhua ham, a traditional Chinese dry-cured meat product with nearly a millennium of production history, derives its characteristic colour, layered aroma, and umami-rich taste from the coordinated biochemical activity of a dynamic microbial ecosystem across an eight-to-ten-month fermentation timeline. This review provides a critical synthesis of research between 2018 and 2025 on microbial composition, community dynamics, functional roles, safety risks, starter culture applications, and multi-omics characterisation of Jinhua ham fermentation, unified by precision fermentation as an organising framework. High-throughput sequencing has established that halotolerant bacterial genera, Staphylococcus, Psychrobacter, Halomonas, and Lactobacillus, and fungal communities comprising Aspergillus, Debaryomyces, Meyerozyma, and Penicillium undergo deterministic, physicochemically driven succession, with their enzymatic activities governing proteolysis, lipolysis, volatile compound formation, colour stabilisation, and the accumulation of biogenic amines, mycotoxins, and antimicrobial resistance genes (ARGs). Autochthonous starter cultures, including Staphylococcus xylosus, Lactiplantibacillus plantarum, and Penicillium aethiopicum, improve process controllability, safety, and sensory consistency, yet their mechanistic basis and validation remain incompletely established. Genomic and metabolomic approaches have generated datasets, but integrated metagenomics-metabolomics coupling, capable of linking microbial gene networks to flavour compound production, and metatranscriptomic characterisation of gene expression remain the unmet methodological needs. Five research directions are proposed: achieving species-level microbial resolution through long-read sequencing and longitudinal sampling; validating flavour-forming pathways through isotopic tracing and controlled inoculation; standardising analytical protocols for cross-study comparability; conducting starter culture and ARG safety validation; and developing low-salt fermentation strategies. Together, these directions define the research investment required to advance Jinhua ham production from empirical tradition to precision-engineered consistency.}, }
@article {pmid42562511, year = {2026}, author = {Lee, JW and Kim, YM and Kim, YJ and Jeong, KC and Kim, SA}, title = {Wastewater irrigation reshapes the microbiome and resistome of radish sprouts: Insights from 16S rRNA and shotgun metagenomic sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119739}, doi = {10.1016/j.foodres.2026.119739}, pmid = {42562511}, issn = {1873-7145}, mesh = {*Raphanus/microbiology/growth &amp; development ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Agricultural Irrigation/methods ; Animals ; Metagenomics/methods ; Shotgun Sequencing ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Swine ; }, abstract = {Water scarcity is increasing the reliance on treated wastewater in fresh produce production, yet its effects on the microbial and hygienic quality of fresh produce remain unclear. This study evaluated the influence of wastewater irrigation on the microbiome and antibiotic resistance gene (ARG) profiles of radish sprouts grown under commercially relevant conditions. Using culture-dependent methods and integrated sequencing (16S rRNA and shotgun metagenomics), we tracked microbial and resistome dynamics across the sprout production process under three irrigation regimes: swine wastewater, treated wastewater, and sterile distilled water. Wastewater irrigation markedly increased microbial loads, with aerobic plate counts exceeding 8.0 log CFU/g in final radish sprouts. Both wastewater treatments were dominated by Pseudomonas and Acinetobacter. Resistome profiling showed persistent multidrug, bacitracin, and polymyxin resistance genes in wastewater-irrigated sprouts, while sulfonamide resistance genes occurred exclusively under wastewater irrigation, suggesting wastewater-associated environmental transmission. Higher ARG subtype richness in wastewater treatments suggested that conventional wastewater treatment processes do not completely eliminate diverse ARGs. ARG-host linkage analysis suggested an elevated potential for horizontal gene transfer within edible plant tissues. Overall, wastewater irrigation altered the microbiological quality of radish sprouts and facilitated ARG persistence, underscoring the need for improved post-treatment and preventive water management to safeguard fresh produce safety.}, }
@article {pmid42562513, year = {2026}, author = {Liu, QJ and Mei, JL and Wen, X and Lu, YH and Zeng, Y and Liu, ZY and Xu, HY and Wang, ST and Jiang, F and Yang, CB and Chi, YL and Xu, ZH}, title = {Cellar age reshapes Huangshui micro-ecosystem and metabolism to drive flavor formation in strong-aroma baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119740}, doi = {10.1016/j.foodres.2026.119740}, pmid = {42562513}, issn = {1873-7145}, mesh = {Fermentation ; Metabolomics ; *Odorants/analysis ; *Taste ; Bacteria/metabolism/genetics ; *Wine/analysis/microbiology ; *Alcoholic Beverages/analysis/microbiology ; Metagenomics ; *Microbiota ; Flavoring Agents ; }, abstract = {Huangshui, a slurry-like liquid exuded during strong-aroma Baijiu fermentation, serves as the core medium for material exchange between pit mud and fermented grains. However, how its micro-ecosystem evolves with cellar age and drives flavor formation remains unclear. Using Huangshui as a dynamic window, this study integrated metagenomics, metabolomics, and flavoromics to compare its temporal dynamics in new and old cellars over a complete fermentation cycle, systematically characterizing how cellar age is associated with the restructuring of the microbial community and metabolic functions of Huangshui, and how these changes are consistent with the flavor profiles observed in the final base liquor. The results showed that Huangshui from old cellars harbored a more diverse and stable microbial community, forming a syntrophic consortium of caproic acid-producing bacteria (Caproicibacterium, Caproiciproducens), syntrophic bacteria (Syntrophomonas), and methanogenic archaea (Methanosarcina), whereas new cellars were dominated by lactic acid bacteria (Acetilactobacillus). Metabolically, the old-cellar community exhibited a clear phase-dependent division. During the acid-producing phase, the TCA cycle, arginine biosynthesis, and pyruvate metabolism were preferentially activated to generate core precursors; during esterification, butanoate metabolism and acyl-CoA supply pathways were enhanced. This orderly shift was associated with higher concentrations of ethyl caproate and ethyl octanoate in old-cellar base liquor. Functional gene analysis revealed coordinated upregulation of chain-elongation, methanogenic, and acetate-activating pathways in old cellars. Network analysis revealed a tightly coupled caproic acid-producing co-occurrence module in old cellars, which was not observed in new ones. Together, these findings suggest that Huangshui may serve as a rapid proxy for assessing both the fermentation status and the maturity level of the cellar. This work identifies potential bioaugmentation targets to accelerate flavor development in new cellars and provides a theoretical basis for the precise micro-ecological management of strong-aroma Baijiu quality.}, }
@article {pmid42562527, year = {2026}, author = {Sun, Y and Guo, S and Kwok, LY and Guo, Y and Jiao, Y and He, Q and Zhang, H and Wang, J}, title = {Fermented milk derived from a novel probiotic strain enhances digestive function and attenuates dextran sulfate sodium-induced colitis via the microbiota-metabolite-immune axis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119757}, doi = {10.1016/j.foodres.2026.119757}, pmid = {42562527}, issn = {1873-7145}, mesh = {Animals ; *Colitis/chemically induced/prevention &amp; control/metabolism ; *Probiotics/pharmacology ; Dextran Sulfate ; Male ; Rats ; *Gastrointestinal Microbiome/physiology ; *Cultured Milk Products/microbiology ; Bifidobacterium animalis/metabolism ; *Digestion ; Rats, Sprague-Dawley ; Cytokines/metabolism ; Colon/pathology/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; }, abstract = {Probiotic-fermented dairy products are increasingly recognized for their dual role in nutrient optimization and disease prevention. This study investigated the mechanisms by which Bifidobacterium animalis subsp. lactis Probio-M8 fermented milk enhances digestive efficiency and protects against dextran sulfate sodium-induced colitis in rats. FM8 supplementation promoted weight gain without excessive adipogenesis, elevated leptin levels, and amplified sucrase, lactase, aminopeptidase, and lipase activities, outperforming conventional fermented milk. Metagenomic analysis revealed microbial restructuring with Corynebacterium glutamicum and Bifidobacterium animalis enrichment, and increased short-chain fatty acids.Untargeted metabolomics identified FM8-responsive metabolites, including p-hydroxybenzaldehyde and indole-3-carboxaldehyde, linked to anti-inflammatory pathways. In dextran sulfate sodium-challenged rats, FM8 pre-administration attenuated colitis severity by reducing disease activity index scores, normalizing colon histology, and suppressing interleukin (IL)-6 and IL-17 while elevating IL-10 and IL-22. Mechanistically, FM8 enriched Bifidobacterium animalis and butyrate levels, which inversely correlated with mucosal injury and pro-inflammatory cytokines. These findings demonstrate that FM8 enhances gastrointestinal health through tripartite microbiota-metabolite-immune interactions, highlighting its functional potential for metabolic optimization and colitis prevention.}, }
@article {pmid42562842, year = {2026}, author = {Lechleiter, N and Wedemeyer, J and Junker, J and Wilczek, M and Klich, D and Olech, W and Anusz, K and Homeier-Bachmann, T and Didkowska, A}, title = {Microbiome and resistome of the European bison (Bison bonasus).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42562842}, issn = {2045-2322}, mesh = {Animals ; *Bison/microbiology ; *Microbiota/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {After facing extinction in the early 20th century, populations of the two remnant genetic lines of European bison are now under continuous health monitoring. Faecal samples were taken from five Polish and one German herd of European bison over the course of several years. Through metagenomic sequencing, the bacterial and archaeal microbiome as well as the resistome of these samples could be characterized. Significant differences were mainly found between the bacterial microbiome of samples taken from droppings as opposed to rectal samples. Apart from this, the microbiome and resistome had low differentiation, showing no significant influence of individual factors or location. Oscillospiraceae, Lachnospiraceae and Bacteroidaceae were the dominant bacterial families, the archaeome was mostly made up by Methanobacteriaceae. Genes from resistance classes like Aminoglycosides and Macrolide, Lincosamide and Streptogramine were present. This study characterises the microbiome and resistome of the European bison with the help of metagenomics, providing novel insights into its biology.}, }
@article {pmid42563165, year = {2026}, author = {Richie, TG and Wiechman, H and Vogt, B and Ingold, C and Heeren, L and Kamke, A and Pogranichniy, S and Monk, K and Summers, T and Ran, Q and Sarkar, S and Plattner, BL and Sidebottom, AM and Chang, EB and Lee, STM}, title = {Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42563165}, issn = {2049-2618}, support = {P20 GM103418/NH/NIH HHS/United States ; U54 HD 090216/NH/NIH HHS/United States ; S10OD021743/NH/NIH HHS/United States ; T32 5T32AI007496-30/NH/NIH HHS/United States ; }, mesh = {*Oxidative Stress/drug effects ; Animals ; *Glutathione/metabolism/pharmacology ; Reactive Oxygen Species/metabolism ; Mice ; Colon/microbiology/metabolism ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; Nitric Oxide/metabolism ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; Metagenomics ; Mice, Knockout ; Interleukin-10/genetics ; }, abstract = {BACKGROUND: Certain microbes inhabiting the gut have been implicated in maintaining gut homeostasis and promoting gut damage repair. Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment.<br><br>RESULTS: We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and reactive oxygen species (ROS) levels. Cell-free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells and colon organoids. CFSM-treated organoids showed reduced ROS accumulation, improved epithelial integrity, and partial recovery of barrier function compared to oxidatively stressed controls. We demonstrated through shotgun metagenomics, metabolomics, host RNA sequencing, and molecular techniques that glutathione (GSH) biosynthesized by E. rectale alleviated host ROS damage. We showed downregulation of cell stress and immune response genes, indicating recovery from ROS stress. Chemical depletion of GSH in CFSM confirmed the role of microbial derived GSH in alleviation of ROS in colon cells.<br><br>CONCLUSIONS: In this study, we identify E. rectale as a potential probiotic by lowering colon inflammation and ROS damage through production of reduced glutathione. Microbially derived GSH has not been well established in the Lachnospiraceae family which are a large member of the overall gut microbiota. Understanding more about the impacts of microbial functions including GSH on lowering inflammation is needed to develop potential probiotics or therapies for chronic inflammatory conditions. Video Abstract.}, }
@article {pmid42564172, year = {2026}, author = {Rojas, L and Zuluaga, J and Cardona, AF}, title = {Microbiome as a prediction of immunotherapy response in lung cancer.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1849553}, pmid = {42564172}, issn = {1664-3224}, mesh = {Humans ; *Lung Neoplasms/immunology/drug therapy/microbiology/therapy ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology/drug effects ; Treatment Outcome ; Animals ; *Microbiota/immunology ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer (LC), offering durable responses in non-small cell lung cancer (NSCLC) and, to a lesser extent, small cell lung cancer (SCLC). Nevertheless, clinical outcomes remain highly heterogeneous, with many patients experiencing primary or acquired resistance and/or immune-related adverse events (irAEs) that impair their quality of life and treatment adherence. The human microbiome, particularly in the gut and oral compartments, has emerged as a critical modulator of systemic antitumor immunity and a promising noninvasive predictive biomarker for ICI efficacy and toxicity. This narrative review synthesizes the current evidence on microbiome composition, diversity, and function in patients with LC receiving ICIs as monotherapy, dual blockade, or in combination regimens, as well as clinically relevant biomarkers associated with treatment response and toxicity. Higher gut microbial alpha diversity and enrichment of beneficial taxa (e.g., Akkermansia muciniphila, Faecalibacterium prausnitzii, and certain Firmicutes) are consistently linked to improved progression-free survival (PFS) and overall survival (OS), mediated by microbial metabolites such as short-chain fatty acids and inosine, which enhance T-cell priming, tumor microenvironment remodeling, and gut-lung axis communication. Microbiome-disruptive exposures, particularly antibiotics and proton pump inhibitors (PPIs), induce dysbiosis and are strongly associated with poorer survival outcomes. Mechanistic insights from preclinical models and clinical cohorts, alongside clinical confounders, underscore the complementary role of the microbiome relative to established markers such as programmed death-ligand 1 (PD-L1) and tumor mutational burden. Prospective standardization of metagenomic profiling and microbiome-modulating interventions represents a key next step in translating these findings into personalized immunotherapy strategies for LC.}, }
@article {pmid42566318, year = {2026}, author = {Beaton, ADM and Croxford, JT and Díaz de Aguinaga, AC and Horsburgh, E and Mark, DR and McQueary, LS and Murray-Clelland, KR and Tucker, SK and Roe, AJ and McHugh, RE}, title = {Interactions at the Streptomyces - animal interface: ecology, defence and disease.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {8}, pages = {}, pmid = {42566318}, issn = {1465-2080}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Streptomyces/physiology/genetics/metabolism ; Animals ; Humans ; Soil Microbiology ; Microbiota ; Insecta/microbiology ; Nematoda/microbiology ; }, abstract = {Streptomyces are filamentous, spore-forming members of the Actinomycetota, renowned for their capacity to produce chemically diverse, specialized metabolites with medically important properties. Traditionally, Streptomyces have been viewed as soil-dwelling microbes, and their roles in soil ecology, plant health and plant disease have been extensively studied. However, advances in metagenomic sequencing and molecular approaches have greatly expanded our ability to investigate interkingdom interactions between Streptomyces and more complex organisms, including animals. In recent years, a growing body of work has revealed diverse and often intimate associations between Streptomyces and members of the Animalia. These include interactions with microfauna such as nematodes (Nematoda), insects (Insecta), including bees and ants, mammals such as bats (Chiroptera) and humans (Homo sapiens). This review consolidates our current knowledge of Streptomyces - animal interactions, with a particular focus on chemical ecology and the roles of specialized metabolites in shaping these relationships. This work highlights the emerging body of work investigating the role of Streptomyces ecology beyond soil ecosystems and draws attention to the importance of exploring non-traditional niches, including animal-associated microbiomes, to deepen our understanding of microbial-animal interactions and to expand opportunities for natural product discovery.}, }
@article {pmid42567235, year = {2026}, author = {Ma, HC and Wang, DJ and Yuan, ZJ and Shi, B and Chen, ZH and Zhuo, M and Zeng, JY and Aqib, AI}, title = {Systematic approach for revealing biomarkers of diarrheal microbiome of yaks through metagenomics sequencings.}, journal = {Microbial pathogenesis}, volume = {219}, number = {}, pages = {108700}, doi = {10.1016/j.micpath.2026.108700}, pmid = {42567235}, issn = {1096-1208}, mesh = {Animals ; Cattle ; *Diarrhea/microbiology/veterinary ; Feces/microbiology ; *Metagenomics/methods ; *Biomarkers/analysis ; *Bacteria/classification/genetics/isolation &amp; purification ; *Cattle Diseases/microbiology ; Phylogeny ; *Microbiota/genetics ; Sequence Analysis, DNA ; Genotype ; DNA, Bacterial/genetics ; }, abstract = {Yaks are important food ruminants on the Plateau, but the presence of a diarrhea disease is seriously threatening the yak sector. To detect bacterial biomarkers of diarrhea in this animal, metagenomics sequencing of fecal samples from diarrhea (group D) and normal (group H) yaks was performed. The results showed 61,963,936,432 and 63,972,070 354 clean samples in the diarrheal and normal yaks, respectively. Genotyping in group D (20,000) was statistically lower than that in group H (80,000) (p < 0.05). Firmicutes and bacteroides levels in diarrheal yaks (1.03) were lower than in normal animals. There were 23 phyla and 696 species significantly different between the two yak groups including species of pathogenic Bacteroides fragilis, Alloprevotella tannerae, Parabacteroides merdae, Anaerococcus marasmi, and beneficial Methanobrevibacter millerae, Elusimicrobium minutum, Adlercreutzia equolifaciens. Our results may contribute to the prevention and treatment of diarrheal in yaks in the cold plains areas.}, }
@article {pmid42568080, year = {2026}, author = {Ma, S and Zhang, C and Yao, Y and Zhou, M and Chen, A and Chen, Y and Chen, Y and Wang, J and Abudushalamu, G and Cai, S and Zhao, F and Chen, D and Li, X and Zheng, Y and Fan, J and Gao, X and Liu, Y and Fan, W and Zhu, F and Yang, J and Miao, M and Fan, X and Wu, G}, title = {A three-metabolite microbiota-associated signature for early risk stratification of gestational diabetes mellitus.}, journal = {Cardiovascular diabetology}, volume = {25}, number = {1}, pages = {}, pmid = {42568080}, issn = {1475-2840}, support = {82302609//National Natural Science Foundation of China/ ; 82373781//National Natural Science Foundation of China/ ; BK20230840//Natural Science Foundation of Jiangsu Province/ ; JSKLCCM202202015//Jiangsu Provincial Key Laboratory of Critical Care Medicine/ ; }, mesh = {Humans ; Female ; *Diabetes, Gestational/diagnosis/microbiology/blood ; Pregnancy ; *Metabolomics ; Risk Assessment ; Prospective Studies ; Risk Factors ; Biomarkers/blood ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Metagenomics ; Predictive Value of Tests ; Gestational Age ; *Propionates/blood ; Prognosis ; *Bacteria/metabolism/classification ; Multiomics ; }, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes and long-term metabolic and cardiovascular risk. However, oral glucose tolerance testing at 24-28 gestational weeks limits early risk stratification. Gut microbiota-associated metabolites may reflect early metabolic abnormalities, including those relevant to cardiometabolic health, but robust early-pregnancy biomarkers remain limited.<br><br>METHODS: We conducted a multicenter nested case-control and prospective study involving 2,693 pregnant women. Untargeted metabolomics and metagenomics were integrated to identify GDM-associated metabolites and gut microbial alterations. Three consistently dysregulated metabolites, 3-hydroxydecanoic acid, &#x3b3;-Glu-Leu, and propionic acid, were quantified by targeted LC-MS/MS. Candidate algorithms were compared using repeated 10-fold cross-validation, and a final generalized linear model was externally and prospectively validated.<br><br>RESULTS: Women who later developed GDM showed an adverse early-pregnancy metabolic profile, including higher BMI, triglycerides, and platelet count. Untargeted metabolomics identified 14 persistently altered metabolites enriched in energy, oxidative stress, and amino acid metabolism pathways. Metagenomics revealed taxonomic restructuring and coordinated microbiota-metabolite associations. The three-metabolite model achieved AUCs of 0.838 (95% CI, 0.791-0.885) in training, 0.840 (95% CI, 0.769-0.911) in internal validation, 0.955 (95% CI, 0.925-0.985) and 0.917 (95% CI, 0.875-0.958) in two external cohorts, and 0.969 (95% CI, 0.937-1.000) in the prospective cohort.<br><br>CONCLUSION: Early microbiota-associated metabolic dysregulation is detectable before routine GDM diagnosis. This compact three-metabolite panel may support early GDM risk stratification and provides metabolic evidence relevant to broader cardiometabolic risk assessment in pregnancy.}, }
@article {pmid42571835, year = {2026}, author = {Wang, G and Li, J and Wang, D and Chen, SS and Zheng, G and Zhou, S and Wang, T and Zhou, Y}, title = {Microbial community structure, function and environmental drivers of the urban soil plastisphere in a typical megacity, China.}, journal = {Environmental research}, volume = {306}, number = {Pt 4}, pages = {125432}, doi = {10.1016/j.envres.2026.125432}, pmid = {42571835}, issn = {1096-0953}, mesh = {China ; *Soil Microbiology ; Fungi/genetics ; *Soil Pollutants/analysis ; Cities ; *Environmental Monitoring ; Bacteria/genetics/classification ; *Microbiota ; Soil/chemistry ; *Microplastics/analysis ; }, abstract = {The plastisphere in urban soils remains poorly understood despite its potential ecological significance. Here, 42 samples, including 21 soil samples and 21 plastisphere samples, were collected from seven functional zones in Nanjing, and metagenomic sequencing, bioinformatics, and quantitative modeling with multisource geographic and soil data were employed to investigate the community structure, function and environmental drivers of the soil plastisphere in this typical megacity, China. Fungi, particularly Ascomycota and the genus Fusarium (LDA score = 4.73), exhibited stronger selective enrichment in the plastisphere than bacteria did, with this pattern being consistent across all functional zones, suggesting that the intrinsic properties of microplastics (MPs) govern taxonomic assembly. Plastisphere co-occurrence networks were simpler, more modular, and less robust than soil networks were, indicating that the structurally vulnerable microbial community was shaped predominantly by stochastic assembly (R[2] > 0.2). Functional analysis further revealed significant alterations in the characteristics of denitrification genes (napA, norB, and narH/narY/nxrB), suggesting modified nitrogen cycling potential. Critically, pollutants, especially MPs themselves, partially overrode geospatial and edaphic factors as direct drivers of plastisphere communities, representing fundamental decoupling from the natural environmental matrix governing bulk soil. Pollutants strongly negatively affected fungal compositions and networks in the plastisphere, amplifying the ecological hazards of coexisting contaminants. These findings revealed that MP pollution modified microbial community assembly in urban soils, creating a decoupled, pollutant-driven microbial system. Integrating these effects into urban environmental risk assessments is therefore urgently needed.}, }
@article {pmid42572222, year = {2026}, author = {Kirilina, IV and Roumiantsev, SA and Gaponov, AM and Savchyk, DV and Khusnutdinova, DR and Grigoryeva, TV and Teplyakova, ED and Shestopalov, AV}, title = {[The contribution of the intestinal microbiome to the formation of the general profile of bacterial DNA in the blood of obese children].}, journal = {Voprosy pitaniia}, volume = {95}, number = {3}, pages = {107-116}, doi = {10.33029/0042-8833-2026-95-3-107-116}, pmid = {42572222}, issn = {0042-8833}, support = {//The research was carried out under the contract no. 0373100122119000041 within the project "Creation of a bank of biosamples of blood serum and feces from healthy donors and patients with obesity, metabolic syndrome, type 2 diabetes mellitus, and impaired mucosal barrier of the gastrointestinal tract, in order to identify candidate species nonspecific mediators of the quorum sensing microbiota systems of human, which modulate the endocrine and metabolic function of adipose tissue"/ ; }, mesh = {Humans ; Child ; *DNA, Bacterial/blood ; Cross-Sectional Studies ; Feces/microbiology ; Adolescent ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/blood ; Lipid Metabolism ; Carbohydrate Metabolism ; Obesity/microbiology/blood ; *Gastrointestinal Microbiome ; }, abstract = {UNLABELLED: Obesity is a multifactorial disease. The gut microbiome disturbances play a significant role in the development of obesity, but emerging data point to a blood microbiome and its association with obesity and other pathologies. Bacterial DNA in the blood represents a pathogen-associated molecular pattern capable of activating the immune system and thereby triggering a cascade of inflammatory responses. The question remains open as to where the bacterial DNA originates, which biotopes shape it, and what role the gut microbiome plays in forming the pool of bacterial DNA in blood. The aim of the study was to compare the bacterial DNA profiles of feces and blood in obese children, to establish relationships between bacterial DNA in blood and feces, and with carbohydrate and lipid metabolism parameters.<br><br>MATERIAL AND METHODS: This single-center, cross-sectional study included children and adolescents aged 10 to 18 years with varying degrees of alimentary-constitutional obesity (n=79) and without obesity (n=84). The taxonomic profile of bacterial DNA in blood and feces was analyzed using metagenomic sequencing. Bacterial DNA was isolated from blood and stool samples, and the v3-v4 variable region of the 16S rRNA gene was sequenced. To identify the relationship between bacterial DNA in blood and feces and lipid and carbohydrate metabolism parameters [glucose, total cholesterol, high-density lipoprotein and low-density lipoprotein (LDL)], Spearman's correlation coefficients were calculated.<br><br>RESULTS: When comparing bacterial DNA from blood and feces, obese children more often isolated DNA from the families Lactobacillaceae (p=0.043), Porphyromonadaceae (p=0.022), Ruminococcaceae (p=0.065) and less often from Prevotellaceae (p=0.028) and Coriobacteriaceae (p=0.085) compared to children and adolescents without obesity. In obese children, the contribution of intestinal taxa (Lachnospiraceae, Ruminococcaceae, Bacteroidaceae) to the formation of the bacterial DNA profile of the blood was significantly reduced, but the contribution of extraintestinal biotopes (skin, soil and water) was more diverse. Positive associations were found between bacterial DNA of fecal Ruminococcaceae taxa and the level of total cholesterol (&#x3c1;=0.347, p=0.002) and LDL (&#x3c1;=0.313, p=0.005) and of fecal Coriobacteriaceae and these lipid metabolism parameters (&#x3c1;=0.304, p=0.007 and &#x3c1;=0.317, p=0.005) in obese children. No positive associations were found between fecal and blood taxa and glucose level.<br><br>CONCLUSION: In obese and non-obese children and adolescents, the general profile of bacterial blood DNA is formed by both intestinal and extra-intestinal biotopes. However, in obese children, taxa from extra-intestinal biotopes predominate in the formation of the blood microbiome, which is confirmed by analyzing the proximity of the taxonomic composition of bacterial DNA in blood and feces based on beta diversity indices. The relationship of taxa with blood cholesterol and LDL levels can be considered as a target for microbiota modification and thus reducing the risks of metabolic complications in obesity.}, }
@article {pmid42573887, year = {2026}, author = {Yang, L and Zhao, J and Han, T and Qi, H and Zhao, F and Sun, Z}, title = {Modulating the gut-joint axis: Bifidobacterium longum subsp. infantis B8762 is associated with selective gut microbial and metabolic alterations in knee osteoarthritis.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42573887}, issn = {1573-0972}, support = {U25A20733//National Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; YLXKZX-NND-006//Inner Mongolia Agricultural University First-Class Discipline Scientific Research Special Program/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; }, mesh = {Humans ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Osteoarthritis, Knee/microbiology/metabolism/therapy ; *Probiotics/administration &amp; dosage ; Metabolome ; *Bifidobacterium/physiology ; Metabolomics ; Male ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenomics ; Female ; Knee Joint/microbiology/metabolism ; *Bifidobacterium longum ; }, abstract = {Knee osteoarthritis (KOA) is a debilitating degenerative joint disorder characterized by chronic low-grade inflammation and metabolic dysregulation. The gut microbiota has emerged as an important regulator of systemic inflammatory responses. Building upon our previous clinical findings that Bifidobacterium longum subsp. infantis B8762 (B8762) improved clinical symptoms and inflammatory markers in patients with KOA, the present study investigated the associated alterations in the gut microbiome and fecal metabolome. Fecal samples were collected from probiotic (n = 20) and placebo (n = 20) groups at baseline (0 M) and after a 1-month intervention (1 M). Integrated metagenomic and untargeted metabolomic analyses were performed to characterize changes in gut microbial composition, functional potential, and metabolic profiles. Metagenomic reads mapped to the B8762 reference genome showed a greater increase in B8762-associated mapping rates in the probiotic group than in the placebo group, supporting an association between B8762 supplementation and longitudinal changes in the gut microbiome. Longitudinal analysis further demonstrated greater increases in microbial alpha diversity in the probiotic group. Species-level analyses suggested selective alterations in gut microbial composition, with nominally higher relative abundances of Bifidobacterium pseudocatenulatum and Anaerostipes caccae and lower relative abundances of Holdemania filiformis and Lachnospira SGB5077 (nominal P < 0.05). HUMAnN3-based functional profiling identified enrichment of microbial pathways related to carbon utilization and amino acid biosynthesis, including the bifidobacterial shunt and branched-chain amino acid biosynthesis pathways. Untargeted metabolomics identified nominal between-group differences in metabolites primarily related to lipid metabolism, including lower relative abundances of aldosterone and 7α-hydroxy-4-cholesten-3-one in the probiotic group (nominal P < 0.05). Correlation analysis further revealed associations between differential taxa and selected metabolites, suggesting potential links between gut microbial alterations and steroid-related metabolic pathways. Overall, B8762 supplementation was associated with longitudinal changes in B8762-associated genomic signals, gut microbial diversity and composition, microbial functional potential, and fecal metabolic profiles. These findings provide exploratory multi-omics evidence supporting an association between B8762 supplementation and gut microbial-metabolic remodeling in KOA and generate hypotheses for future mechanistic studies of the gut-joint axis.}, }
@article {pmid42576510, year = {2026}, author = {Nio, SA and Mantilen Ludong, DP}, title = {Water Deficit During the Vegetative Stage Alters the Structure of Root-Associated Microbial Communities in Local North Sulawesi Rice.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {29}, number = {5}, pages = {243-250}, doi = {10.3923/pjbs.2026.243.250}, pmid = {42576510}, issn = {1812-5735}, mesh = {*Oryza/microbiology/growth &amp; development/metabolism ; *Plant Roots/microbiology ; Droughts ; Water/metabolism ; *Microbiota/physiology ; Indonesia ; Rhizosphere ; }, abstract = {Background and Objective: Changes in rhizosphere microbial populations have been reported in response to drought, temperature fluctuations, CO2 levels and other environmental factors. However, the structure of the root-associated microbes in local North Sulawesi rice using a metagenomic approach has not yet been investigated. This study examined the microbial community structure in local North Sulawesi rice (cv. Superwin) under drought (water deficit) conditions compared to well-watered conditions at the vegetative phase. Materials and Methods: Rice plants were grown in polybags filled with a 5:1:1 mixture of garden soil, compost and rice husks and were allowed to grow until the four-fully-expanded leaf stage. They were then subjected to two treatments for 14 days: well-watered conditions (irrigated to 100% field capacity) and water deficit conditions (0% field capacity). Root samples were collected for next-generation sequencing analysis to assess molecular response of Superwin rice to water deficit. Results: During drought, several root-associated microbes were more prevalent, including Nitrospirota at the phylum level, Rubrobacteria at the class level, Micrococcales at the order level, Gaiellaceae at the family level, Gaiella at the genus level and Gaiella occulta at the species level. Conclusion: Root-associated microbes, including taxa Nitrospirota, Rubrobacteria, Micrococcales, Gaiellaceae, Gaiella and Gaiella occulta, have a higher relative abundance in rice plants under water deficit. Gaiella occulta serves as sensitive indicator of water deficit in North Sulawesi local rice, i.e. Superwin.}, }
@article {pmid42577578, year = {2026}, author = {Song, Y and Zhang, X and Wang, H and Wang, Y and Zhang, S and Li, Y and Cui, X and Li, X and Li, Y and Wang, J and Su, J and Zheng, Y and Gai, W and Liu, W}, title = {Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799148}, pmid = {42577578}, issn = {2235-2988}, mesh = {Humans ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Microbiota ; *Endosonography/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; *Neoplasms/complications/drug therapy ; Bacteria/classification/genetics/isolation &amp; purification ; Bronchoscopy ; Aged, 80 and over ; Adult ; Sepsis ; }, abstract = {INTRODUCTION: Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.<br><br>METHODS: This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score &#x2265;2, n=32) and non-sepsis (SOFA score <2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.<br><br>RESULTS: mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%, P <&#xa0;0.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.<br><br>DISCUSSION: EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.}, }
@article {pmid42583788, year = {2026}, author = {Han, L and Wu, X and Gong, B and Li, X and Li, X and Wang, Z}, title = {A Two-Sample Mendelian Randomisation Analysis of the Oral Microbiome and Oral/Oropharyngeal/Tongue Cancers.}, journal = {Oral health &amp; preventive dentistry}, volume = {24}, number = {}, pages = {613-621}, pmid = {42583788}, issn = {1757-9996}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Tongue Neoplasms/microbiology ; *Oropharyngeal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Mouth Neoplasms/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Tongue/microbiology ; }, abstract = {OBJECTIVE: To assess the potential causal relationships of the oral microbiome with the risks of oral cancer, oropharyngeal cancer, and tongue cancer using two-sample Mendelian randomisation (MR) analysis, while distinguishing these from reverse causal effects of the cancers on microbial abundance.<br><br>METHODS AND MATERIALS: Using single-nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance-weighted approach to evaluate the effects of the dorsal-tongue and salivary microbiomes on oral, oropharyngeal, and tongue cancers. Analyses were conducted with the R package TwoSampleMR, leveraging genome-wide association study (GWAS) summary statistics from CNGBdb, the FinnGen consortium, and other sources. Sensitivity, heterogeneity, and pleiotropy assessments were performed. Additionally, reverse MR sensitivity analyses were conducted to explore the possible causal influence of cancers on the oral microbiota.<br><br>RESULTS: Using a single nucleotide polymorphism (SNP) significance threshold of p 5 &#xd7; 10-6, our large-scale MR study revealed genetically supported causal relationships between microbial taxa derived from saliva and the tongue and the risk of oral, oropharyngeal, and tongue cancers. Integrating these results, we found that both 's Veillonella_rogosae_mgs_2008' and 's unclassified_mgs_1048' conferred a reduced risk of oropharyngeal and tongue cancers. Sensitivity analyses based on heterogeneity tests and pleiotropy evaluations further corroborated the robustness of our findings, lending additional credibility to the conclusions.<br><br>CONCLUSION: This study leveraged large-scale publicly available genetic data and identified significant causal relationships between the oral microbiota and cancers of the oral cavity, oropharynx, and tongue. Reverse MR analyses indicated that oral and tongue cancers may in turn alter the abundance of specific oral microbes, suggesting a potential bidirectional causal loop. Future work should integrate metagenomic data to further validate these microbiota-cancer associations.}, }
@article {pmid42584931, year = {2026}, author = {Kaszecki, E and Azimychetabi, Z and Emery, RJN and Saville, BJ}, title = {Integrated transcriptomic and hormonomic insights into cadmium tolerance of a Euglena mutabilis fungal-algal-bacterial consortium.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {8}, pages = {}, pmid = {42584931}, issn = {1465-2080}, mesh = {*Cadmium/metabolism/toxicity ; *Transcriptome ; *Euglena/genetics/metabolism/drug effects ; *Microbial Consortia/genetics ; *Fungi/genetics/metabolism ; Gene Expression Profiling ; *Bacteria/genetics/metabolism/classification ; Chloroplasts/metabolism ; }, abstract = {Acidic, metal-contaminated environments harbour specialized microbial consortia adapted to extreme stress. We examined an environmental Euglena mutabilis culture naturally associated with Talaromyces and Acidiphilium acidophilum and exposed it to cadmium (Cd). Integrated transcriptomic, hormonal, structural and taxonomic analyses revealed a coordinated Cd-tolerance strategy. RNA sequencing showed differential regulation of metal transporters consistent with a shift from Cd uptake to intracellular sequestration. Transmission electron microscopy confirmed Cd compartmentalization within chloroplasts and increased paramylon granules. Cd exposure suppressed light-harvesting complex genes and formate/nitrite transporters while maintaining core photosynthetic function. Hormone profiling indicated strong repression of bioactive auxin and cytokinin (CK) free bases, alongside accumulation of CK nucleotides and downregulation of CK biosynthetic and activation genes. Metagenomics revealed Cd-driven enrichment of Talaromyces and Acidiphilium, implicating them in detoxification and stress support. Together, these responses highlight early Cd uptake followed by chloroplast-based detoxification, metabolic buffering via paramylon, hormonal downregulation of growth and community-mediated resilience.}, }
@article {pmid42585955, year = {2026}, author = {Han, X and Gao, Y and Chen, J and Yang, P and Liang, X and Wang, L and Ge, Y and Gui, H and He, Y and Zhan, F and Zhang, X and Kuzyakov, Y}, title = {Microplastics disrupt bacterial defense within the plant-AMF-bacteria continuum to amplify Cd bioavailability.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143257}, doi = {10.1016/j.jhazmat.2026.143257}, pmid = {42585955}, issn = {1873-3336}, mesh = {*Cadmium/metabolism/toxicity ; *Soil Pollutants/toxicity/metabolism ; *Mycorrhizae/drug effects/metabolism ; *Zea mays/microbiology/metabolism/drug effects ; Rhizosphere ; *Microplastics/toxicity ; Biological Availability ; Soil Microbiology ; Microbiota/drug effects ; *Bacteria/drug effects/metabolism ; }, abstract = {The plant-arbuscular mycorrhizal fungi (AMF)-bacteria continuum provides a critical barrier against heavy-metal toxicity, but how microplastics (MPs) disrupt rhizosphere functions and exacerbate phytotoxicity remains unresolved. Using a maize-AMF-bacteria system in cadmium (Cd)-contaminated soil, we investigated two MP fractions differing in size and morphology added at increasing Cd contents. Although AMF colonization remained resilient, MPs induced fraction-dependent bacterial functional decoupling. Small MPs shifted the microbiome from extracellular Cd-immobilizing taxa (Sphingomonadaceae and Rhizobiaceae) toward intracellular stress-tolerant lineages. Large MPs restricted bacterial contacts, suppressing density-dependent cooperation. Metagenomic profiling and analysis of metagenome-assembled genomes (MAGs) revealed reduced potential for quorum sensing, ABC transporters, and alpha-linolenic acid metabolism under large MP exposure, compromising biofilm formation and extracellular Cd sequestration. Partial least squares path modeling indicated that bulk-soil chemistry did not define Cd uptake by plants. Instead, depletion of available Cd in soil reflected a biological sink associated with enhanced plant uptake. Enhanced Cd accumulation was associated with loss of rhizosphere defense mechanisms: potential root-barrier disruption by large MPs and weakened microbial buffering. Consequently, large MPs increased the Cd bioconcentration factor by 57.5%, compared with 32.1% for small MPs. These findings show that MPs amplify legacy Cd risks without increasing bulk-soil Cd availability, through disruption of root-interface integrity and microbial protection.}, }
@article {pmid42587419, year = {2026}, author = {Chang, H and Yang, Y and Zhang, P and Lei, Z and Zhang, Y and Li, S and Wang, L and Wang, Y and Jiang, J and Li, L and Shi, H and Shi, A}, title = {Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {46}, number = {9}, pages = {e70836}, pmid = {42587419}, issn = {1478-3231}, support = {2025JC-YBQN-1179//Natural Science Basic Research Program of Shaanxi Province/ ; 2025SCIPT-63//Scientific Research Supporting Fund of the Second Affiliated Hospital of Xi'an Jiaotong University/ ; }, mesh = {Humans ; *Liver Cirrhosis/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/genetics ; Case-Control Studies ; Metagenome ; Metagenomics ; Male ; }, abstract = {BACKGROUND: The gut microbiota contributes to liver cirrhosis (LC), yet the gut virome and its cross-kingdom ecology with bacteria are less well defined.<br><br>METHODS: To characterize LC-associated virome alterations and assess their clinical relevance, we reanalyzed publicly available faecal metagenomes from patients with LC and healthy controls. After quality control and removal of human reads, sequences were mapped to the Chinese Gut Viral Catalogue at 95% nucleotide similarity, viral operational taxonomic units (vOTUs) were annotated using the latest ICTV framework, and viral functions were inferred by KEGG annotation. Differential vOTUs and bacterial species, virus-bacteria networks and random forest classifiers were constructed with internal and external validation.<br><br>RESULTS: LC showed reduced viral richness and Shannon diversity, and a distinct Bray-Curtis separation from controls. Ten viral families and 473 vOTUs differed between groups (59 LC-enriched). KEGG-based profiling highlighted functional shifts in LC-enriched viruses, including increased K01185 (lysozyme) and K02172 (blaR1). Virus-bacteria networks were markedly sparser in LC than in controls (130 vs. 509 significant correlations). A virome-based random forest model distinguished patients from controls with high accuracy in internal (optimal AUC&#x2009;=&#x2009;0.911) and external (optimal AUC&#x2009;=&#x2009;0.773) validation cohorts, and the model combining viral and bacterial features achieved similarly robust performance.<br><br>CONCLUSIONS: LC is associated with disrupted gut viral-bacterial ecology, and virome features show promise as non-invasive biomarkers, warranting longitudinal and mechanistic follow-up.}, }
@article {pmid42588064, year = {2026}, author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA}, title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.}, journal = {Nutrients}, volume = {18}, number = {15}, pages = {}, pmid = {42588064}, issn = {2072-6643}, support = {E022 Program Recursos Fiscales para la Investigaci&#xf3;n//Instituto Nacional de Pediatria/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration &amp; dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration &amp; dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; }, abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.}, }
@article {pmid42589241, year = {2026}, author = {Wang, Q and Wang, BY and Wilus, D and Xie, H}, title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, pmid = {42589241}, issn = {1422-0067}, support = {R16GM149359/GM/NIGMS NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; R16 GM149359/GM/NIGMS NIH HHS/United States ; U01 DE033241/DE/NIDCR NIH HHS/United States ; UG3 HG013248/HG/NHGRI NIH HHS/United States ; U54MD007586/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; Female ; Male ; Adult ; Middle Aged ; *Periodontitis/microbiology/therapy ; Metagenome ; Dental Scaling ; Root Planing ; Metagenomics/methods ; }, abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced probing depth, clinical attachment level, bleeding on probing, and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of the microbial community. Established periodontal pathogens, including Porphyromonas gingivalis, as well as the emerging pathogens Escherichia coli and Burkholderia multivorans, decreased following treatment. Tannerella forsythia also showed a marked reduction after treatment, although this decrease was not significant after false discovery rate (FDR) correction. In contrast, health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus, increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified significant treatment-associated differences in carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.}, }
@article {pmid42589351, year = {2026}, author = {Shen, H and Huang, S and Wang, Z and Zhou, S and Huang, L and Zhang, H and Han, Y and Jiang, J and Guo, H}, title = {Glycyrrhizic Acid Alleviates Atherosclerosis in ApoE[-/-] Mice via Microbial Indole-3-Lactic Acid-Mediated AhR-p65 Interaction in the Endothelium.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, pmid = {42589351}, issn = {1422-0067}, support = {No. 3332025150//Fundamental Research Funds for the Central Universities/ ; No. 2025-I2M-KJ-016//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Animals ; *Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology ; Mice ; *Glycyrrhizic Acid/pharmacology/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism ; Male ; *Transcription Factor RelA/metabolism ; *Apolipoproteins E/deficiency/genetics ; Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Humans ; Fecal Microbiota Transplantation ; Endothelium, Vascular/metabolism/drug effects ; Mice, Knockout ; }, abstract = {Glycyrrhizic acid (GL), a natural triterpenoid glycoside extracted from the "medicine food homology" herb Glycyrrhiza glabra L., exhibits potent anti-atherosclerotic effects; yet its underlying mechanisms remain unclear due to its poor oral bioavailability. The gut microbiota plays a pivotal role in the development of atherosclerosis (AS). In this study, the microbiota-dependent anti-AS effects of GL were evaluated in high-fat diet (HFD)-fed ApoE[-/-] mice using antibiotic depletion and fecal microbiota transplantation (FMT). Integrated metagenomic and metabolomic analyses were performed to identify the key bioactive microbial metabolite. Further in vivo and in vitro experiments, including co-immunoprecipitation and dual-luciferase reporter assays, were utilized to elucidate the underlying molecular mechanisms. It was demonstrated that oral administration of GL alleviated AS in a microbiota-dependent manner by reversing gut dysbiosis, improving intestinal barrier function, and reducing pro-inflammatory lipopolysaccharide (LPS) levels. GL shifted intestinal tryptophan metabolism toward bacterial-derived indole-3-lactic acid (ILA) production, suppressing LPS-induced vascular endothelial adhesion dysfunction by activating the aryl hydrocarbon receptor (AhR). Mechanistically, ILA-activated AhR interacted with the NF-κB subunit p65 in the cytoplasm, effectively preventing the nuclear translocation of p65 and suppressing the promoter activities of adhesion molecules (VCAM1 and ICAM1), resulting in the amelioration of HFD-induced AS. These findings elucidate the microbiota-dependent mechanism of orally administered GL against AS, and highlight the therapeutic potential of targeting the ILA-AhR-p65 axis in the vascular endothelium as a strategy for AS.}, }
@article {pmid42589527, year = {2026}, author = {Coppini, M and Mauceri, R and Vacca, D and Bertolazzi, G and Caponio, VCA and Rodolico, V and Belmonte, B and Campisi, G}, title = {Longitudinal Exploratory Analysis of Salivary Microbiota Profiles in Patients with Oral Squamous Cell Carcinoma Before and After Surgery: A Pilot Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, pmid = {42589527}, issn = {1422-0067}, mesh = {Humans ; *Saliva/microbiology ; Pilot Projects ; *Mouth Neoplasms/microbiology/surgery ; Female ; Male ; *Microbiota ; *Carcinoma, Squamous Cell/surgery/microbiology ; Middle Aged ; Aged ; Longitudinal Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; Adult ; Metagenome ; }, abstract = {Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally assess salivary microbiota profiles in patients with oral squamous cell carcinoma (OSCC) before and after tumor resection using Oxford Nanopore Technology. Unstimulated saliva samples were collected from 16 patients with OSCC at two time points (before and after tumor resection) and from 10 OSCC-free reference subjects. Microbial DNA was extracted using the QIAamp DNA Blood Kit (QIAGEN GmbH, Hilden, Germany) and subjected to long read metagenomic sequencing using the Oxford Nanopore MinION platform (v. 20.06.4, Oxford Nanopore Technologies, Oxford, UK). Taxonomic profiling was performed to longitudinally characterize salivary microbiota composition within patients and to provide descriptive comparisons with the OSCC-free reference cohort. Longitudinal analysis identified differences in salivary microbiota profiles between pre- and post-resection samples. Before surgery, an increased relative abundance of Neisseria subflava and Leptotrichia buccalis was observed. Post-surgical samples showed higher levels of Glaesserella parasuis, Streptomyces anulatus, and Lactobacillus species. Distinct microbial patterns were also descriptively observed between OSCC patients and OSCC-free controls, suggesting disease-associated dysbiosis. This exploratory longitudinal pilot study suggests differences in salivary microbiota profiles between samples collected before and after tumor resection in patients with OSCC, including changes in taxonomic composition and reduced alpha diversity. Given the limited sample size and the potential influence of unmeasured perioperative factors, these findings should be considered hypothesis-generating. Larger, well-controlled longitudinal studies incorporating standardized oral health assessment and detailed perioperative metadata are required to clarify the biological and clinical relevance of these observations.}, }
@article {pmid42589672, year = {2026}, author = {Zeng, C and Chen, J and Yong, X and Xie, Y}, title = {Convergent Gut Microbiome Remodeling Across Ischemic Stroke, Myocardial Infarction, and Longevity Reveals a Shared Ecological Signature of Aging and Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, pmid = {42589672}, issn = {1422-0067}, support = {cstc2021jcyj-msxmx0848//Natural Science Foundation of Chongqing/ ; BSKJ2022006//Bishan District Science and Technology Bureau/ ; 81773954//National Natural Science Foundation of China (NSFC)/ ; 202310617015//National College Student Innovation and Entrepreneurship Program/ ; X2024160170123, X2026106170029//Chongqing College Students' Innovation and Entrepreneurship Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Aging ; *Myocardial Infarction/microbiology ; *Longevity ; *Ischemic Stroke/microbiology ; Male ; Female ; Aged ; Dysbiosis/microbiology ; }, abstract = {Gut microbiota dysbiosis has been associated with ischemic stroke (IS), myocardial infarction (MI), and aging, but whether these contexts share reproducible microbial features remains unclear. We conducted an exploratory and hypothesis-generating descriptive study of genus-level microbiota patterns across an internal IS cohort and publicly available external IS, MI, and age-stratified or longevity-associated datasets. Analyses were performed within predefined age strata and interpreted cautiously because of the small internal cohort, cross-cohort heterogeneity, and the absence of direct metabolite, intestinal barrier, inflammatory, or microbial activity measurements. No taxon in the internal cohort remained statistically significant after false-discovery-rate correction; therefore, all taxonomic observations were treated as descriptive. Candidate overlapping features included repeated detection of Escherichia-Shigella and Klebsiella and non-uniform patterns among genera previously associated with short-chain fatty acid metabolism, including Faecalibacterium, Blautia, and Roseburia. Lachnoclostridium and Bacteroides showed opposite abundance gradients in selected cross-dataset comparisons. These observations suggest possible ecological overlap across ischemic disease and age-associated microbiome contexts, but they do not establish causality, disease-specific biomarkers, or shared microbial function. The mechanistic models discussed in this manuscript are literature-informed hypotheses based on exploratory compositional data and require future validation in larger, harmonized longitudinal cohorts using metagenomic, metabolomic, clinical, and experimental measurements.}, }
@article {pmid42593705, year = {2026}, author = {Wei, W and Zhou, L and Huang, Y and Lu, Z and Zhang, R and Zeng, M and Wang, X}, title = {Association Between Gut Microbiota Dysbiosis and Bilirubin Metabolism Dysregulation in Children with Heart Failure.}, journal = {Journal of cardiovascular translational research}, volume = {19}, number = {1}, pages = {}, pmid = {42593705}, issn = {1937-5395}, mesh = {Humans ; *Heart Failure/microbiology/diagnosis/blood ; *Bilirubin/blood ; *Dysbiosis ; *Gastrointestinal Microbiome ; Female ; Child, Preschool ; Male ; Child ; Case-Control Studies ; Biomarkers/blood ; Feces/microbiology ; Age Factors ; Metabolomics ; Infant ; Ribotyping ; Clostridium/genetics ; Adolescent ; Eubacteriales ; }, abstract = {Patients with heart failure (HF) demonstrate dysregulation in bilirubin metabolism. The specific characteristics of intestinal bilirubin metabolism in HF remain unclear. This study involved metagenomic sequencing and metabolomic profiling of fecal samples from 45 children with HF and 32 healthy children. Serum total bilirubin levels were 11.3umol/L, 19.4umol/L and 5.0umol/L in HF New York Heart Association (NYHA) I-II, NYHA III-IV and control group (p < 0.001), and the median gut microbiome health index (GMHI) were - 0.78, -1.53 and 0.09 in each (p < 0.001). The abundance of 2 bacteria species containing bilirubin reductase, Ruminococcus gnavus (p = 0.028) and Clostridium sp.M62/1 (p = 0.002) significantly decreased in NYHA III-IV group. The gut downstream bilirubin products, urobilinogen and stercobilin were decreased in the HF group; while the upstream bilirubin products, unconjugated and conjugated bilirubin increased. Dysbiosis of the gut microbiome and the decrease of bilirubin reductase containing bacteria in pediatric HF patients related to a reduction in gut bilirubin metabolism.}, }
@article {pmid42595349, year = {2026}, author = {Yang, Z and Ramakrishnan, M and Wang, B and Wei, Q and Ahmad, Z}, title = {Optimized Controlled-Release Fertilization Improves Productivity and Reshapes the Rhizosphere Microbiome in Lei Bamboo: A Metagenomic Assessment.}, journal = {Environmental microbiology}, volume = {28}, number = {8}, pages = {e70401}, pmid = {42595349}, issn = {1462-2920}, support = {2018YFD060010403//National Key Research and Development Program of China/ ; 2021F1065-10//Special Project of Zhejiang Provincial Scientific Research Institutes/ ; }, mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Poaceae/microbiology/growth &amp; development ; Nitrogen/metabolism ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Soil/chemistry ; Urea/metabolism ; }, abstract = {Intensive nitrogen fertilization in Lei bamboo (Phyllostachys praecox) plantations has increased productivity but has also reduced nitrogen-use efficiency (NUE), accelerated nutrient losses, and contributed to soil degradation. How nutrient-release strategies influence rhizosphere microbiome assembly and ecosystem functioning remains poorly understood. Here, we developed a bamboo shoot-specific controlled-release fertilizer (CRF) and evaluated different urea-CRF blending ratios to identify sustainable fertilization strategy for Lei bamboo production. Mixed CRF-urea treatments outperformed both sole-fertilizer applications and the unfertilized control. T2 (30% urea + 70% CRF) achieved the highest shoot yield, whereas T3 (50% urea + 50% CRF) enhanced NUE. Optimized fertilization improved soil nutrient availability and organic matter accumulation without significantly affecting soil pH. Metagenomic analysis revealed the enrichment of taxa associated with nutrient transformation, organic matter turnover, and plant growth. However, pathway-level analysis revealed shifts in carbon, nitrogen, and sulfur cycling activities under optimized nutrient-release regimes. Our results demonstrate that synchronizing nitrogen release with plant and microbial demand enhances rhizosphere function, productivity and NUE. T2 delivered the strongest overall agronomic performance by maximizing shoot yield while maintaining improved nutrient retention and ecological stability. These findings provide a mechanistic link between fertilization strategy, rhizosphere microbial dynamics, and ecosystem function, supporting sustainable Lei bamboo production.}, }
@article {pmid42595551, year = {2026}, author = {Wang, L and Yang, J and Li, D and Zhang, F and Yan, JA and Wang, YY and Sun, J and Cao, H}, title = {[Tremella fuciformispolysaccharide retards the progression of colorectal cancer by regulating the gut microbiota-metabolome axis].}, journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]}, volume = {48}, number = {8}, pages = {975-982}, doi = {10.3760/cma.j.cn112152-20250925-00485}, pmid = {42595551}, issn = {0253-3766}, support = {MS2024064//Jiangsu Province Science and Technology Development Program of Traditional Chinese Medicine (General Project)/ ; YJZ202305//the Jiangnan University Affiliated Hospital Research-Oriented Hospital Medical Research Project (General Project)/ ; KX-25-C166//Wuxi City 2025 Soft Science Research Project/ ; }, mesh = {Animals ; *Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced ; Humans ; Mice ; HT29 Cells ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Male ; *Basidiomycota/chemistry ; *Metabolome/drug effects ; Azoxymethane ; Apoptosis/drug effects ; Dextran Sulfate ; Cell Proliferation/drug effects ; Feces/chemistry/microbiology ; Disease Progression ; Colon/pathology/metabolism ; }, abstract = {Objective: To investigate the anti-colorectal cancer effect of tremella fuciformis polysaccharides (TFP) via the gut microbiota-metabolite axis. Methods: Colorectal cancer was induced in C57BL/6J mice using azoxymethane/dextran sulfate sodium. TFP or distilled water was administered by gavage for 3 weeks. Disease activity index (DAI), colon length, tumor burden, histopathology, gut microbiota (metagenomics), fecal metabolites (untargeted metabolomics), and colonic protein expression (Western blot) were assessed. Pyridoxic acid's effect on HT-29 cells was tested in vitro. Results: TFP significantly reduced DAI [2.0(1.8, 3.3) vs. 3.5(2.8, 4.5), P＜0.01], increased colon length [(7.2±1.1) vs. (5.5±0.5) cm, P＜0.05], lowered pathological score [6(3, 8) vs. 9(8, 10), P＜0.05], and decreased tumor number [2(1, 3) vs. 4(3, 4), P＜0.05] and volume [(11.02±7.88) vs. (24.99±3.38), P＜0.01]. Metagenomics revealed that TFP significantly reshaped gut microbiota (R[2]=0.173, P=0.027), enriching Candidatus Amulumruptor, Helicobacter, and Akkermansia. Metabolomics showed distinct profiles (R[2]=0.159, P=0.004), with pyridoxic acid elevated 1.20 fold (P＜0.001). Pyridoxic acid suppressed HT-29 cell viability and migration, and correlated positively with several upregulated bacteria, suggesting a microbiota-metabolite axis underlying its anti-tumor effect. TFP downregulated nuclear factor-κB (NF-κB) (P＜0.01) and upregulated phosphorylated AMP-activated protein kinase alpha (p-AMPKα) (P＜0.001), BAX (P＜0.001), and cleaved caspase-3 (P＜0.05). Conclusion: TFP inhibits colorectal cancer progression by modulating gut microbiota, elevating pyridoxic acid, suppressing NF-κB, and activating AMPK-mediated apoptosis.}, }
@article {pmid42595876, year = {2026}, author = {Knuth, D and Mäder, P and Boekhorst, J and Poll, C and Kandeler, E and Alaoui, A and Pasković, I and Polić Pasković, M and Baldi, I and Bureau, M and Alcon, F and Contreras, J and Glavan, M and Abrantes, N and Campos, I and Norgaard, T and Huerta Lwanga, E and Geissen, V and Harkes, P}, title = {Beneath the surface: non-target effects of multiple pesticides on the soil microbiome in organic and conventional agricultural European fields.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {26}, pages = {13432-13448}, pmid = {42595876}, issn = {1614-7499}, support = {862568//HORIZON EUROPE Framework Programme/ ; }, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Pesticides ; Soil/chemistry ; Agriculture ; Europe ; Soil Pollutants ; }, abstract = {Previous studies have shown that diverse cocktails of pesticide mixtures are omnipresent in agricultural soils yet miss a clear link to the effects on the soil microbiome. In this study, we linked the occurrence of pesticides in conventional and organic agricultural soils of the SPRINT (Sustainable plant protection transition) projects' Case Study Sites to the composition and function of soil microbial communities. Metagenomic sequencing, phospholipid fatty acids analysis and enzyme activity measurements were used to characterize the soil microbiome and effects of site-specific parameters such as pH and SOC, and pesticide residues. Differences in the soil microbiome were strongly influenced by the geographic origin of the samples, with the pH value as dominant driver. Against our hypothesis, effects of the investigated management systems were limited, yet significant at the European level. Notably, an association between some pesticides could still be observed after accounting for the variation explained by the environmental factors. Among these, especially fungicides, with modes of action that aim to interfere with processes in microorganisms, seemed to affect the soil microbiome. This might occur either by directly affecting these processes in non-target organisms or by changing co-dependencies between fungi and bacteria. Next to fungicides, aminomethylphosphonic acid showed a significant effect on the soil microbial composition and an interactive, possibly synergistic effect with the persistent pesticide hexachlorobenzene. The latter raises concerns about a possible interaction of recently applied pesticides and persistent "legacy" pesticides. This work highlights that even though environmental parameters can overshadow the effects of pesticides, especially the identity of the pesticides present, can have an influence on the soil microbiome.}, }
@article {pmid42598412, year = {2026}, author = {Wang, X and Chen, W and Zhang, H and Cao, D and Sun, J and Hu, H}, title = {Gut microbial biomarkers for major depressive disorder: a cross-sectional study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1690285}, pmid = {42598412}, issn = {2235-2988}, mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/virology ; *Biomarkers/analysis/blood ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Female ; Adult ; Male ; Metagenomics ; Bacteria/genetics/classification/isolation &amp; purification ; Middle Aged ; Viruses/genetics/classification/isolation &amp; purification ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Alterations in the gut microbiota have been associated with a variety of psychiatric disorders, including major depressive disorder (MDD). However, the relationship between MDD and gut microbial communities remains incompletely understood. Most previous studies have primarily focused on gut bacteria, with relatively limited attention to other microbial components.<br><br>METHODS: In this study, we analyzed gut microbial profiles from 36 patients with MDD and 36 healthy controls using metagenomic sequencing data. The MaAsLin2 algorithm was applied to identify potential microbial biomarkers associated with MDD.<br><br>RESULTS: A total of 6 bacterial biomarkers and 7 viral biomarkers were identified. The models based on these features demonstrated strong predictive performance, with area under the curve (AUC) values of 0.891 for bacteria and 0.878 for viruses. Notably, the combined bacterial-viral model achieved an AUC of 0.946. These findings were further evaluated through external testing in two unrelated research cohorts. In the Shanxi cohort, the AUC values were 0.825 (bacteria), 0.803 (viruses), and 0.972 (combined model). In the Wuhan cohort, the AUC values were 0.683 (bacteria), 0.693 (viruses), and 0.784 (combined model).<br><br>CONCLUSION: In summary, our results highlight the potential of gut bacterial and viral biomarkers as candidate biomarkers and potential auxiliary tools for MDD assessment and suggest that integrating multi-domain microbial features may improve prediction accuracy.}, }
@article {pmid42599548, year = {2026}, author = {Medeiros, WB and Hidalgo-Martinez, KJ and Penna, DDPS and Oliveira, VM}, title = {Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {9}, pages = {}, pmid = {42599548}, issn = {1573-0972}, mesh = {Antarctic Regions ; *Microbiota/genetics ; Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.}, }
@article {pmid42600761, year = {2026}, author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z}, title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.}, journal = {Pharmacological research}, volume = {231}, number = {}, pages = {108398}, doi = {10.1016/j.phrs.2026.108398}, pmid = {42600761}, issn = {1096-1186}, mesh = {Humans ; *Muscle, Skeletal/physiology ; *Tea ; *Gastrointestinal Microbiome ; Male ; Proteomics ; Female ; Prospective Studies ; Middle Aged ; Multiomics ; Biomarkers/blood ; Hand Strength ; *Muscle Strength ; Adult ; }, abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.}, }
@article {pmid42601633, year = {2026}, author = {Albastaki, A and Naji, M and Moussa, M and Smith, J}, title = {Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {4}, pages = {e70403}, pmid = {42601633}, issn = {1758-2229}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Ecosystem ; Soil/chemistry ; Metagenomics ; Forensic Sciences ; Phylogeny ; }, abstract = {Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m[-1]) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.}, }
@article {pmid42605509, year = {2026}, author = {Xiao, L and Fu, C and Santos, IR and Duarte, CM and Liu, J and Zhou, L and Zhou, M and Dang, R and Lin, J and Xiao, K and Luo, Y and Han, G}, title = {Microbial Decomposition of Lignin to Methane Reduces Net Blue Carbon Benefit Across China's Saltmarshes.}, journal = {Global change biology}, volume = {32}, number = {8}, pages = {e71059}, pmid = {42605509}, issn = {1365-2486}, support = {2022YFF0802101//National Key Research and Development Program in China/ ; U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 41991330//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Methane/metabolism ; *Lignin/metabolism ; China ; *Wetlands ; Carbon/metabolism ; *Microbiota ; Biodegradation, Environmental ; }, abstract = {CH4 emissions from mangrove, saltmarsh, and seagrass ecosystems partially offset carbon sequestration, potentially diminishing the climate mitigation capacity of these blue carbon habitats. However, a mechanistic understanding of the processes governing CH4 production potential across large spatial scales remains limited. By integrating incubation-based measurements from 116 sites, we reveal significant ecosystem-specific differences in CH4 production potential, with saltmarshes emerging as CH4 production hotspot relative to mangroves and seagrass meadows. Using an integrated analytical approach encompassing more than 30 environmental, biogeochemical, and microbial parameters, we demonstrate that CH4 production potential converges on sediment organic carbon availability, particularly plant-derived carbon, as a key regulatory axis. Additionally, metagenome-assembled genomes (MAGs) recovered from saltmarshes show a functional bias toward lignin degradation, thereby fueling downstream CH4 production via methylotrophic pathways. Lignin-addition and stable carbon isotope experiments further provide supportive evidence that lignin decomposition enhances Chinese saltmarsh CH4 production potential, revealing a pathway that may reduce net blue carbon benefit. Together, these findings underscore that saltmarsh plant-derived lignin is less stable than conventionally assumed, as microbial processing redirects stored carbon toward CH4 production, challenging current blue carbon accounting frameworks at a continental scale within China.}, }
@article {pmid42608979, year = {2026}, author = {Wang, P and Wang, C and Zhang, Y and Bi, L and Zhao, H and Xu, Z and Wang, Z and Sheng, Y and Cui, Y}, title = {Topical Application of Indole-3-Acetic Acid, Present in S. epidermidis Supernatant, Alleviates Atopic Dermatitis in Mice at Least via the Aryl Hydrocarbon Receptor Signalling Pathway.}, journal = {Experimental dermatology}, volume = {35}, number = {8}, pages = {e70329}, pmid = {42608979}, issn = {1600-0625}, support = {201920102303//Peking Union Medical College/ ; 2024-ZX-019//Project of Integrated Traditional Chinese Medicine Collaboration "Flagship" Department Development/ ; ZRJY2023-GG14//China-Japan Friendship Hospital Youth Science and Technology Excellence Project/ ; 2208085Y25//Outstanding Youth Project of Natural Science Foundation of Anhui Province/ ; 2022YFC3602002//China National Key R&amp;D Program of China/ ; 2022-NHLHCRF-LX-02-03//National High-Level Hospital Clinical Research Funding/ ; }, mesh = {Animals ; *Dermatitis, Atopic/drug therapy/metabolism/microbiology ; *Indoleacetic Acids/administration &amp; dosage/pharmacology/therapeutic use/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism/antagonists &amp; inhibitors ; *Staphylococcus epidermidis/metabolism ; Signal Transduction/drug effects ; Mice ; Humans ; Skin Microbiome ; Skin/metabolism/microbiology ; Keratinocytes/metabolism ; Administration, Topical ; Disease Models, Animal ; Female ; Molecular Docking Simulation ; }, abstract = {Dysbiosis of the skin microbiome, characterised by Staphylococcus aureus overgrowth and imbalance of commensals such as Staphylococcus epidermidis (S. epidermidis), is closely associated with atopic dermatitis (AD). However, the therapeutic relevance of defined S. epidermidis-associated indole metabolite, especially indole-3-acetic acid (IAA), in AD-like inflammation remains incompletely characterised. Here, we investigated the role of IAA, a tryptophan-derived metabolite enriched in the culture supernatant of the tested S. epidermidis strain, in AD-like inflammation. Public transcriptomic analyses suggested impaired AHR-associated and tryptophan-metabolism signatures in AD skin, particularly in lesional skin, while human metagenomic data indicated AD-associated staphylococcal alterations. Targeted metabolomics identified IAA as an enriched indole metabolite in S. epidermidis culture supernatant. In an MC903-induced AD-like mouse model, cutaneous IAA levels and S. epidermidis abundance were reduced. Topical IAA attenuated AD-like phenotypes, improved barrier-related proteins and reduced inflammatory indices. These protective effects were diminished by the AHR antagonist CH223191. Molecular docking predicted a possible interaction between IAA and AHR, and in vitro assays showed that IAA modulated keratinocyte AHR-associated inflammatory and barrier-related responses. Together, our findings support IAA as a microbiome-associated postbiotic candidate for AD management, at least partly through AHR-associated signalling.}, }
@article {pmid42611116, year = {2026}, author = {Ajagbe, MA and Ahmed, SF and Ouf, A and Abdoullateef, BMT and Abdallah, RZ and Siam, R and Elbehery, AHA}, title = {Siwa spring microbiomes as reservoirs of biosynthetic gene clusters: Unlocking natural product potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {9}, pages = {}, pmid = {42611116}, issn = {1573-0972}, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; Metagenomics ; Metagenome ; Archaea/genetics/classification/metabolism/isolation &amp; purification ; Phylogeny ; Biosynthetic Pathways/genetics ; Computational Biology ; }, abstract = {The rising demand for novel therapeutics, including antimicrobial, anticancer, and anti-inflammatory agents, underscores the need for new drug discovery strategies. Microbial communities represent rich reservoirs of bioactive compounds encoded by biosynthetic gene clusters (BGCs), yet traditional approaches remain limited by the inability to culture most microorganisms and the frequent rediscovery of known metabolites. Sequence-based metagenomics provides a transformative solution by directly identifying BGCs from environmental DNA. Using NovaSeq X Plus shotgun sequencing, we explored the biosynthetic potential of microbial communities in two previously unstudied brackish springs of the Siwa Oasis, Cleopatra and Fatnas. These ecosystems were dominated by bacteria (99.2%), with archaea being nearly absent (< 0.1%), and the microbial composition consisted largely of mesophilic taxa from Pseudomonadota, Bacteroidota, Actinomycetota, and Planctomycetota, which together accounted for 98.2% of the community. Our integrated bioinformatics pipeline enabled the reconstruction of 37 medium-to-high-quality metagenome-assembled genomes (MAGs), and recovered 147 BGCs mostly from Pseudomonadota, Actinomycetota, and Acidobacteriota phyla. Terpene (n = 23) and ribosomally synthesized and post-translationally modified peptide (RiPPs; n = 22) BGCs predominated within Cleopatra Spring, whereas RiPPs (n = 20) represented the dominant class recovered from Fatnas Spring. None of the recovered gene clusters mapped to experimentally validated entries in the MIBiG database (distance > 0.4), and 96.6% displayed structural divergence from the gene cluster families catalogued in the BGC Atlas. These results highlight the Siwa Oasis as a promising reservoir of unexplored biosynthetic potential and a valuable resource for natural product discovery to address global health challenges.}, }
@article {pmid42611121, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {SARS‑CoV‑2 Associated Shifts in the Upper Respiratory Tract Mycobiome in Non-hospitalized Cases.}, journal = {Mycopathologia}, volume = {191}, number = {5}, pages = {}, pmid = {42611121}, issn = {1573-0832}, support = {OLP-57//CSIR-NEERI/ ; }, mesh = {Humans ; *COVID-19/microbiology ; SARS-CoV-2 ; *Mycobiome ; Male ; *Fungi/classification/genetics/isolation &amp; purification ; Female ; India ; Metagenomics ; Adult ; Middle Aged ; *Respiratory System/microbiology ; }, abstract = {SARS‑CoV‑2 infection is associated with marked changes of the upper respiratory tract mycobiome. URT mycobiome Changes in non-hospitalized patients however, remains poorly defined. We performed shotgun metagenomic sequencing of 95 upper respiratory tract swab samples from 48 symptomatic SARS‑CoV‑2-positive individuals and 47 healthy controls from central India. Fungal diversity and community structure were compared using alpha- and beta-diversity analyses, while differential taxa were identified using prevalence-based testing and a Directional Significance Score (DSS). SARS‑CoV‑2-positive samples showed significantly higher fungal alpha diversity than controls, with increased Shannon diversity (p = 0.000319) and Simpson diversity (p = 0.017). Beta-diversity analysis showed significant separation between groups for both Bray-Curtis and Jaccard distances (PERMANOVA p = 0.001), with significant dispersion effects as well (PERMDISP p = 0.001). DSS analysis showed certain fungal taxa associated with the SARS-CoV-2 group, including enrichment of Candida orthopsilosis, Malassezia furfur, Aspergillus glaucus, Aspergillus terreus, and Aspergillus niger, while Malassezia arunalokei, Aspergillus chevalieri, and Aspergillus sydowii were enriched in controls. These findings indicate that SARS‑CoV‑2 infection is associated with URT mycobiome dysbiosis and enrichment of clinically relevant opportunistic fungi in community cases.}, }
@article {pmid42611234, year = {2026}, author = {Zhu, Y and Deng, X and Wang, Q and Song, H and Wang, L and Zhou, D and Gao, C and Gardea-Torresdey, JL and White, JC and Zhao, L}, title = {SiO2@CuO Nanozyme Reinforces Plant-Microbiome Synergies for Simultaneous Yield Enhancement, Nutritional Fortification, and a Beneficial Soil Legacy.}, journal = {ACS nano}, volume = {20}, number = {32}, pages = {22762-22777}, doi = {10.1021/acsnano.6c06987}, pmid = {42611234}, issn = {1936-086X}, support = {2026ZD1211704//Jing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project/ ; CX (23)3015//Independent Innovation Fund for Agricultural Science and Technology in Jiangsu Province/ ; }, mesh = {*Microbiota/drug effects ; *Copper/chemistry/pharmacology ; *Silicon Dioxide/chemistry/pharmacology ; Soil Microbiology ; Soil/chemistry ; *Zea mays/growth &amp; development/microbiology/drug effects/metabolism ; Rhizosphere ; Seeds ; }, abstract = {Plant associated microbes play pivotal role in promoting host fitness and health. However, modern agricultural practices, such as agrochemicals use and domestication are eroding plant-microbe partnership. Here, we show that nanoenabled seed priming strengthens plant-microbe interactions, enhancing the plant holobiont performance. We found that SiO2@CuO nanozymes (NZs) with peroxidase (POD)-like activities, as seed priming agent, initiate earlier and stronger seed respiration and boost exudates release (sugars, amino acids, and fatty acids), creating a nutrient-rich and transiently hypoxic spermosphere microenvironment. Field trials revealed that by day 40, rhizosphere microbiome diversity increased, with enrichment of functional taxa involved in carbon and nitrogen metabolism, as determined by 16S rRNA and metagenomic sequencing. Throughout the growing season, above-ground tissues in the nanopriming group consistently outperformed the hydropriming control in photosynthetic pigment content and plant height. At harvest, without additional fertilizers or other inputs, nanopriming increased maize yield by 8.1% and improved kernel nutritional quality: starch (21.0%), protein (24.5%), and iron (24.2%). Soil nutrient availability (N, P, K, Ca) and cation exchange capacity also increased, indicating the improved soil quality. Notably, the soil from nanopriming group confers the subsequent maize crop with better drought tolerance and enhanced P uptake capacity, compared to the soil from hydropriming group, indicating beneficial legacy effect. This study demonstrates that a simple seed nanopriming can steer a positive feedback loop between plant and microbe, cascading into multifaceted holobiont benefits. This offers a sustainable strategy to harness plant microbiomes and promote sustainable and climate resilient agriculture.}, }
@article {pmid42615753, year = {2026}, author = {Sillos, MD and Matsuo, JSS and Morais, MB}, title = {GUT MICROBIOTA IN INFANTS WITH COW MILK ALLERGY: A SYSTEMATIC REVIEW OF CONTROLLED STUDIES.}, journal = {Arquivos de gastroenterologia}, volume = {63}, number = {}, pages = {e25133}, pmid = {42615753}, issn = {1678-4219}, mesh = {Humans ; *Milk Hypersensitivity/microbiology ; *Gastrointestinal Microbiome/physiology ; Infant ; Animals ; Immunoglobulin E/immunology ; }, abstract = {BACKGROUND: Alterations in the gut microbiota may be involved in the pathophysiology of cow milk allergy (CMA). However, whether gut microbiota abnormalities contribute to the diagnostic confirmation of CMA through specific microbiome signatures is still unknown.<br><br>OBJECTIVE: To conduct a systematic review of the literature on the gut microbiota of infants with CMA.<br><br>METHODS: This systematic review included studies on the gut microbiota of infants aged <2 years with CMA at diagnosis and at follow-up after different interventions to control clinical manifestations and compared them with that of healthy controls. The PubMed database was used for literature search. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses protocol was applied. This review was registered on the PROSPERO platform (CRD42024574354).<br><br>RESULTS: A total of 1,096 articles were identified. After applying inclusion and exclusion criteria, 18 studies were selected for the systematic review. Clinical manifestations included infants with immunoglobulin E (IgE)-mediated CMA (n=7), those with non-IgE-mediated CMA (n=10), or both (n=1). An oral challenge test for CMA diagnosis was mentioned in 11 studies, and in seven of them, a double-blind placebo-controlled challenge test was used. Most studies (n=13) used 16S rRNA gene sequencing to investigate the intestinal microbiota, and only three studies used shotgun metagenomic analysis. There was significant heterogeneity in the expression of results on microbiota characteristics. Alpha diversity was similar in the control group in most studies. A low abundance of Bifidobacteria was observed in some studies (n=5).<br><br>CONCLUSION: The results of this systematic review did not identify a typical microbiota pattern in infants with CMA. Studies including infants before elimination diet and with a diagnosis confirmed by an oral challenge test, and studies including one group of infants of the same age on exclusive breastfeeding and another group of infants of the same age on formula feeding as a control group are needed. Therefore, currently available data do not allow CMA diagnosis through a microbiota signature.}, }
@article {pmid42615833, year = {2026}, author = {Masiá, M and Gutiérrez, F}, title = {Microbial metabolite-driven mechanisms linking the gut microbiome to atherosclerosis: multi-omic and translational perspectives.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2718621}, pmid = {42615833}, issn = {1949-0984}, mesh = {Humans ; *Atherosclerosis/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Bacteria/metabolism/classification/genetics ; Metabolomics ; }, abstract = {Atherosclerotic cardiovascular disease remains the leading cause of mortality worldwide, and a substantial residual risk persists despite optimal management of traditional risk factors. Increasing evidence implicates the gut microbiome as a mechanistic contributor to atherogenesis, not merely through taxonomic shifts but via the production of bioactive microbial metabolites that link diet, microbial metabolism, and host vascular biology. These metabolites have emerged as central effectors of the gut-artery axis, influencing intestinal barrier integrity, systemic immunity, lipid handling, and thrombosis. Among the best-characterized pathways, trimethylamine N-oxide and phenylacetylglutamine have been robustly linked to macrophage lipid accumulation, platelet hyperreactivity, and adverse cardiovascular outcomes. More recently, imidazole propionate, a histidine-derived microbial metabolite, has emerged as a candidate mediator of vascular inflammation and plaque development through imidazoline-1 receptor-dependent activation of mTORC1 signaling, supported by mechanistic and experimental evidence. Advances in metagenomics, metabolomics, and proteomics now enable systems-level interrogation of microbiome-host interactions, facilitating causal inference through integrative metabolite-protein and pathway-level analyses. These approaches have revealed reproducible molecular networks associated with subclinical and clinical atherosclerosis, providing a framework for biomarker discovery and therapeutic targeting. People with HIV represent a particularly informative human model, in which persistent gut barrier disruption and dysbiosis sustain immune activation and confer excess cardiovascular risk, with distinct microbial and metabolite signatures linked to vascular inflammation and plaque progression. This review synthesizes current evidence linking gut microbial function to atherosclerosis, with a specific focus on metabolite-driven mechanisms, multi-omic integration, and translational relevance. We highlight emerging biomarkers and therapeutic strategies targeting microbial metabolic pathways and discuss methodological challenges that must be addressed to advance the gut-artery axis toward precision cardiovascular medicine.}, }
@article {pmid42615987, year = {2026}, author = {Comba, IY and Mars, RAT and Yang, L and Dumais, M and Chen, J and Van Gorp, TM and Harrington, JJ and Sinnwell, JP and Johnson, S and Holland, LA and Khan, AK and Lim, ES and Aakre, C and Athreya, AP and Gerber, GK and O'Horo, JC and Lazaridis, KN and Kashyap, PC}, title = {Gut microbiome signatures during acute infection are associated with long COVID.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2718581}, pmid = {42615987}, issn = {1949-0984}, support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; R01 DK138818/DK/NIDDK NIH HHS/United States ; R01 GM144351/GM/NIGMS NIH HHS/United States ; R35 GM149270/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/microbiology ; Female ; Longitudinal Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Post-Acute COVID-19 Syndrome ; Male ; SARS-CoV-2 ; Middle Aged ; Adult ; Machine Learning ; Metagenomics ; Acute Disease ; }, abstract = {BACKGROUND: Long COVID (LC) manifests in 10%-30% of non-hospitalized individuals post-SARS-CoV-2 infection, leading to significant morbidity. The predictive role of gut microbiome composition during acute infection in the development of LC is not well understood, partly because of the heterogeneous nature of the disease.<br><br>OBJECTIVES: To determine whether the gut microbiome composition in the acute phase of SARS-CoV-2 infection predicts subsequent LC and to investigate the role of microbiome signatures in disease subphenotypes.<br><br>DESIGN: We conducted a longitudinal cohort study involving 799 outpatient participants tested for SARS-CoV-2 due to similar symptom presentation, including 380 SARS-CoV-2 positive and 419 negative individuals. Stool samples were collected at two time points for metagenomic sequencing. Logistic regression with L1 regularization was employed to predict LC based on the microbiome and clinical metadata.<br><br>RESULTS: The individuals who developed LC harbored a distinct gut microbiome during acute infection compared to those who recovered fully and uninfected controls with similar symptomatology. However, the temporal changes in the gut microbiome between the acute (0-1 month) and post-acute (1-2 months) phases were similar across the three cohorts. Using machine learning, we showed that the gut microbiome carried a modest signal for subsequent LC, but model performance was insufficient for clinical prediction, likely reflecting the heterogeneous nature of LC. Finally, we identified four LC symptom clusters, with gastrointestinal and fatigue-only groups strongly linked to gut microbiome alterations.<br><br>CONCLUSION: The gut microbiome can potentially offer solutions for understanding the heterogeneous nature of LC. Larger cohorts and phenotype-aware computational algorithms may help overcome current model performance limitations and support the development of targeted diagnostic and therapeutic strategies.}, }
@article {pmid42618929, year = {2026}, author = {Issilbayeva, A and Vinogradova, E and Chulenbayeva, L and Kozhakhmetov, S and Jarmukhanov, Z and Myrzakhmetova, G and Umriukhin, A and Andossova, S and Bekbossynova, M and Kushugulova, A}, title = {Distinct gut microbiome profiles characterize obese and non-obese patients with atherosclerosis: a metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42618929}, issn = {1479-5876}, mesh = {Humans ; *Obesity/microbiology/complications ; *Metagenomics/methods ; Female ; *Atherosclerosis/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Dysbiosis/microbiology ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: Obesity is widely recognized as an aggravating risk factor for atherosclerosis (AS), yet the effects of obesity on AS-associated microbiome dysbiosis are not sufficiently characterized. This study aims to identify the contribution of obesity-related dysbiosis in AS.<br><br>METHODS: Using shotgun metagenomic sequencing, we studied gut microbiome composition and functional capacity across non-obese AS patients (AS-NOB, BMI&#x2009;<&#x2009;30, n&#x2009;=&#x2009;93), age-sex-matched non-obese controls (Ctrl-NOB, BMI&#x2009;<&#x2009;30, n&#x2009;=&#x2009;27), and obese AS patients (AS-OB, BMI&#x2009;&#x2265;&#x2009;30, n&#x2009;=&#x2009;68).<br><br>RESULTS: Gut community composition differed significantly across study groups (PERMANOVA F&#x2009;=&#x2009;3.23, p&#x2009;=&#x2009;0.001). Among metadata, obesity had the strongest effect (F&#x2009;=&#x2009;3.1, p&#x2009;<&#x2009;0.01) on the microbiome structure of AS patients. Furthermore, obese AS patients demonstrated a decrease in species richness and evenness (p&#x2009;<&#x2009;0.05). Taxonomic and functional analysis further suggested that obesity does not simply aggravate AS-associated gut dysbiosis but instead redirects it towards a distinct community state, characterized by a Prevotella expansion that consistently opposes the rest of the bacterial community. Among AS microbiome markers, an increase was detected in Pseudomonadota (Proteobacteria), Bilophila, Dysosmobacter, and Faecalibacterium.<br><br>CONCLUSION: Taken together, these results suggest that pathological expansion of Prevotella, potentially in conjunction with reduced alpha diversity, may represent a putative indicator of increased risk in AS patients, particularly within populations where the Prevotella enterotype or subtype is prevalent, warranting further investigation.}, }
@article {pmid42625439, year = {2026}, author = {Hilliard, MA and Oliver, A and Wilson, SMG and Shahab-Ferdows, S and Hampel, D and Bennett, BJ and Allen, LH and G Lemay, D}, title = {High dietary B12 is associated with reduced gut microbial B12 biosynthesis capacity and lower fecal short-chain fatty acids in healthy United States adults.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2718567}, pmid = {42625439}, issn = {1949-0984}, mesh = {*Feces/chemistry/microbiology ; Humans ; *Fatty Acids, Volatile/analysis/metabolism ; *Vitamin B 12/blood/metabolism/administration &amp; dosage ; Male ; Adult ; *Gastrointestinal Microbiome ; Female ; United States ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Middle Aged ; Diet ; Young Adult ; }, abstract = {Vitamin B12 is acquired through the consumption of animal-source foods and supplements. In animal models, interventions with B12 and/or methionine influence fecal short-chain fatty acid (SCFA) concentration. Yet the relevance of dietary B12 to microbially produced SCFAs in humans is unknown. This study determined associations between dietary B12 and the gut microbiome in a deeply phenotyped cohort of healthy U.S. adults. Habitual diet and fecal shotgun metagenomes were integrated alongside measurements of fecal SCFAs, plasma SCFAs, and plasma B12 (n = 277). Vitamin B12 intake ranged from 2.4 to 1062 µg/day, and nearly all participants were B12 replete. Stratification of participants into adequate (2.4-8.51 µg/day) and high B12 intake (>8.51 µg/day) groups revealed the association of high intake with a reduction in bacteria capable of anaerobic B12 biosynthesis. High B12 intake was also associated with lower fecal SCFA concentrations even after controlling for fiber and methionine intake. Differences in microbial taxa between dietary groups were limited. However, machine learning models demonstrated the ability to predict fecal propionate and butyrate from microbial pathways in the adequate or no supplement groups, but not in the high intake or supplement groups. Our results indicate that dietary B12 greater than 8.51 µg/day may be associated with reduced microbial synthesis of B12 and lower fecal SCFA production.}, }
@article {pmid42629006, year = {2026}, author = {Asadi, A and Sarand, I and Spuul, P and Fanning, S and Macori, G}, title = {Mapping spoilage microbiota in complex food systems: organisms, mechanisms, and omics-based characterization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 1}, pages = {119633}, doi = {10.1016/j.foodres.2026.119633}, pmid = {42629006}, issn = {1873-7145}, mesh = {*Food Microbiology/methods ; *Microbiota ; Multiomics ; *Bacteria/classification/genetics ; Food Storage ; Food Loss and Waste ; }, abstract = {Food spoilage is a major cause of food loss, while it remains less understood in complex, multi-component foods than in single-ingredient products. This review reframes spoilage in such foods as a community-driven ecological process, not simply the result of single dominant organisms, and argues that spoilage is best understood through microbial activity rather than microbial presence or relative abundance alone. We develop this framework around three central ideas: (i) ingredient-derived microbiotas interact within a shared matrix, so spoilage depends on microbial succession and competition during storage; (ii) predictions based on individual specific spoilage organisms often perform poorly in heterogeneous mixed foods; and (iii) taxonomic dominance does not necessarily indicate spoilage activity. On this basis, we examine key spoilage-associated groups, including Leuconostoc gelidum, Lactococcus piscium, Latilactobacillus sakei, Latilactobacillus curvatus, Pseudomonas spp., Enterobacteriaceae, yeasts, and moulds, and link them to characteristic metabolites and spoilage patterns under refrigerated and modified-atmosphere storage. We then evaluate analytical approaches, from culture-based methods and MALDI-TOF MS to 16S rRNA and ITS sequencing, shotgun metagenomics, and activity-resolved multi-omics, according to what each can and cannot reveal about viable populations, microbial activity, community succession, and spoilage causation. We also discuss how bioinformatic choices influence interpretation and why gene detection does not necessarily indicate spoilage activity. Finally, we propose an integrated framework for study design and data integration to support more reliable quality control and shelf-life assessment in complex food systems.}, }
@article {pmid42629009, year = {2026}, author = {Tong, Y and Wei, Y and Yang, Y and Jiang, M and Li, S and Liu, X and Wang, S and Huang, H and Liu, M and Song, P}, title = {Metagenomics-based insights into the microbial community succession and metabolic potential of flavor in Qingke high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 1}, pages = {119674}, doi = {10.1016/j.foodres.2026.119674}, pmid = {42629009}, issn = {1873-7145}, mesh = {Volatile Organic Compounds/analysis ; *Metagenomics/methods ; *Microbiota/genetics ; *Taste ; Fermentation ; *Hot Temperature ; Bacteria/metabolism/classification/genetics ; *Food Microbiology ; *Edible Grain/microbiology ; }, abstract = {Raw grain selection profoundly influences the flavor and quality of high-temperature Daqu (HTD). However, the microbial and flavor profiles of Daqu made with Qingke (highland barley) remain unclear. This study explored how varying Qingke addition affects physicochemical indicators, volatile organic compounds (VOCs), and microbial succession, ultimately impacting the formation of characteristic flavor compounds. Results showed that Qingke high-temperature Daqu (QHTD) underwent notable physicochemical changes, with the 30%and 50% addition groups exhibiting higher moisture and total acid levels (P < 0.01). Eleven characteristic VOCs were identified in QHTD, primarily represented by tetramethyl-pyrazine, phenylethyl alcohol, benzaldehyde, and specific alcohols, aldehydes, and acids. Dominant taxa in mature QHTD included Pseudonocardiales (mainly Saccharopolyspora), Bacillales (mainly Kroppenstedtia and Lentibacillus), and Eurotiales (mainly Paecilomyces). Temperature, moisture, and total acid were the main drivers of microbial succession in QHTD, and Qingke supplementation shaped microbial co-occurrence patterns by altering the fermentation environment. Key genera such as Kroppenstedtia and Paecilomyces were positively correlated with pyrazines and aldehydes. Metabolic network analysis based on metagenomic prediction revealed that functional bacteria (mainly Bacillales and Lactobacillales) were extensively involved in macromolecular degradation and flavor synthesis, exhibiting higher enzyme abundances in QHTD. Fungi primarily drove macromolecule degradation, phenylethyl alcohol synthesis, and metabolism of acetate and ethanol. In summary, the addition of Qingke modified the physicochemical indicators, altered functional microbial abundance, and enriched the flavor compounds in HTD. These insights offer theoretical and practical guidance for enhancing multi-grain Daqu production and the quality of Sauce-flavor Baijiu.}, }
@article {pmid42629115, year = {2026}, author = {Li, Y and Zhang, J and Li, S and Zhu, R and Ou, F and Xu, H and Wang, Y and Liu, Y and Tang, S and Xu, J}, title = {Astragalus polysaccharide ameliorates ischemic stroke via modulating the microbiota-gut-brain axis.}, journal = {Chinese journal of natural medicines}, volume = {24}, number = {9}, pages = {1081-1093}, doi = {10.1016/S1875-5364(26)61206-X}, pmid = {42629115}, issn = {1875-5364}, mesh = {Animals ; *Polysaccharides/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Astragalus Plant/chemistry ; *Ischemic Stroke/drug therapy/metabolism/microbiology ; *Brain/drug effects/metabolism ; Humans ; Mice, Inbred C57BL ; Toll-Like Receptor 4/metabolism ; Disease Models, Animal ; *Neuroprotective Agents/pharmacology ; }, abstract = {Ischemic stroke (IS) remains a major contributor to global disability and mortality. Astragalus polysaccharide (ASP), a naturally active component derived from Astragalus membranaceus, exhibits therapeutic potential against IS. However, their mechanism against IS via the microbiota-gut-brain axis remains unclear. Our study aimed to evaluate the mechanism of ASP against IS by middle cerebral artery occlusion (MCAO)-induced animal models combined with antibiotics (ABX) and fecal microbiota transplantation (FMT) experiments. In MCAO mice, our results showed that ASP significantly attenuated brain injury and intestinal barrier dysfunction. Transcriptomics, network pharmacology, and western blot identified LPS-TLR4-MAPK pathway as a key regulatory pathway in the regulation of IS-induced intestinal barrier dysfunction by ASP. Metagenomics and metabolomics indicated that ASP modulates SCFA-producing and anti-inflammatory bacterial genera (g_Anaerobutyricum and g_Caproiciproducens). Critically, ABX and FMT experiments confirmed that ASP's neuroprotective effects in MCAO mice receiving gut microbiota from IS patients, with this therapeutic benefit being microbiota-dependent. Additionally, LPS levels were upregulated in clinical patients with IS. In conclusion, our findings indicated that ASP alleviates IS-induced brain injury via the microbiota-gut-brain axis.}, }
@article {pmid42632657, year = {2026}, author = {Chen, B and Su, S and Lu, R and Lv, J and Pang, X and Wang, X and Zhang, S}, title = {Integrated sensory evaluation, flavoromics, untargeted metabolomics, and metagenomics analysis reveal the effects of fermentation time on the flavor quality of koumiss.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 2}, pages = {119801}, doi = {10.1016/j.foodres.2026.119801}, pmid = {42632657}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Fermentation ; *Metabolomics/methods ; Volatile Organic Compounds/analysis ; *Taste ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Time Factors ; Amino Acids/analysis ; Microbiota ; Humans ; Multiomics ; }, abstract = {Koumiss is valued for its nutritional and potential health benefits, whereas its undesirable flavor and excessive sourness often reduce consumer acceptance and limit its wider utilization. In this study, flavoromics, metabolomics, metagenomics, and sensory evaluation were integrated to investigate the mechanisms underlying characteristic flavor formation and sensory changes during koumiss fermentation. Fermentation time significantly affected sensory quality, metabolite profiles, and microbial community composition. Compared with commercial-fermented koumiss (CFK), laboratory-fermented koumiss (LFK) samples fermented for ≤72 h exhibited better overall sensory quality, with 72 h koumiss sample showing the best sensory performance. Esters, acids, alkanes, aldehydes, and alcohols were the predominant volatile organic compounds (VOCs). Pathway analysis indicated that phenylalanine, tyrosine, and branched-chain amino acid metabolism were the main differential pathways. Spearman correlation analysis indicated that free amino acids, VOCs, key microbial species, metabolite classes, and fatty acids were closely associated with sensory quality. In addition, Lactococcus raffinolactis and Streptococcus parauberis were negatively associated with aldehydes compounds, suggesting an important role of microbial succession in characteristic flavor formation. Excessive accumulation of organic acids and free amino acids may contribute to the sour and bitter attributes of koumiss. These findings provide a theoretical basis for quality evaluation of koumiss and offer practical guidance for fermentation optimization, particularly through the regulation of key microbial species and associated metabolites to improve flavor development and sensory quality.}, }
@article {pmid42632665, year = {2026}, author = {Zhuang, Y and Sun, T and Hu, F and Bi, Y and Lv, X and Ma, T}, title = {Dietary resveratrol improves meat quality in lambs via the rumen-muscle axis mediated by reshaped microbial metabolism.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 2}, pages = {119868}, doi = {10.1016/j.foodres.2026.119868}, pmid = {42632665}, issn = {1873-7145}, mesh = {Animals ; *Resveratrol/pharmacology/administration &amp; dosage ; *Rumen/microbiology/metabolism/drug effects ; *Diet/veterinary ; *Muscle, Skeletal/metabolism/drug effects ; Sheep ; Animal Feed/analysis ; *Red Meat/analysis ; *Gastrointestinal Microbiome/drug effects ; Fatty Acids, Volatile/metabolism ; Amino Acids/metabolism ; }, abstract = {Resveratrol (RSV) is a plant-derived polyphenol known to enhance host health and growth in animals. In this study, we used integrated metagenomic and metabolomic approaches to show that dietary RSV reshapes the rumen microbiome and its metabolism. Specifically, RSV upregulated volatile fatty acid (VFA) and amino acid synthesis pathways while suppressing methanogenesis in finishing lambs. These microbial metabolic changes propagated along a rumen-muscle axis, driving compositional improvements, as evidenced by elevated polyunsaturated fatty acids (gamma-linolenic acid) and key amino acids (Ser, Ala, Ile, and Leu), as well as enhanced meat quality traits, including reduced drip loss, increased eye muscle area, and improved color stability. Microbiota-muscle correlation analyses further linked the signature rumen microbes with muscle nutritional indicators. Our findings delineate a clear microbe-metabolite-tissue pathway through which RSV influences mutton quality, offering a mechanistic basis for microbiome-guided strategies to optimize meat production in ruminants.}, }
@article {pmid42632691, year = {2026}, author = {Rahman, AU and Valentino, V and Cobo-Díaz, JF and Sequino, G and Ordóñez, AA and Ercolini, D and De Filippis, F}, title = {Metagenomic profiling reveals how ecological and processing drivers shape the beef microbiome from farm to fork.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 2}, pages = {119939}, doi = {10.1016/j.foodres.2026.119939}, pmid = {42632691}, issn = {1873-7145}, mesh = {Animals ; Cattle ; *Microbiota/genetics ; *Red Meat/microbiology ; *Food Handling/methods ; *Metagenomics/methods ; *Food Microbiology ; Farms ; *Bacteria/genetics/classification/isolation &amp; purification ; Seasons ; Biofilms ; }, abstract = {Meat processing environments harbor complex microbial ecosystems that may be transferred to the final product, thus influencing product quality and safety. Several factors may affect microbiome composition, such as seasonality and sanitation procedures. In this study, we carried out a metagenomic analysis over two seasons across four beef processing facilities, following beef carcasses from farm-to-fork. The pre-maturation environment was dominated by Corynebacterium xerosis and Acinetobacter johnsonii in summer, and by Bifidobacterium pseudolongum and Cutibacterium acnes in winter, whereas meat maturation environments were colonized by a specialized lactic acid bacterial community. The long-term maturation stage was led by Carnobacterium divergens and Carnobacterium maltaromaticum, whereas Pseudolactococcus carnosus and Pseudolactococcus paracarnosus prevailed during the retail stage. The environmental microbiome exhibited broad metabolic potential, in contrast to the specialized, low-diversity profiles of mature meat. Routine sanitation practices did not fully remove detectable microbial DNA signatures from environmental surfaces and were associated with shifts in taxonomic and functional profiles, including a greater representation of biofilm-associated genes. We also identified a diverse phage community, and statistical modeling revealed strong negative predictive associations with Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Collectively, our findings demonstrate that the beef processing microbiome is shaped by the interaction of multiple ecological forces. Understanding these interactions provides a comprehensive framework for ecology-based strategies to improve meat quality, safety, and shelf-life.}, }
@article {pmid42634048, year = {2026}, author = {Cheng, C and Cheng, S and Jiang, W and Fu, S and Shang, Y and Tang, X and Zhao, J and Wang, H}, title = {Microbiota-derived 4-HPAA alleviates Crohn's disease by stabilizing SIRT1 and reprogramming macrophage immunometabolism.}, journal = {Apoptosis : an international journal on programmed cell death}, volume = {31}, number = {9}, pages = {}, pmid = {42634048}, issn = {1573-675X}, support = {No.M2025006//Jiangsu Provincial Commission of Health and Family Planning/ ; }, mesh = {Animals ; *Macrophages/immunology/metabolism/drug effects ; *Crohn Disease/microbiology/immunology/metabolism/pathology/genetics ; Mice ; *Sirtuin 1/metabolism/genetics ; Colitis/chemically induced ; Intestinal Barrier Function ; Humans ; Intestinal Mucosa/drug effects ; *Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Interleukin-10/genetics ; }, abstract = {Crohn's disease (CD) is characterized by mucosal immune dysregulation, gut microbiota disturbance, and epithelial barrier dysfunction. This study investigated whether an Aronia berry polyphenol-rich diet attenuates CD-related intestinal inflammation through microbiota-derived metabolic signals. IL-10[-/-] and TNBS-induced colitis mouse models were used to evaluate the effects of dietary intervention, bacterial strain supplementation, and candidate metabolite administration. Integrated metagenomic, metabolomic, and transcriptomic analyses were combined with in vivo and in vitro mechanistic experiments to identify diet-responsive microbial taxa, metabolites, and host regulatory pathways. This diet alleviated colitis, reduced mucosal injury, and improved epithelial barrier integrity. Multi-omics analyses identified Flavonifractor plautii enrichment and increased microbiota-derived 4-hydroxyphenylacetic acid (4-HPAA) levels as major diet-associated changes. F. plautii supplementation was associated with increased 4-HPAA production, while 4-HPAA administration partially reproduced the intestinal protective phenotype in vivo. In macrophages, 4-HPAA suppressed pro-inflammatory activation and promoted oxidative metabolic remodeling. Mechanistically, 4-HPAA stabilized SIRT1 by limiting ubiquitination-mediated proteasomal degradation, thereby activating SIRT1-PGC-1α signaling. Myeloid SIRT1 deficiency attenuated the effects of 4-HPAA on macrophage polarization, inflammatory cytokine expression, and epithelial barrier-associated proteins. These findings identify a diet-associated microbial metabolite pathway involving F. plautii, 4-HPAA, and SIRT1 signaling, linking polyphenol-rich dietary intervention to macrophage immunometabolic regulation and intestinal barrier protection. This microbial metabolite-centered mechanism may provide insight into nutritional intervention strategies for CD-related intestinal inflammation.}, }
@article {pmid42634100, year = {2026}, author = {Shi, R and Yang, Z and Zhou, X and Xu, D and Xue, W and An, L and Zhang, X and Huang, Y}, title = {Immune Cell-Mediated Causal Link Between Gut Microbiota Traits and Childhood Asthma: Evidence From Mendelian Randomization and Metagenomic Sequencing.}, journal = {The clinical respiratory journal}, volume = {20}, number = {8}, pages = {e70227}, pmid = {42634100}, issn = {1752-699X}, support = {82403847//National Natural Science Foundation of China/ ; 2023D43//Special Fund for Nursing Research of Tongji Hospital/ ; }, mesh = {Humans ; *Asthma/immunology/microbiology/genetics ; Child ; *Gastrointestinal Microbiome/immunology/genetics ; Metagenomics/methods ; Female ; *Mendelian Randomization Analysis/methods ; Male ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiota may be involved in childhood asthma. However, the causal relationship between the gut microbiota and childhood asthma remains obscure. Whether immune cells mediate the pathway from gut microbiota to childhood asthma has not been elucidated.<br><br>METHODS: Genetic data of 196 gut microbiota taxa, 731 immune cell phenotypes, and childhood asthma were retrieved from the MiBioGen consortium and the MRC-IEU OpenGWAS database. Bidirectional Mendelian randomization (MR) analysis was first performed to verify the causal association between gut microbiota and childhood asthma, with reverse MR analysis conducted to rule out reverse causality. Mediation analysis was subsequently applied to identify the immune cell-mediated regulatory pathways. Additionally, a clinical validation cohort including childhood asthma patients and healthy controls was enrolled. Fecal samples from all subjects were subjected to metagenomic sequencing for microbial species identification and functional annotation. Linear discriminant analysis effect size (LEfSe) was used to screen differential gut microbiota taxa, whereas alpha diversity analysis was performed to evaluate microbial community richness. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was utilized for microbial functional pathway annotation, and Python-based bioinformatics analysis was adopted to quantify the abundance of microbial virulence factors based on Virulence Factor Database (VFDB) annotation results.<br><br>RESULTS: MR analysis confirmed significant causal associations between seven gut microbiota taxa and childhood asthma, among which four taxa exhibited robust causal effects, and no reverse causal relationship was detected. A total of 25 immune cell types showed statistically significant effects on childhood asthma risk. Mediation analysis further validated two key immune cell-mediated pathways: the CD64 phenotype on CD14-CD16 immune cells mediated the causal effect of s_Paraprevotella_unclassified on childhood asthma, and the CD45 phenotype on HLA-DR T cells mediated the association of s_Bacteroides_thetaiotaomicron with childhood asthma. Clinical metagenomic sequencing revealed distinct gut microbial signatures between the two groups: The asthma group was characterized by enriched Bacteroides, whereas healthy controls had predominant Akkermansia and Lachnospiraceae, which was consistent with the MR findings. Alpha diversity analysis showed a trend of higher microbial species abundance in children with asthma without statistical significance. KEGG functional analysis indicated that differential microbial pathways between groups were primarily enriched in glucose metabolism, genetic information processing, and immune regulation. Moreover, the abundance of virulence factors including mrkl, mrkJ, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, impF, and hcp/tssD was significantly elevated in the childhood asthma group.<br><br>CONCLUSIONS: Specific gut microbiota taxa exert definitive causal effects on childhood asthma. Two immune cell phenotypes serve as crucial intermediate mediators linking gut microbiota dysbiosis to childhood asthma development. These novel findings elucidate the microbiota-immune regulatory mechanism underlying childhood asthma, providing a solid theoretical basis for the development of gut microbiota-targeted intervention strategies for childhood asthma prevention and treatment.}, }
@article {pmid42634387, year = {2026}, author = {Alomeir, N and Chinchilli, E and Terio, C and Zhang, L and Beck, LA and Assery, N and Mao, X and Wolf, JR and Xiao, J and Wu, T}, title = {Salivary OMICS factors associated with atopic dermatitis in early infancy.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {8}, pages = {e70468}, pmid = {42634387}, issn = {1399-3038}, support = {R01 DE031025/DE/NIDCR NIH HHS/United States ; U01 AI152011/AI/NIAID NIH HHS/United States ; R01DE031025/NH/NIH HHS/United States ; U01AI152011/NH/NIH HHS/United States ; }, mesh = {Humans ; *Dermatitis, Atopic/epidemiology/diagnosis/microbiology/metabolism ; Female ; Male ; *Saliva/microbiology/metabolism ; Biomarkers/metabolism/analysis ; Infant ; Prospective Studies ; Microbiota ; Cytokines/metabolism ; Infant, Newborn ; Child, Preschool ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) often develops in early childhood and may persist into adulthood. Noninvasive measures to identify infants at risk for AD are limited. We investigated whether oral biomarkers and oral microbiota are associated with AD onset within the first 2 years of life.<br><br>METHODS: In this prospective cohort study, we followed 119 infants residing in Upstate New York from birth to 24&#x2009;months (2018-2023). AD diagnoses were obtained from electronic health records. Saliva samples were collected at seven time points (1, 2, 4, 6, 12, 18, and 24&#x2009;months) and analyzed for 5 hormones and 23 cytokines using multiplex immunoassays. Salivary microbiome profiles were characterized via metagenomic sequencing.<br><br>RESULTS: Nearly half (48%) of infants developed AD by age 2, with most cases manifesting by 12&#x2009;months (42%) and peak incidence occurring between months 2-4. Infants who developed AD by 1&#x2009;year demonstrated significantly elevated estradiol (p&#x2009;=&#x2009;.007) and progesterone (p&#x2009;=&#x2009;.046) at 1&#x2009;month, and a significantly lower salivary cortisol level (p&#x2009;=&#x2009;.019) at 6&#x2009;months. Additionally, these infants exhibited higher sIL-1ra (p&#x2009;=&#x2009;.024) and IL-9 (p&#x2009;=&#x2009;.034) in saliva at 4&#x2009;months and lower IL-1&#x3b1; (p&#x2009;=&#x2009;.038) at 6&#x2009;months. Salivary microbiome beta diversity differed significantly at 2&#x2009;months between infants with and without AD by 1&#x2009;year (p&#x2009;=&#x2009;.038), with lower differential abundances of Bifidobacterium breve and Veillonella atypica in early infancy prior to AD onset.<br><br>CONCLUSION: Early-life salivary biomarkers, including hormonal, cytokine, and microbiome signatures, may serve as noninvasive indicators of infants at risk for early AD onset.}, }
@article {pmid42635214, year = {2026}, author = {Muller, E and Baum, S and Borenstein, E}, title = {MAAMOUL: metabolic network-based discovery of microbiome-metabolome shifts in disease.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {Supplement_2}, pages = {}, pmid = {42635214}, issn = {1367-4811}, support = {//Raymond and Beverly Sackler Chair in Bioinformatics at Tel Aviv University/ ; U19AG057377/NH/NIH HHS/United States ; U19 AG057377/AG/NIA NIH HHS/United States ; 2266/25//Israel Science Foundation/ ; //Safra Center for Bioinformatics at Tel-Aviv University/ ; }, mesh = {*Metabolic Networks and Pathways ; Humans ; *Metabolome ; *Metabolomics/methods ; *Inflammatory Bowel Diseases/metabolism/microbiology/genetics ; *Irritable Bowel Syndrome/metabolism/microbiology ; *Microbiota ; Metagenomics/methods ; *Computational Biology/methods ; *Gastrointestinal Microbiome ; }, abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.<br><br>RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.<br><br>MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL.}, }
@article {pmid42635406, year = {2026}, author = {Hirayama, M and Takame, F and Maeda, T and Kashihara, K and Ito, M and Ohno, K and Ueyama, J}, title = {Separating extracellular from intracellular fecal metabolites exposes cross-feeding architecture in the gut: exploring metabolite partitioning and ecological associations.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2719062}, pmid = {42635406}, issn = {1949-0984}, mesh = {Humans ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metabolomics ; Metabolome ; *Gastrointestinal Tract/microbiology ; Vitamins/metabolism/analysis ; }, abstract = {The gut microbiota forms a complex ecosystem through metabolic interdependence (cross-feeding). However, conventional fecal metabolomics typically quantifies only total metabolite pools, making it difficult to distinguish extracellular-enriched metabolite pools from predominantly cell-associated ones, and thus limiting reconstruction of in situ metabolic networks. Here, we quantified fecal metabolites in paired fractions from the same specimen: an undisrupted fraction representing the extracellular pool and a strongly bead-beaten fraction representing the total pool; the intracellular pool was defined as the difference between total and extracellular measurements. Stool samples from 63 healthy individuals were analyzed for short-chain fatty acids, polyamines, and water-soluble vitamins, and the results were integrated with shotgun metagenomic profiles of species composition and functional genes. Vitamins exhibited two distinct behaviors. Adenosylcobalamin (a vitamin B12 coenzyme) was detectable only after disruption, and together with thiamine (B1) and niacin (B3) was classified as an intracellular-retained type (Type 1). In contrast, biotin (B7) and pantothenate (B5) showed higher extracellular proportions (Type 2). Integrative analyses further indicated that Type 1 thiamine was negatively associated with Blautia, consistent with intensive microbial utilization, whereas Type 2 biotin was strongly positively associated with Alistipes, suggesting links to ecological niches shaped by luminal pH and fermentation modes (carbohydrate vs protein fermentation). Fraction-resolved quantification provides a practical operational framework to differentiate extracellular from cell-associated metabolite pools, helping reconcile metagenomic potential with metabolomic reality and enabling deeper inference of cross-feeding structure in the gut ecosystem.}, }
@article {pmid42636187, year = {2026}, author = {Qin, W and Huo, J and Xiao, X and Li, S and Luo, H and Wu, Y and Chen, W and Chen, Z and Zheng, C and Liu, M and Li, B and Zhou, G and Huang, Z and Li, X and Li, J and Zhang, Z and Ye, J}, title = {Metagenomic analysis of gut microbiota and its correlation with thyroid hormones in papillary thyroid cancer before and after operation.}, journal = {PloS one}, volume = {21}, number = {8}, pages = {e0356770}, pmid = {42636187}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Thyroid Cancer, Papillary/surgery/microbiology/blood ; *Thyroid Hormones/blood/metabolism ; *Metagenomics/methods ; *Thyroid Neoplasms/surgery/microbiology/blood ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The changes of intestinal flora and thyroid hormone levels before and after operation for papillary thyroid cancer (PTC) and their relationship are not clear. It may interfere with the intestinal thyroid axis, change the systemic thyroid hormone regulation and exogenous treatment response. It is recognized that this microbial involvement is clinically related to long-term metabolic outcomes, and future strategies for microbial targeted adjuvant therapy are suggested. This study aims to provide direct evidence and a comprehensive understanding of the relationship between intestinal flora and thyroid hormone levels before and after surgical treatment of papillary thyroid cancer through metagenomic analysis.<br><br>METHODS: As a paired before and after observation study, 20 patients diagnosed with papillary thyroid cancer were included in the study. Fecal samples and thyroid hormone levels were collected within 3 days before operation and 72 hours after operation. First, the intestinal microbiota of these 20 patients was analyzed for metagenomic differences, such as &#x3b1; and &#x3b2; diversity analysis, PCoA, ANOSIM, Spearman correlation analysis, FDR correction, KEGG pathway enrichment and correlation network analysis. Subsequently, the changes of hormone levels were examined in combination with the collected intestinal microbiota.<br><br>RESULTS: There were significant differences in the diversity and composition of the gut microbiota in patients with papillary thyroid cancer before and after surgery. At the species level, the eight most significantly different groups identified were Bacteroides sp., Clostridium sp., Bacteroides fragilis, Alistipes sp., Parabacteroides sp., Bacteroides thetaiotaomicron, Phocaeicola dorei, and Oscillibacter sp. Notably, Clostridium sp. higher abundance in the pre-operative group, whereas Bacteroides sp., Bacteroides fragilis, Alistipes sp., Parabacteroides sp., Phocaeicola sp., and Bacteroides thetaiotaomicron were more prevalent in the post-operative group. After operation, FT4 showed an upward trend, while TSH, PTH and HTG showed a downward trend. The primary differential pathways associated with these changes pertained to iron uptake and regulation, polysaccharide utilization and transport, as well as metabolism and stress response. The pre-operative group was predominantly involved in ribosome biosynthesis, along with amino acid synthesis for valine and leucine. In contrast, the post-operative group primarily engaged in lipoic acid metabolism, glycosaminoglycan degradation, and bacterial secretion systems.<br><br>CONCLUSION: This study found that the composition, diversity and function of intestinal flora changed in patients with papillary thyroid cancer after operation. Specific microbial taxa may be associated with fluctuations in thyroid hormone levels. In the future, regulating intestinal flora can be used as an adjuvant therapy for hormone regulation in patients undergoing PTC surgery.}, }
@article {pmid42636377, year = {2026}, author = {Nearing, JT and Kuntz, T and Perdomo, V and Nickols, WA and Branck, T and Bhosle, A and Badri, DV and Huttenhower, C and Jackson, M and Thompson, KN}, title = {Gut microbiome-metabolome interactions during varied low-carbohydrate food consumption.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {35}, pages = {e2533462123}, doi = {10.1073/pnas.2533462123}, pmid = {42636377}, issn = {1091-6490}, support = {Hills internal funding HSPH//Hills Pet Nutrition Inc./ ; }, mesh = {Animals ; Dogs ; *Metabolome ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/physiology ; *Diet, Carbohydrate-Restricted ; *Dietary Carbohydrates/metabolism ; Cross-Over Studies ; Male ; }, abstract = {Low-carbohydrate (LC) foods have been associated with weight loss, insulin resistance, and reduced inflammation. Gut microbes may drive these effects by changing the host's immune and metabolic state, yet the optimal replacement strategies (e.g., protein vs. fat) and the biochemical impacts are still uncertain. Thus, we conducted a randomized cross-over study in canines (n = 35) using a high-carbohydrate food for 4 wk, followed by two 5-wk intervals of LC foods replacing carbohydrates with fat or protein. Feces and blood samples collected after each interval underwent metabolome profiling, as well as shotgun metagenomic and metatranscriptomic sequencing from feces. We observed strong associations between food and overall fecal and serum chemical and gut microbial composition. Bifidobacterium spp. were significantly reduced during consumption of either LC food, whereas many species from Firmicutes increased. In addition to broad taxonomic changes, we also found that several microbially associated metabolites (tryptophan derivatives, secondary bile acids, and short-chain fatty acid fermentation) shifted in abundance in response to differing LC foods. Broadly, we also identified a strong trend toward decreased amino acids in the feces of dogs fed LC foods, particularly the high fat food. Coupled with decreased fecal dipeptide levels and increased fecal ammonia, these findings indicate a broad metabolic shift within the gut microbiome, potentially toward protein catabolism. Together, the data suggest that diverse carbohydrate replacement strategies induce extensive gut reprogramming, with some changes dependent on whether carbohydrate energy was replaced with fat or protein.}, }
@article {pmid42637340, year = {2026}, author = {Li, Q and Feng, H and Wang, J and Han, L and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Microbial community succession, functional dynamics, and fermentative characteristic of yeasts in the fermented grains of strong-flavor Baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 5}, pages = {120183}, doi = {10.1016/j.foodres.2026.120183}, pmid = {42637340}, issn = {1873-7145}, mesh = {*Fermentation ; *Yeasts/metabolism/classification/genetics ; *Wine/microbiology ; *Food Microbiology ; Taste ; *Microbiota ; *Edible Grain/microbiology ; *Alcoholic Beverages/microbiology ; Ethanol/metabolism ; }, abstract = {To elucidate the succession patterns and functional characteristics of microbial community during the fermentation of Strong-flavor Baijiu, this study integrated metagenomics, flavor analysis, and pure culture approaches to systematically investigate the dynamic changes in the microecosystem of fermented grains over 0-60 days of fermentation. In addition, the fermentative performance and environmental adaptability of the core yeast strains were evaluated. The results showed that Daqu-derived microorganisms (e.g., Kroppenstedtia and Rhizopus) dominated the early fermentation stage, whereas lactic acid bacteria (e.g., Lactobacillus and Acetilactobacillus) and yeasts (e.g., Pichia) became predominant in the late stage. Fungal community succession occurred earlier than that of bacteria. Functional annotation revealed that metabolic pathways related to carbohydrate metabolism and pyrimidine biosynthesis continuously increased throughout fermentation, with Firmicutes being the primary contributors. In the middle and late fermentation stages, the abundance of alcohol dehydrogenase (ADH) genes increased significantly, with Saccharomyces and the non-Saccharomyces yeast Pichia being the main contributors. Acidity and ethanol were identified as key drivers shaping microbial community succession, and most flavor compounds, such as ethyl acetate, predominantly accumulated during the middle-to-late fermentation stages. The two non-Saccharomyces yeasts, Pichia kudriavzevii Pk1 and Wickerhamomyces anomalus Wa9, exhibited both robust ethanol fermentation capacity and a desirable metabolic profile characterized by "high ester production with low 3-methyl-1-butanol formation." This study systematically reveals the temporal succession and functional dynamics of the microbial community during strong-flavor Baijiu fermentation and provides valuable microbial resources for targeted fermentation enhancement and the development of functional starter cultures.}, }
@article {pmid42637407, year = {2026}, author = {Wang, Q and Zhang, J and Li, J and Borjihan, Q and Wusigale,  and Dorjgotov, D and Jambal, T and Tseveen, S and Xia, Y and Chen, Y}, title = {Integrated metagenomics and metabolomics reveal geographical signatures in the microbiome and metabolome of Jiaoke from Inner Mongolia, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 4}, pages = {120052}, doi = {10.1016/j.foodres.2026.120052}, pmid = {42637407}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; China ; *Metabolomics/methods ; *Microbiota/genetics ; *Metabolome ; *Cultured Milk Products/microbiology/analysis ; Fermentation ; Food Microbiology ; Animals ; Bacteria/classification/genetics/metabolism ; Multiomics ; }, abstract = {Jiaoke is a traditional fermented dairy product from Inner Mongolia, China, and its characteristic flavor and quality attributes are shaped by region-specific microbial communities. In this study, shotgun metagenomic sequencing combined with untargeted metabolomics was used to systematically characterize Jiaoke samples collected from three distinct ecological production regions: Hulun Buir (HLB), Xilingol (XLG), and Bayan Nur (BYN). The results demonstrated pronounced regional specificity in both microbial composition and metabolite profiles across the three regions. BYN samples were dominated by Lactococcus lactis and Bifidobacterium spp. with enrichment of lipid-derived metabolites. HLB samples were characterized by Lactococcus raffinolactis and psychrotolerant bacteria, together with elevated levels of sphingolipids. In contrast, XLG samples were dominated by Streptococcus macedonicus and exhibited high abundances of amino acids and dipeptides. Correlation analysis indicated that Lactococcus raffinolactis and Streptococcus macedonicus may contribute to Jiaoke flavor formation by promoting milk protein hydrolysis and dipeptide accumulation. These findings provide a basis for understanding regional flavor formation, developing tailored starter cultures, and establishing geographically indicated products in the future.}, }
@article {pmid42637484, year = {2026}, author = {Zhou, H and Yan, L and Zhang, L and Wang, R and Xu, S and Xu, B and Wu, X and Li, X}, title = {Insights into the analysis of microbial communities in fermented foods from the perspective of DNA-based techniques.}, journal = {Food research international (Ottawa, Ont.)}, volume = {242}, number = {Pt 4}, pages = {120175}, doi = {10.1016/j.foodres.2026.120175}, pmid = {42637484}, issn = {1873-7145}, mesh = {*Fermented Foods/microbiology ; *Food Microbiology/methods ; Fermentation ; High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The quality, flavor, and stability of fermented foods depend on the microbial community. However, microbial dynamics are difficult to observe directly, leading to limited control over fermentation. High-throughput sequencing is a revolutionary tool for microbial characterization, among which DNA-based amplicon and metagenomic sequencing are core techniques. Nevertheless, the related data processing workflows in the context of fermented foods have not yet been systematically summarized, hindering the translation of research findings into fermentation practices. This review clarifies the applications of amplicon and metagenomic sequencing in fermented foods. For amplicon sequencing, the impacts of target regions, data preprocessing, and reference databases are addressed. For metagenomic sequencing, sequencing strategies, read-based and binning-based analytical methods, functional annotation, and species-specific databases are discussed. In addition, major strategies for downstream analysis of community data are summarized, including microbial diversity, co-occurrence networks, niche and community assembly, key environmental drivers, and machine learning-based prediction. Amplicon sequencing efficiently reveals microbial succession during fermentation but has limitations in functional annotation. Metagenomic sequencing is notable for functional annotation, enabling the linkage between microbial communities and metabolic potential alongside community characterization. Standardized data preprocessing and specific databases are critical for improving characterization. For community data, integrated analysis allows uncovering the driving factors of microbial succession, thereby helping to regulate fermentation. Notably, the compositional nature of the data must be considered and validated to avoid spurious associations. In summary, the exponential growth of sequencing data will propel the era of precision fermentation.}, }
@article {pmid42640339, year = {2026}, author = {Li, J and Zhang, Y and Yang, K and Yang, Y and Chang, Z and Xu, T and Song, F and Chang, W}, title = {Arbuscular mycorrhizal fungi reshape rhizosphere microbial communities to alleviate phosphorus deficiency in soda-saline soils.}, journal = {Mycorrhiza}, volume = {36}, number = {5}, pages = {}, pmid = {42640339}, issn = {1432-1890}, support = {No. 32571883//The National Natural Science Foundation of China/ ; No. LH2024C091//Natural Science Foundation (Joint Guidance) of Heilongjiang Province/ ; No. 2025-KYYWF-ZR0407//Basic Scientific Research Business Expenses for Provincial Universities of Heilongjiang Province/ ; }, mesh = {*Mycorrhizae/physiology ; *Rhizosphere ; *Phosphorus/metabolism/deficiency ; *Soil Microbiology ; *Soil/chemistry ; Bacteria/metabolism/classification ; *Microbiota/physiology ; }, abstract = {Phosphorus availability is severely constrained in soda saline-alkali soils; yet the mechanisms by which arbuscular mycorrhizal (AM) fungi modulate rhizosphere microbial communities to alleviate the limitation are still unresolved. In the research, a microcosm experiment is conducted with metagenomic sequencing to investigate how inoculation with Rhizophagus intraradices influenced rhizosphere properties, phosphorus fractions, phosphatase activities, microbial community structure, P-cycling gene networks, and growth of Elaeagnus angustifolia under soda saline-alkali stress. The results demonstrated that AM inoculation was associated with enhanced plant growth and root development, ameliorated rhizosphere physicochemical conditions, elevated phosphatase activities, and enrichment of organic phosphorus-mineralizing bacteria, primarily Actinobacteria (Streptomyces) and Proteobacteria (Pseudoxanthomonas, Sphingomonas, Variovorax). Critically, the P-cycling gene network was reorganized, with hubs shifting from inorganic phosphorus transport genes toward organic phosphorus mineralization genes. Variance partitioning analysis further indicated that AM fungi independently contributed to variation in P-cycling functional genes, whereas their influence on soil phosphorus pools and phosphatase activity appeared to be largely indirect and associated with changes in soil chemical properties. Collectively, these findings support the hypothesis that AM fungi may promote phosphorus mobilization and transfer toward plants by restructuring microbial community composition and functional potential, providing a foundation for microbial management strategies in soda saline-alkali soils.}, }
@article {pmid42640403, year = {2026}, author = {Parveen, S and Tak, H and Ganai, BA and Aien, Q and Wana, GM and Kousar, A}, title = {Host-parasite-microbiome interactions in gastrointestinal trematodes and cestodes of small ruminants: current advances and future perspectives.}, journal = {Veterinary research communications}, volume = {50}, number = {6}, pages = {}, pmid = {42640403}, issn = {1573-7446}, support = {23D/23J00547//Human Resource Development Centre, Council of Scientific And Industrial Research/ ; }, mesh = {Animals ; *Trematoda/physiology ; *Cestoda/physiology ; *Host-Parasite Interactions ; *Trematode Infections/veterinary/parasitology ; *Cestode Infections/veterinary/parasitology ; Sheep ; Goats ; *Goat Diseases/parasitology/microbiology ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; Rumen/parasitology/microbiology ; Ruminants/parasitology ; }, abstract = {Gastrointestinal helminth infections remain a major problem for sheep and goat farming worldwide. In the past, research mainly focused on the shape, classification, spread, health effects, and genetic makeup of the parasites. With the advent of new next-generation sequencing technologies, we now better understand the gut ecosystem and the important roles of host-parasite-microbiome interactions in animal health. The digestive tract of sheep and goats contains microbes that aid digestion, nutrient utilization, immune function, and the maintenance of homeostasis. New research shows that helminths can change these microbial communities by affecting the immune system, damaging tissues, and competing for nutrients. At the same time, the existing microbes can affect how parasites settle, survive, and cause disease. Unlike studies on other parasites, research on the microbiomes of rumen flukes (Paramphistomum, Cotylophoron, and Calicophoron) and cestodes (Moniezia, Avitellina, and Stilesia) remains very limited, despite these parasites inhabiting environments rich in microbes, such as the rumen and small intestine. This review brings together what is currently known about the diversity, distribution, preferred habitats, and interactions among hosts, parasites, and microbiomes of gastrointestinal trematodes and cestodes in small ruminants. It focuses on metagenomic methods, the microbiota linked to these parasites, and new possibilities for microbiome research. The review also highlights important gaps in our knowledge and emphasizes the need for combined morphological, molecular, and next-generation sequencing studies, especially in areas such as Kashmir, where these parasites are common. Learning more about the microbes associated with these helminths could offer new insights into parasite biology and help develop better ways to diagnose, monitor, and control infections, supporting more sustainable small-ruminant farming.}, }
@article {pmid42640703, year = {2026}, author = {Lewandowski, R}, title = {Emergent function, not microbial conformity: functional redundancy and the limits of taxonomic inference in microbiome genomics.}, journal = {Microbial genomics}, volume = {12}, number = {8}, pages = {}, pmid = {42640703}, issn = {2057-5858}, mesh = {*Microbiota/genetics ; *Genomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification ; Host Microbial Interactions ; }, abstract = {Microbiome genomics has achieved remarkable resolution of community structure, yet composition alone remains an unstable basis for inferring host-relevant biology. That instability reflects a broader interpretive problem in which taxonomically distinct communities can converge on similar outputs, while superficially similar communities can diverge in behaviour because of strain variation, gene content, regulatory state, ecological context, spatial organization and host physiology. Functional redundancy is therefore better understood not as a reserve of interchangeable organisms but as a distributed functional architecture through which host-relevant outputs can persist across variation in membership. The central question for microbial genomics is not whether composition matters, but when community structure can be expected to predict function, host consequence or recovery. A more rigorous framework must distinguish membership from encoded capacity, realized activity, ecological interaction and host-relevant effect, while also recognizing that host physiology and spatial context shape which microbial functions become possible and which outputs are ultimately encountered. Progress will depend first on matching the evidentiary layer to the claim and then on selecting proportionate additions, from strain-resolved genomics and pathway-level interpretation to targeted metatranscriptomic, metaproteomic, metabolomic, spatial, perturbation-recovery or host-response measurements. In that framework, reproducibility may reside less in recurring taxa than in conserved biological outputs, and restoration less in compositional resemblance than in recovery of the functions and host-facing consequences that were actually disrupted.}, }
@article {pmid42640706, year = {2026}, author = {Whelan, FJ and Hall, LJ}, title = {An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.}, journal = {Microbial genomics}, volume = {12}, number = {8}, pages = {}, pmid = {42640706}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Metagenomics/methods ; Humans ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The 16S rRNA gene has - and continues to - play an important role in microbiology. It's universality across prokaryotes and variation across species has allowed the sequencing of its hypervariable regions to be used to distinguish taxa within complex mixed bacterial communities. Although 16S rRNA gene sequencing has transformed our understanding of microbial communities, its use comes with important caveats and considerations, especially in light of the availability of whole-genome metagenomic sequencing. Within, we discuss the 16S rRNA gene and its important role in microbiome research, in the past, present, and future.}, }
@article {pmid42642381, year = {2026}, author = {Birkeland, EE and Kværner, AS and Avershina, E and Bucher-Johannessen, C and Bemanian, V and Blix, HS and Hjartåker, A and de Vos, WM and Ursin, G and Hoff, G and Randel, KR and Botteri, E and Berstad, P and Rounge, TB}, title = {Microbiome signatures for detection of colorectal lesions in population-based FIT screening.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42642381}, issn = {2041-1723}, support = {190179//Kreftforeningen (Norwegian Cancer Society)/ ; 198048//Kreftforeningen (Norwegian Cancer Society)/ ; 2020056//Ministry of Health and Care Services | Helse S&#xf8;r-&#xd8;st RHF (Southern and Eastern Norway Regional Health Authority)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; Female ; Feces/microbiology ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Early Detection of Cancer/methods ; Aged ; Occult Blood ; Bacteria/genetics/classification/isolation &amp; purification ; Norway ; Metagenome ; Precancerous Conditions/diagnosis/microbiology ; Mass Screening/methods ; }, abstract = {The gut microbiome has been linked to colorectal cancer (CRC) development, with microbe-based classifiers distinguishing between CRC patients and healthy controls. However, there is a lack of studies addressing the utility of the microbiome in screening-relevant settings, including both precancers and CRC. In this Norwegian population-based study, we used fecal immunochemical test (FIT) leftovers from 1034 FIT-positive (i.e. positive for occult blood) screening participants for gut metagenome profiling using shotgun sequencing. Using comprehensive clinical, demographic, and lifestyle data, we modeled gut microbiome associations with CRC screening outcomes. Combining microbial profiles with quantitative FIT values improved detection of premalignant lesions beyond optimizing the FIT value alone, even after incorporating established CRC risk factors. Still, the FIT value maintained superior discriminative ability for CRC. We confirmed enrichment of bacteria such as Fusobacterium nucleatum and Peptostreptococcus stomatis in CRC. In contrast, other bacteria previously associated with the presence of CRC, including Hungatella hathewayi and Clostridium symbiosum, as well as pks-negative Escherichia coli, were enriched in those with no neoplastic findings, suggesting that in a FIT-positive population their presence may reflect other conditions causing intestinal bleeding rather than underlying neoplasia. Microbial profiles were predominantly associated with distal rather than proximal lesions. Together, our findings highlight the potential for microbial markers to improve FIT-based CRC screening, especially by differentiating those with premalignant lesions from those who test FIT-positive for other reasons.}, }
@article {pmid42642622, year = {2026}, author = {Bushnell, B and Villada, JC}, title = {Deployable high-fidelity metagenome binning at scale with QuickBin.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {42642622}, issn = {2399-3642}, mesh = {*Metagenomics/methods ; *Algorithms ; *Metagenome ; *Software ; Microbiota/genetics ; }, abstract = {Reconstructing genomes from metagenomic assemblies is foundational to microbiome research, yet binning faces a persistent trade-off between fidelity and throughput. Many high-accuracy methods rely on GPU-intensive workflows, marker-gene postprocessing, or heavy computational resources, limiting reproducible use at scale. Here, we present QuickBin, a CPU-native, marker-free binning algorithm designed to recover near-complete, ultra-low-contamination metagenome-assembled genomes (MAGs) efficiently. QuickBin pairs a GC-coverage spatial index (BinMap) with an early-exit Oracle cascade of similarity tests (scalar composition/coverage filters and SIMD-accelerated k-mer comparisons), reserving a compact neural network exclusively for ambiguous merges. Across synthetic communities, evaluated by marker-based and contig-origin ground truth, QuickBin maximizes high-fidelity sequence recovery. In benchmarking 297 diverse real metagenomes, QuickBin completed all runs, recovering more high-quality MAGs (≥95% completeness, ≤1% contamination) than resource-intensive alternatives that frequently failed. QuickBin provides a practical path to reproducible, genome-resolved metagenomics at scale for downstream comparative analyses. Open-source at: https://github.com/bbushnell/BBTools .}, }
@article {pmid42644416, year = {2026}, author = {Cavani, E and Edbom Devall, A and Chen, Y and Grompone, G and Brusselaers, N and Vlajic, M and de Vos, WM}, title = {Nationwide cohort study reveals low bifidobacteria and distinct microbiota composition and function in Swedish newborns.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2719244}, doi = {10.1080/19490976.2026.2719244}, pmid = {42644416}, issn = {1949-0984}, mesh = {Humans ; *Bifidobacterium/isolation &amp; purification/classification/genetics/physiology ; Infant, Newborn ; Sweden ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Female ; }, abstract = {NCT06285630.}, }
@article {pmid42653097, year = {2026}, author = {Lima, O and Rodríguez-Costas, N and Pérez-Rodríguez, MT and Davina-Nunez, C and Represa, M and Rubiñán, P and Alvarez, M and Ávila-Nuñez, M and Filgueira, A and Portela, C and Sopeña, B and Vasallo Vidal, FJ and Pérez-Castro, S}, title = {KEGG-Based Functional Signatures Complement Taxonomic Profiles Associated with Spontaneous Decolonisation of Carbapenem-Resistant Enterobacterales.}, journal = {International journal of molecular sciences}, volume = {27}, number = {16}, pages = {}, pmid = {42653097}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/classification ; *Carbapenems/pharmacology ; *Enterobacteriaceae Infections/microbiology ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; }, abstract = {Understanding the functional potential of the gut microbiota for carbapenem-resistant Enterobacterales (CRE) decolonisation is essential for developing novel non-antibiotic strategies to promote their clearance. In a previous study, we identified distinct taxonomic signatures associated with spontaneous CRE decolonisation (DeCol). Here, we aimed to determine whether these taxonomic differences were accompanied by differences in the predicted functional potential of the gut microbiota. Patients were identified from a database of individuals colonised with CRE. We performed Illumina shotgun metagenomic sequencing on 14 persistent CRE carriage (Col) and 23 DeCol patients with OXA-48-producing isolates. Bioinformatic analysis was performed using SqueezeMeta and differential abundance of functional and metabolic genes was assessed using DESeq2. Several antimicrobial resistance genes, including blaOXA-48, were underrepresented in DeCol patients. In contrast, DeCol patients showed an overrepresentation of genes associated with motility, regulated adhesion, short-chain fatty acid (SCFA)-related pathways and alternative carbohydrate metabolism. These orthologue enrichment patterns are consistent with functions previously linked to intestinal homeostasis in the literature. Conversely, Col patients exhibited an overrepresentation of genes associated with redox defence, biofilm formation and amino acid metabolism, suggesting distinct predicted functional profiles between persistent carriage and spontaneous decolonisation. Spontaneous CRE decolonisation was associated with distinct KEGG-based functional signatures and a lower abundance of antimicrobial resistance determinants. These functional profiles were consistent with the taxonomic differences previously identified in the same cohort and generate hypotheses regarding microbiome functions that may contribute to colonisation clearance. Because these findings are based on gene-content analysis, they reflect predicted functional potential rather than direct evidence of metabolic activity. Further multi-omics and experimental studies are required to validate these observations.}, }
@article {pmid42655634, year = {2026}, author = {La Vignera, S and Condorelli, RA}, title = {Non-Sexual Transmission of Papillomavirus: Is It Part of Our Virome?.}, journal = {Viruses}, volume = {18}, number = {8}, pages = {}, pmid = {42655634}, issn = {1999-4915}, mesh = {Humans ; *Papillomavirus Infections/transmission/virology/epidemiology ; Female ; *Human Papillomavirus Viruses/genetics/classification/physiology ; Infectious Disease Transmission, Vertical ; *Virome ; Infant, Newborn ; Pregnancy ; Fomites/virology ; Prevalence ; *Papillomaviridae/genetics ; Milk, Human/virology ; Infant ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) has traditionally been considered a sexually transmitted infection, yet accumulating evidence demonstrates that HPV can be acquired through multiple non-sexual routes. Understanding these alternative transmission pathways is critical for interpreting HPV detection in non-sexually active populations and for refining public health strategies.<br><br>METHODS: This review synthesizes current evidence on non-sexual HPV transmission routes, including vertical (transplacental, intrapartum), perinatal oropharyngeal colonization, fomite contamination, breast milk transmission, and horizontal non-sexual contact. We examine HPV prevalence data from female virgins, neonates, infants, and children, and evaluate metagenomic evidence positioning HPV as a component of the human virome across multiple body sites.<br><br>RESULTS: Published studies report that vertical transmission occurs in approximately 18.2% of HPV-positive mothers, with neonatal HPV positivity of 3.4% at birth and 100% genotype concordance in transmission pairs. Transplacental transmission has been documented in 10.2% of concordant mother-placenta-newborn triads. Reviewed studies report oropharyngeal colonization at birth reaching 58.2% following vaginal delivery, with 94.3% of colonized neonates clearing infection by 24 months. HPV DNA has been detected on fomites and medical devices, in breast milk (8.6-15%), and across body sites in healthy adults (skin 61.3%, vagina 41.5%, oral cavity 30%, gut 17.3%). Metagenomic studies identify HPV DNA in 68.9% of healthy individuals, with 109 distinct types detected. Female virgins show HPV prevalence ranging from 0-51.1% across studies.<br><br>CONCLUSIONS: The reviewed evidence suggests that HPV exhibits characteristics of a ubiquitous virome component with multiple non-sexual acquisition routes. These findings have important implications for vaccination strategies, screening interpretation, infection control in healthcare settings, and counseling of pediatric cases and non-sexually active individuals.}, }
@article {pmid42658871, year = {2026}, author = {Gonzales-Rodriguez, AO and Gonzales-Huerta, LE and Wong Chero, PA and Vera-Silva, LE and Uceda-Campos, G and Reale, FA}, title = {Breastmilk microbiota and its association with infant iron deficiency anaemia: A 16S rRNA metagenomic study in Peruvian mothers cohort.}, journal = {PloS one}, volume = {21}, number = {8}, pages = {e0352428}, pmid = {42658871}, issn = {1932-6203}, mesh = {Humans ; Peru/epidemiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Anemia, Iron-Deficiency/microbiology/epidemiology ; Infant ; *Milk, Human/microbiology ; *Microbiota/genetics ; Mothers ; Adult ; Metagenomics ; Metagenome ; Bacteria/genetics/classification ; Male ; Cohort Studies ; }, abstract = {Anaemia is one of the most important public health challenges in developing countries. The global burden is estimated at 1.8 billion people, affecting approximately 30% of all children. Despite the implementation of multiple strategies over several decades, up to 42.5% of children under 3 years of age suffer anaemia in rural areas of Peru. We studied the microbiota of breastmilk (hBM) from mothers with children under the age of 1 and analysed its association with their iron deficiency anaemia. 46 mother-child pairs were recruited from Talara, a town on the northern coast of Peru and classified according to the clinical status of the children. Children with anaemia were also tested for ferritin level to classify them as iron deficiency anaemia (IDA) or non-iron deficiency anaemia (non-IDA). hBM samples were taken from the mothers after careful instruction to reduce the risk of sample contamination and the microbiome was analyzed using 16S rRNA sequencing. Streptococcus and Staphylococcus were the predominant genera, with 90% of bacterial abundance being explained by 14 genera. Alpha diversity analysis showed that hBM from mothers of children with non-IDA had higher levels of bacterial richness than hBM from healthy (p < 0.01) and IDA (p < 0.05) participants. Principal coordinates analysis did not yield differential clusters but showed a disparity in the spread of samples for non-IDA group when compared with the other groups. IDA group showed higher burden of Corynebacterium, Acinetobacter, Paludibacter and Nitrospira, while exhibiting a trend towards a lower burden of Streptococcus. No statistically significant differences were identified on demographic characteristics. This study suggests that hBM microbiota may differ in mothers of children with IDA and non-IDA, highlighting the necessity of further in-depth research to elucidate potential factors associated with its pathogenesis.}, }
@article {pmid42664252, year = {2026}, author = {Abdelghany, S and Helmkampf, M and Schechter, MS and Veseli, IA and Leray, M and Eren, AM and Puebla, O}, title = {Proteobacteria with chemosynthetic potential are highly prevalent in the gills of Hypoplectrus reef fishes.}, journal = {PLoS genetics}, volume = {22}, number = {8}, pages = {e1012266}, doi = {10.1371/journal.pgen.1012266}, pmid = {42664252}, issn = {1553-7404}, abstract = {Fishes host a diverse microbiome in their gills, but a broad characterization of this microbiome at the metagenomic level is lacking. Here, we apply genome-resolved metagenomics to the gills of the hamlets (Hypoplectrus spp), a group of reef fishes from the Greater Caribbean. The analysis of 353 gill samples from 15 hamlet species collected at eight locations over 13 years revealed a stark contrast between the gill microbiota and reef water microbial communities, indicating a distinct and specific gill microbiome. A total of 70 gill-associated metagenome-assembled genomes (MAGs) were recovered. These MAGs belong to 17 lineages, most of which are novel. They relate to known fish gill pathogens, fish gut microbes, free-living and biofilm-associated taxa, indicating that the gill microbiome was assembled from a collection of distinct eco-evolutionary trajectories. The MAGs harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. One lineage in the Burkholderiaceae family was outstandingly prevalent across fish host species, sampling locations and years. Its genome encoded complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. To the best of our knowledge, this is the first line of evidence that fishes may host sulfur-oxidizing chemosynthetic bacteria in their gills. The functional significance of this chemosynthetic potential for the fish host or other members of the gill microbiome remains to be established. The high prevalence of this lineage allowed to build a pangenome. It revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), which parallels the phylogenomic pattern observed in the hamlets. Overall, our findings point to complex fish host-microbe and microbe-microbe eco-evolutionary interactions in the gills that may influence fish physiology, homeostasis and immune response.}, }
@article {pmid42665338, year = {2026}, author = {Orwa, S and Vlajic, M and Cavani, E and Devall, AE and Hugerth, LW and Brusselaers, N and De Vos, WM}, title = {PREVENT 1, a nationwide Swedish infant cohort for longitudinal gut microbiome profiling and early-life health outcomes: cohort profile.}, journal = {BMJ open}, volume = {16}, number = {8}, pages = {e118233}, doi = {10.1136/bmjopen-2026-118233}, pmid = {42665338}, issn = {2044-6055}, mesh = {Humans ; Infant ; Sweden/epidemiology ; Female ; *Gastrointestinal Microbiome ; Male ; Feces/microbiology ; Prospective Studies ; Infant, Newborn ; Surveys and Questionnaires ; Longitudinal Studies ; Breast Feeding/statistics &amp; numerical data ; Metagenomics ; Child Development ; }, abstract = {PURPOSE: PREVENT 1 is a nationwide, prospective Swedish infant cohort established to characterise gut microbiome development during the first 2 years of life and to relate microbial trajectories to feeding, infections, growth and everyday well-being. The study integrates repeated infant stool sampling with shotgun metagenomics analysis with aligned parental questionnaires, stool photographs and infant cry recordings collected at three approximately 3-month intervals for each infant.<br><br>PARTICIPANTS: Families were recruited nationwide in Sweden from September 2023 through targeted digital channels. Eligible participants were term-born infants residing in Sweden and aged <1 year at enrolment. Baseline questionnaire data and stool samples were collected from 253 infants. Parents completed questionnaires covering socio-demographic characteristics and health, pregnancy and delivery, postnatal factors, infant environment, feeding and growth, infections and other health outcomes, gastrointestinal symptoms and everyday well-being.<br><br>FINDINGS TO DATE: Retention was high, with 248 families completing at least one follow-up questionnaire at Phase 2 and 243 at Phase 3. For stool samples, 250 infants provided at least two samples and 241 provided all three. At enrolment, 42.3% of infants were older than 7 months, 73.9% had weight-for-length z-scores in the normal range and exclusive breastfeeding at 4&#x2009;months was reported for 58.9%.<br><br>FUTURE PLANS: Three-phase sample and questionnaire data collection was completed in December 2024. Future analyses will examine microbiome features, resistome profiles and functional pathways in relation to antibiotic exposure, feeding, growth and infant health outcomes. Subject to ethical approval and participant consent, follow-up may include further stool collection and Swedish register linkage.<br><br>TRIAL REGISTRATION NUMBER: NCT06285630.}, }
@article {pmid41118252, year = {2025}, author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z}, title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {72}, number = {4}, pages = {287-295}, doi = {10.1556/030.2025.02690}, pmid = {41118252}, issn = {1588-2640}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diarrhea/chemically induced/therapy/microbiology ; *Anti-Bacterial Agents/adverse effects ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Dysbiosis/chemically induced/therapy ; Animals ; }, abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.}, }
@article {pmid41118772, year = {2025}, author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH}, title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {11}, pages = {1873-1885.e7}, pmid = {41118772}, issn = {1934-6069}, support = {R35 GM146969/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Steroids/metabolism ; *Clostridium/metabolism/genetics/enzymology/isolation &amp; purification ; Crohn Disease/microbiology/drug therapy ; Germ-Free Life ; Hydrocortisone/metabolism ; Prednisolone/metabolism ; Metabolic Networks and Pathways ; *Oxidoreductases/metabolism/genetics ; *Gastrointestinal Tract/microbiology ; Glucocorticoids/metabolism ; Oxidation-Reduction ; }, abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.}, }
@article {pmid41120531, year = {2025}, author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P}, title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36670}, pmid = {41120531}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; }, abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.}, }
@article {pmid41121093, year = {2025}, author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S}, title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {447}, pmid = {41121093}, issn = {1478-811X}, support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Proteins/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; }, abstract = {BACKGROUND &amp; AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.<br><br>METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.<br><br>RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.<br><br>CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.}, }
@article {pmid41121668, year = {2025}, author = {Enagbonma, BJ and Modise, DM and Babalola, OO}, title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.}, journal = {MicrobiologyOpen}, volume = {14}, number = {5}, pages = {e70085}, pmid = {41121668}, issn = {2045-8827}, support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; }, mesh = {*Sorghum/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fabaceae/growth &amp; development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth &amp; development ; *Edible Grain/growth &amp; development/microbiology ; Agriculture/methods ; }, abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.}, }
@article {pmid41122237, year = {2025}, author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT}, title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20232}, pmid = {41122237}, issn = {2167-8359}, mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Bacillota/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; }, abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.}, }
@article {pmid41123352, year = {2025}, author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL}, title = {Metagenomic study of food waste anaerobic digestion.}, journal = {Microbiology spectrum}, volume = {13}, number = {12}, pages = {e0208725}, pmid = {41123352}, issn = {2165-0497}, mesh = {Anaerobiosis ; *Metagenomics ; Methane/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Archaea/metabolism/genetics/classification ; Biofuels ; Fermentation ; Microbiota/genetics ; Food ; Food Loss and Waste ; }, abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.}, }
@article {pmid41124778, year = {2025}, author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L}, title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.}, journal = {EBioMedicine}, volume = {121}, number = {}, pages = {105978}, pmid = {41124778}, issn = {2352-3964}, mesh = {Humans ; Female ; *Dihydrotestosterone/blood ; Male ; Middle Aged ; *Testosterone/blood ; *Gastrointestinal Microbiome ; Aged ; *3-Oxo-5-alpha-Steroid 4-Dehydrogenase/metabolism/genetics ; Cross-Sectional Studies ; Animals ; }, abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.<br><br>METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.<br><br>FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P = 3 &#xd7; 10[-4]), but not &#x3b2;-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P < 2 &#xd7; 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 &#xd7; 10[-6]; P. distasonis P = 5 &#xd7; 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).<br><br>INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5&#x3b1;-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.<br><br>FUNDING: See Acknowledgements.}, }
@article {pmid41125958, year = {2025}, author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G}, title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.}, journal = {Nature microbiology}, volume = {10}, number = {12}, pages = {3258-3271}, pmid = {41125958}, issn = {2058-5276}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {*Fecal Microbiota Transplantation ; *Metagenomics/methods ; Humans ; Clostridium Infections/therapy/microbiology ; Feces/microbiology ; Clostridioides difficile/genetics/classification/isolation &amp; purification ; Inflammatory Bowel Diseases/therapy/microbiology ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.}, }
@article {pmid41128412, year = {2025}, author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H}, title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.}, journal = {ACS nano}, volume = {19}, number = {43}, pages = {37758-37782}, pmid = {41128412}, issn = {1936-086X}, mesh = {Animals ; *Manganese/chemistry/administration &amp; dosage/pharmacology ; *Sepsis/complications/drug therapy/metabolism ; Mice ; *Carbon/chemistry/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Lung Injury/drug therapy/etiology/metabolism/pathology ; Administration, Oral ; Male ; *Quantum Dots/chemistry/administration &amp; dosage ; Lung/drug effects/metabolism ; }, abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.}, }
@article {pmid41128541, year = {2025}, author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S}, title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0095625}, pmid = {41128541}, issn = {2379-5077}, support = {2023YFD1702200//National Key Research and Development Program of China/ ; 42277357//National Natural Science Foundation of China/ ; 2022RC3057//Science and technology innovation Program of Hunan Province/ ; YLS-2025-ZY02039//Yuelushan Laboratory Breeding Program/ ; }, mesh = {*Composting/methods ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Hot Temperature ; Soil Microbiology ; Metagenome ; Metagenomics ; Transcriptome ; }, abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.<br><br>IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.}, }
@article {pmid41128819, year = {2025}, author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y}, title = {Olsenella scatoligenes-derived skatole promotes smooth muscle cell proliferation and migration to aggravate atherosclerosis.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41128819}, issn = {1751-7370}, support = {2025QNPY01//Fundamental Research Funds for the Central Universities/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; 82273611//National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 82330105//Key Program of National Natural Science Foundation of China/ ; }, mesh = {*Cell Proliferation ; Humans ; *Cell Movement ; *Atherosclerosis/microbiology/pathology ; *Myocytes, Smooth Muscle/physiology ; Male ; Animals ; Calcium-Binding Proteins/metabolism/genetics ; Microfilament Proteins/metabolism/genetics ; Calponins ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/genetics ; Female ; Muscle, Smooth, Vascular ; *Actinobacteria/metabolism ; Mice ; Middle Aged ; Coronary Artery Disease/microbiology ; }, abstract = {Coronary artery disease (CAD) remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of CAD through unclear mechanisms. Here, we demonstrate that the abundance and interspecies interactions of Olsenella scatoligenes are 4.7- and 1.6-fold higher in patients with CAD, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of O. scatoligenes. Consistently, supplementation with O. scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, O. scatoligenes-derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates ~40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking O. scatoligenes to aggravated atherosclerosis through activation of the aryl hydrocarbon receptor-calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of CAD.}, }
@article {pmid41130000, year = {2025}, author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z}, title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140201}, doi = {10.1016/j.jhazmat.2025.140201}, pmid = {41130000}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects/genetics ; Trimethoprim/pharmacology ; Nitrogen/metabolism ; Lincomycin/pharmacology ; Carbon/metabolism ; *Genes, Bacterial ; Sulfur/metabolism ; Drug Resistance, Microbial/genetics ; *Water Microbiology ; *Bacteria/genetics/drug effects/metabolism ; }, abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.}, }
@article {pmid41130504, year = {2026}, author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G}, title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.}, journal = {Environmental research}, volume = {288}, number = {Pt 1}, pages = {122995}, doi = {10.1016/j.envres.2025.122995}, pmid = {41130504}, issn = {1096-0953}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Microplastics/analysis ; Pilot Projects ; Metagenomics ; Female ; Male ; Young Adult ; China ; Feces/chemistry/microbiology ; *Environmental Exposure ; Students ; *Environmental Pollutants/analysis ; Adolescent ; Bacteria ; Adult ; }, abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.<br><br>METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry (Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.<br><br>RESULTS: The detection rate of microplastics in the stool samples was 98.5&#xa0;%, with a median mass concentration of 54.7&#xa0;&#x3bc;g/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.<br><br>CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.}, }
@article {pmid41130610, year = {2025}, author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K}, title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.}, journal = {BMJ open respiratory research}, volume = {12}, number = {1}, pages = {}, pmid = {41130610}, issn = {2052-4439}, mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; }, abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.<br><br>METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.<br><br>RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.<br><br>CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.<br><br>PROSPERO REGISTRATION NUMBER: CRD42023436934.}, }
@article {pmid41131078, year = {2025}, author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B}, title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37098}, pmid = {41131078}, issn = {2045-2322}, support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; }, mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; }, abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.}, }
@article {pmid41131367, year = {2025}, author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C}, title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2686-2701}, pmid = {41131367}, issn = {2058-5276}, support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; }, mesh = {*Hydrogenase/metabolism/genetics ; Humans ; Hydrogen/metabolism ; *Gastrointestinal Microbiome ; Fermentation ; *Bacteria/genetics/enzymology/classification/growth &amp; development/metabolism/isolation &amp; purification ; Metagenomics ; Feces/microbiology ; Bacteroidetes/growth &amp; development/metabolism/genetics ; Bacillota/growth &amp; development/genetics/metabolism/enzymology ; Crohn Disease/microbiology ; *Gastrointestinal Tract/microbiology ; Iron-Sulfur Proteins/metabolism/genetics ; Healthy Volunteers ; }, abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.}, }
@article {pmid41131583, year = {2025}, author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y}, title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1162}, pmid = {41131583}, issn = {1479-5876}, support = {No. CCCF-QF-2022B04-4//the China Crohn's &amp; Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&amp;D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; }, abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.<br><br>METHODS: A cohort of treatment-na&#xef;ve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.<br><br>RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p&#x2009;=&#x2009;0.02) compared to HC, which was restored after EEN treatment at remission status (p&#x2009;<&#x2009;0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r&#x2009;=&#x2009;0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-&#x3b1;, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).<br><br>CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.}, }
@article {pmid41131656, year = {2025}, author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S}, title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {215}, pmid = {41131656}, issn = {2049-2618}, mesh = {*Rumen/cytology/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics/immunology ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Inflammation/immunology/metabolism/microbiology/veterinary ; *Acidosis/immunology/metabolism/microbiology/veterinary ; Animals ; *Goat Diseases/immunology/metabolism/microbiology ; Goats ; Metagenomics ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Female ; Dairying ; Animal Feed ; Fermentation/immunology ; Th17 Cells/immunology/metabolism ; Interleukin-17/metabolism ; Signal Transduction/immunology ; }, abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.<br><br>RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the &#x3b2; diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.<br><br>CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.}, }
@article {pmid41135463, year = {2025}, author = {Zhang, A and Pan, P and Zhou, NY and Li, T}, title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140176}, doi = {10.1016/j.jhazmat.2025.140176}, pmid = {41135463}, issn = {1873-3336}, mesh = {*Benzophenones/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Wastewater/microbiology ; *Sunscreening Agents/metabolism ; *Microbial Consortia ; Bacteria/metabolism/genetics ; }, abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.}, }
@article {pmid41135729, year = {2025}, author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J}, title = {Deciphering microbial dynamics in coastal ecosystems under polycyclic aromatic hydrocarbon stress: Community assembly, interaction networks, and metabolic adaptations.}, journal = {Environmental research}, volume = {287}, number = {}, pages = {123179}, doi = {10.1016/j.envres.2025.123179}, pmid = {41135729}, issn = {1096-0953}, mesh = {*Polycyclic Aromatic Hydrocarbons/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Geologic Sediments/microbiology/chemistry ; Estuaries ; Ecosystem ; Environmental Monitoring ; Rivers/microbiology/chemistry ; China ; }, abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.}, }
@article {pmid41136135, year = {2026}, author = {Du, R and Li, X and Xu, Y and Jing, K and Ao, L and Deng, B and Xu, Q and Song, P and Yu, J}, title = {Metagenomics reveals potential antimicrobial peptides in Chinese baijiu fermentation.}, journal = {Food microbiology}, volume = {134}, number = {}, pages = {104918}, doi = {10.1016/j.fm.2025.104918}, pmid = {41136135}, issn = {1095-9998}, mesh = {Metagenomics ; Fermentation ; Food Microbiology ; *Fermented Beverages/microbiology ; *Antimicrobial Peptides/biosynthesis/chemistry/pharmacology ; Cell Line, Tumor ; Phylogeny ; Genome, Bacterial ; Microbiota ; Genome, Archaeal ; Cell Survival/drug effects ; Bacterial Proteins/chemistry/metabolism ; Escherichia coli/drug effects ; Molecular Docking Simulation ; }, abstract = {Antimicrobial peptides (AMPs) from food fermentation microbiota hold promise for food preservation and as potential antimicrobial agents. However, the biosynthetic potential of AMPs in food fermentations remains largely unclear. Here, using Chinese baijiu fermentation as a model, we provided a workflow for AMP mining by combining metagenomics and machine learning. We recovered 389 metagenome-assembled genomes (MAGs) spanning both bacteria and archaea from 18 fermented samples. In total, 414 AMPs, including 290 novel AMPs, were predicted in 59.38 % of these MAGs using a machine learning model. Correlation network analysis showed that AMP-producing microorganisms potentially mediated negative microbial interactions. We selected ten AMPs for experimental validation, and eight AMPs exhibited antimicrobial activity against five human pathogens and two food spoilage microorganisms. One peptide, AMP_22, showed a broad-spectrum activity (all seven test strains) with high potency (MIC = 3.06-200 μg/mL) and cytotoxicity was not observed below 25 μg/mL using HepG2 and A549 cell lines. We further investigated the antimicrobial mechanism of AMP_22 using Escherichia coli as a model. Treatment with AMP_22 caused severe damage to the bacterial cell membrane, inhibited intracellular protein synthesis, and led to a significant accumulation of reactive oxygen species (ROS). Furthermore, molecular docking analysis indicated that AMP_22 can bind to DNA gyrase and dihydrofolate reductase via hydrogen bonding. This study highlights the potential of food-derived AMPs for application as preservatives and antimicrobial agents.}, }
@article {pmid41136439, year = {2025}, author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z}, title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9353}, pmid = {41136439}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; }, abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.}, }
@article {pmid41136898, year = {2025}, author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S}, title = {Prevalence of oxalotrophy in the human microbiome.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {954}, pmid = {41136898}, issn = {1471-2164}, support = {40B2-0_194701//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert R&#xfc;f Stiftung/ ; }, mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.<br><br>RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.<br><br>CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.}, }
@article {pmid41137068, year = {2025}, author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM}, title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {426}, pmid = {41137068}, issn = {1756-3305}, mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.<br><br>METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Ba&#xf1;os, Laguna, Philippines, that differ in topography and land use transformations.<br><br>RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.<br><br>CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.}, }
@article {pmid41137451, year = {2025}, author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J}, title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.}, journal = {Molecular ecology}, volume = {34}, number = {22}, pages = {e70156}, doi = {10.1111/mec.70156}, pmid = {41137451}, issn = {1365-294X}, support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; }, mesh = {*Methane/biosynthesis ; *Soil Microbiology ; *Soil/chemistry ; Temperature ; *Food Chain ; Microbiota/genetics ; Oryza ; Metagenomics ; Anaerobiosis ; Climate Change ; }, abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.}, }
@article {pmid41137517, year = {2025}, author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S}, title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2568706}, pmid = {41137517}, issn = {1949-0984}, support = {GRANT NO. 1022149//USDA/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation &amp; purification ; Models, Animal ; Disease Models, Animal ; }, abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.}, }
@article {pmid41137523, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2569739}, pmid = {41137523}, issn = {1949-0984}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; T32 AI141349/AI/NIAID NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; T32 AI179595/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; }, abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.}, }
@article {pmid41138002, year = {2025}, author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M}, title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {178}, pmid = {41138002}, issn = {1572-9699}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.}, }
@article {pmid41138182, year = {2025}, author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF}, title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116477}, doi = {10.1016/j.celrep.2025.116477}, pmid = {41138182}, issn = {2211-1247}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; *Primates/microbiology ; Feces/microbiology ; *Microbial Interactions ; Metagenome ; Bacteria/genetics/metabolism/classification ; }, abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.}, }
@article {pmid41138185, year = {2025}, author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C}, title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116431}, doi = {10.1016/j.celrep.2025.116431}, pmid = {41138185}, issn = {2211-1247}, mesh = {Humans ; *Probiotics/therapeutic use ; *Sepsis/microbiology/prevention &amp; control ; Infant, Newborn ; Female ; Male ; Gastrointestinal Microbiome ; Infant, Very Low Birth Weight ; Infant ; Metabolome ; Risk Factors ; *Bacteria/metabolism ; }, abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.}, }
@article {pmid41138328, year = {2025}, author = {Bai, X and Bi, J and Li, A and Deng, X and Zhao, Z and Hu, H and Pan, H}, title = {Walnut cake meal improves amino acids, fatty acid composition and flavor of egg yolk via the microbiota-yolk metabolites crosstalk in Jingfen-1 laying hens.}, journal = {Poultry science}, volume = {104}, number = {12}, pages = {105981}, pmid = {41138328}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/microbiology/metabolism ; Female ; Animal Feed/analysis ; *Egg Yolk/chemistry ; *Amino Acids/analysis/metabolism ; Diet/veterinary ; *Fatty Acids/analysis/metabolism ; *Juglans/chemistry ; Random Allocation ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena/drug effects ; Taste ; }, abstract = {Egg production is important for both human nutrition and its economic contribution. However, regions with a shortage of soybean meal (SM) may not meet the nutritional needs of the laying hen industry. Walnut cake meal (WM), a by-product of walnut processing, can be reused in laying hen production. In this study, we evaluated the feasibility of using WM to reduce the demand for SM in the laying hen industry. A total of 144 47-week laying hens (with similar performance) were randomly assigned to two groups (12 hens in each replicate and six replicates for each group). One group was fed a maize-SM diet (SM group), and the other was fad a maize-WM diet (WM group). The diets of both groups had similar crude protein and ME contents. After replacing SM with WM, the laying rate, egg weight, and feed efficiency did not significantly change (P > 0.05). WM increased (P < 0.05) the polyunsaturated fatty acids content, particularly linoleic acid, as well as umami and essential amino acids, in the eggs. WM diet also enhanced the flavor of eggs by enriching multiple volatile organic compounds that smell of sweet and herb-like foods. In addition, probiotic bacteria such as Cyanobacteriota and Prevotella, were enriched in the cecal microbiota of laying hens fed WM. Moreover, targeted metabolomics revealed the enrichment of butyric acid, 4-methylvaleric acid, isoleucine, and valine in the cecal digesta of laying hens fed with WM. Metagenomic sequencing revealed genes in the cecal microbiota associated with the synthesis of these enriched metabolites. Increased isoleucine and 4-methylvaleric acid in the digestive system contributed to the enrichment of fatty acids and amino acids in the yolks, whereas elevated flavor substances in the yolk could be associated with more amino acids in the intestine of laying hens. In conclusion, WM can reduce the need for soybean meal, improve cecal metabolism and egg quality, and ultimately achieve sustainable agriculture.}, }
@article {pmid41138387, year = {2025}, author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T}, title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127698}, doi = {10.1016/j.jenvman.2025.127698}, pmid = {41138387}, issn = {1095-8630}, mesh = {Microbiota ; Animals ; *Methane/chemistry/metabolism ; Chickens ; *Propionates/metabolism ; Anaerobiosis ; }, abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.}, }
@article {pmid41138814, year = {2025}, author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K}, title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.}, journal = {Clinical nutrition ESPEN}, volume = {70}, number = {}, pages = {427-433}, doi = {10.1016/j.clnesp.2025.10.015}, pmid = {41138814}, issn = {2405-4577}, mesh = {Humans ; *Polypharmacy ; Male ; Aged ; *Gastrointestinal Microbiome/drug effects ; Female ; Cross-Sectional Studies ; *Stroke/microbiology/drug therapy ; Aged, 80 and over ; Inpatients ; Feces/microbiology ; Phylogeny ; Stroke Rehabilitation ; }, abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.<br><br>METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4 years; 55.8 % male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9 % of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (&#x3b2; = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (&#x3b2; = -0.159, p = 0.067) and Faith's PD (&#x3b2; = -0.38, p = 0.111).<br><br>CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.}, }
@article {pmid41138869, year = {2025}, author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M}, title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.}, journal = {International journal of biological macromolecules}, volume = {332}, number = {Pt 2}, pages = {148387}, doi = {10.1016/j.ijbiomac.2025.148387}, pmid = {41138869}, issn = {1879-0003}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/chemistry/pharmacology ; Humans ; *Fatty Acids, Volatile/biosynthesis ; *Selenium/chemistry/pharmacology ; *Nanoparticles/chemistry ; Antioxidants/pharmacology/chemistry ; Caco-2 Cells ; Prebiotics ; }, abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.}, }
@article {pmid41139486, year = {2025}, author = {Tran, T and Duong, DV and Le, TD and Bui, XT}, title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {10}, pages = {e70072}, doi = {10.1111/apm.70072}, pmid = {41139486}, issn = {1600-0463}, mesh = {*Biofilms/growth &amp; development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; }, abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.}, }
@article {pmid41142817, year = {2025}, author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER}, title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1610360}, pmid = {41142817}, issn = {1664-3224}, mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; }, abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.<br><br>METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).<br><br>RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 &#xb1; 13.19 years, and the mean BMI was 25.25 &#xb1; 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (&#x3b2;=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (&#x3b2;=0.32; p<0.01) and Faecalicatena fissicatena (&#x3b2;= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.<br><br>CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.}, }
@article {pmid41143528, year = {2025}, author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW}, title = {Evaluating the use of biobanked urine specimens for human urobiome studies.}, journal = {Microbiology spectrum}, volume = {13}, number = {12}, pages = {e0216424}, pmid = {41143528}, issn = {2165-0497}, support = {R01 DK121689/DK/NIDDK NIH HHS/United States ; //Lerner Research Institute, Cleveland Clinic/ ; }, mesh = {Humans ; *Biological Specimen Banks ; *Microbiota/genetics ; Male ; Female ; *Urine/microbiology ; *Urinary Tract/microbiology ; Metagenomics/methods ; Middle Aged ; Specimen Handling/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Aged ; }, abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.}, }
@article {pmid41143690, year = {2026}, author = {Kim, KJ and Garcia, MM and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY}, title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {209}, number = {1}, pages = {}, pmid = {41143690}, issn = {1096-0929}, support = {R01 ES032037/ES/NIEHS NIH HHS/United States ; T32ES007032//UW Environmental Pathology/Toxicology Training/ ; 5P30ES007033-27//UW EDGE Center/ ; //Environmental Health and Microbiome Research Center (EHMBRACE)/ ; //Sheldon Murphy Endowment/ ; 1R01AG070776/GF/NIH HHS/United States ; 1U01AG088557/GF/NIH HHS/United States ; //Dianne Isakson Distinguished Professorship/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Mice, Inbred C57BL ; *Microplastics/toxicity ; *Metabolome/drug effects ; Feces/microbiology ; Mice ; Metabolomics ; }, abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. MPs, defined as plastic particles less than 5 mm in diameter, are formed through the degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, and food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested MPs. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged with mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1,162 bacterial species and 1,437 metabolites were evaluated for downstream analysis. MPs' exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition, along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways, such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, short-chain fatty acid (SCFA)-targeted metabolomics showed significant changes in neuroprotective SCFA levels in both sexes. Our study demonstrates that MPs dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.}, }
@article {pmid41145643, year = {2025}, author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K}, title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37529}, pmid = {41145643}, issn = {2045-2322}, support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; }, abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.}, }
@article {pmid41147731, year = {2025}, author = {Jones, JA and Moczek, AP and Newton, ILG}, title = {The dung beetle microbiome complements host metabolism and nutrition.}, journal = {mSystems}, volume = {10}, number = {11}, pages = {e0117225}, pmid = {41147731}, issn = {2379-5077}, support = {2243725//National Science Foundation/ ; 1901680//National Science Foundation/ ; 2141416//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism ; *Microbiota ; Amino Acids/metabolism/biosynthesis ; Bacteria/genetics/metabolism/classification ; }, abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.}, }
@article {pmid41147782, year = {2026}, author = {Zhang, L and Yang, G and Zhang, C and Ji, B and Wu, D}, title = {Symbiotic nitrogen fixation and recycling in xylophagous insects: insights from gut microbiota of Apriona swainsoni larvae.}, journal = {Pest management science}, volume = {82}, number = {2}, pages = {1789-1804}, doi = {10.1002/ps.70323}, pmid = {41147782}, issn = {1526-4998}, support = {81503115//National Natural Science Foundation of China/ ; JNFX2025192//Domestic Visiting Program for Young Key Teachers of Anhui Province/ ; BK2012816//Natural Science Foundation of Jiangsu Province/ ; 201409/WT_/Wellcome Trust/United Kingdom ; CX (16)1005//Jiangsu Agricultural Science and Technology Independent Innovation Project/ ; 2023AH050727//Natural Science Foundation (Key project) of the University in Anhui Province/ ; 2024AH050921//Natural Science Foundation (Key project) of the University in Anhui Province/ ; HZR2436//Hefei Municipal Natural Science Foundation/ ; 2024A755//Anhui Postdoctoral Scientific Research Program Foundation/ ; 201409/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Symbiosis ; *Nitrogen Fixation ; Larva/microbiology/growth &amp; development/physiology/metabolism ; *Coleoptera/microbiology/growth &amp; development/physiology/metabolism ; Nitrogen/metabolism ; Klebsiella oxytoca/physiology/metabolism ; }, abstract = {BACKGROUND: Xylophagous insects, as nitrogen-limited organisms, face severe nutritional constraints due to the inherently low nitrogen content of lignocellulosic substrates-insufficient for growth. To alleviate this limitation, they rely on gut microbiota-mediated symbiotic nitrogen fixation and nitrogenous waste recycling. Apriona swainsoni, a model wood-boring cerambycid, exemplifies this adaptation: under extreme nitrogen scarcity in its xylem diet. While gut symbionts are hypothesized to overcome nitrogen limitation, the underlying mechanisms remain unclear.<br><br>RESULTS: First, metagenomic sequencing and functional gene analysis revealed enrichment of nitrogenase and urease genes in the posterior hindgut (PHG). Metaproteomics detected the nitrogenase gene nifU but no urease proteins, identifying nitrogen fixation as the primary nitrogen limitation mitigation strategy in A. swainsoni larvae. Subsequently, in vivo/in vitro [15]N isotope tracing showed peak [15]N in the PHG (105.02% higher than the natural environment) and&#x2009;~&#x2009;25-fold greater [15]N incorporation in cultured Klebsiella oxytoca versus controls. Targeted amino acid profiling further demonstrated [15]N enrichment in both essential and non-essential amino acids, with a spatial gradient (intestinal tissues > extra-intestinal tissues > frass)-indicating efficient microbial conversion of nitrogen into host-utilizable amino acids. Importantly, we identified that intestinal microbiota primarily mediate ammonia-to-amino acid conversion via the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the PHG. This is the first reported GS/GOGAT-mediated nitrogen fixation pathway in cerambycids.<br><br>CONCLUSIONS: Our comprehensive analysis of gut microbial nitrogen metabolism might elucidate a set of mechanisms by which some xylophagous insects may overcome nutritional constraints in nitrogen-deficient niches, via evolutionarily optimized host-microbe metabolic interactions. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid41147939, year = {2025}, author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F}, title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.}, journal = {Food &amp; function}, volume = {16}, number = {22}, pages = {8846-8861}, doi = {10.1039/d5fo03604f}, pmid = {41147939}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Dextran Sulfate/adverse effects ; *Colitis/chemically induced/drug therapy/microbiology ; *Polyphenols/pharmacology/administration &amp; dosage/chemistry ; Mice ; Male ; Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; *Plant Extracts/pharmacology/chemistry/administration &amp; dosage ; Disease Models, Animal ; Cytokines/metabolism ; Humans ; }, abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.}, }
@article {pmid41148242, year = {2025}, author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R}, title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {72}, number = {4}, pages = {296-312}, doi = {10.1556/030.2025.02725}, pmid = {41148242}, issn = {1588-2640}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases/diagnosis/microbiology ; *Artificial Intelligence ; Machine Learning ; Dysbiosis ; }, abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.}, }
@article {pmid41148302, year = {2026}, author = {Hirayama, M and Maeda, T and Kashihara, K and Tsuboi, Y and Ito, M and Nishiwaki, H and Ohno, K and Ueyama, J}, title = {Linking diet, gut microbiota, and metabolites to Parkinson's disease risk: a shotgun metagenomic comparison of Japanese and Taiwanese cohorts.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {133}, number = {7}, pages = {1357-1368}, pmid = {41148302}, issn = {1435-1463}, support = {24K10657//Japan Society for the Promotion of Science/ ; 23H02794//Japan Society for the Promotion of Science/ ; 2022G025//Smoking Research Foundation/ ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Cohort Studies ; *Diet ; *Gastrointestinal Microbiome/genetics/physiology ; Japan/epidemiology ; Metagenomics ; *Parkinson Disease/metabolism/microbiology/epidemiology ; Taiwan/epidemiology ; East Asian People ; }, abstract = {Emerging evidence suggests that gut microbiota and its metabolites play pivotal roles in the pathogenesis of Parkinson's disease (PD). However, cross-national differences in diet and microbial composition may account for the striking variability in PD prevalence worldwide. To address this, we performed a comparative shotgun metagenomic analysis between Japanese and Taiwanese individuals, two genetically similar East Asian populations with distinct dietary habits and differing PD incidence rates. Our analysis revealed marked differences in dietary intake: Taiwanese individuals consumed higher amounts of animal fats and tropical fruits, whereas the Japanese diet was characterized by greater intake of seafood, root vegetables, and traditional fermented foods such as natto. These dietary patterns were reflected in gut microbiota profiles. Japanese individuals exhibited a higher abundance of Blautia, Faecalibacterium, and Bifidobacterium, while Taiwanese samples were enriched in Bacteroides and Alistipes. Functionally, genes involved in short-chain fatty acid (SCFA), vitamin, and polyamine biosynthesis were significantly reduced in PD patients and in the Taiwanese cohort. Metabolomic analyses corroborated these findings, showing decreased levels of SCFAs, polyamines, and key vitamins such as nicotinate and pantothenate in PD patients. Notably, Blautia abundance correlated positively with a broad range of beneficial metabolites, highlighting its potential role as a central modulator of host-microbe metabolic interactions. Our findings suggest that traditional Japanese dietary practices may shape a gut microbial environment that confers resistance to PD, underscoring the need for future interventional studies targeting diet-microbiota interactions in PD prevention and treatment.}, }
@article {pmid41148396, year = {2025}, author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q}, title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.}, journal = {International ophthalmology}, volume = {45}, number = {1}, pages = {447}, pmid = {41148396}, issn = {1573-2630}, support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical &amp; Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; }, abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.<br><br>METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n&#x2009;=&#x2009;5959), 233 blood metabolites (n&#x2009;=&#x2009;136,016), and RVO cases and controls from the FinnGen consortium (cases, n&#x2009;=&#x2009;775; controls, n&#x2009;=&#x2009;308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.<br><br>RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.<br><br>CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.}, }
@article {pmid41151484, year = {2025}, author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J}, title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.}, journal = {International immunopharmacology}, volume = {167}, number = {}, pages = {115730}, doi = {10.1016/j.intimp.2025.115730}, pmid = {41151484}, issn = {1878-1705}, mesh = {*Melatonin/pharmacology/therapeutic use ; *NF-kappa B/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bronchopulmonary Dysplasia/drug therapy/chemically induced/metabolism/pathology ; *Fatty Acids, Volatile/metabolism ; Mice ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Bleomycin ; Cell Line ; Lung/pathology/drug effects/metabolism ; Male ; }, abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).<br><br>METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-&#x3ba;B signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.<br><br>RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-&#x3ba;B pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-&#x3ba;B pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-&#x3ba;B activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-&#x3ba;B and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.<br><br>CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-&#x3ba;B pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.}, }
@article {pmid41151807, year = {2025}, author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M}, title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70112}, pmid = {41151807}, issn = {1758-2229}, support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; }, mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; }, abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.}, }
@article {pmid41152000, year = {2025}, author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, &#xc4; and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H}, title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70222}, pmid = {41152000}, issn = {1758-2229}, support = {2020-02710//Svenska Forskningsr&#xe5;det Formas/ ; 20-102//Svenskt Vatten/ ; }, mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.}, }
@article {pmid41152332, year = {2025}, author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L}, title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1702}, pmid = {41152332}, issn = {2052-4463}, support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; }, mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; }, abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.}, }
@article {pmid41152726, year = {2025}, author = {Zou, Y and Zou, Q and Wang, Y and Han, C}, title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {693}, pmid = {41152726}, issn = {1471-2180}, support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; China ; Feces/microbiology ; }, abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.<br><br>RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of &#x3b1;-galactosidase and &#x3b2;-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.<br><br>CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.}, }
@article {pmid41152727, year = {2025}, author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S}, title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {691}, pmid = {41152727}, issn = {1471-2180}, support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, mesh = {*Thyroid Cancer, Papillary/microbiology ; *Dysbiosis/complications ; *Thyroid Nodule/microbiology ; Humans ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification ; China ; Male ; Female ; Adult ; Middle Aged ; Phylogeny ; }, abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.<br><br>METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16&#xa0;S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.<br><br>RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.<br><br>CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.}, }
@article {pmid41155136, year = {2025}, author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T}, title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.}, journal = {International journal of molecular sciences}, volume = {26}, number = {20}, pages = {}, pmid = {41155136}, issn = {1422-0067}, support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; }, mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation &amp; purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; }, abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.}, }
@article {pmid41156563, year = {2025}, author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M}, title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {20}, pages = {}, pmid = {41156563}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; }, abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.}, }
@article {pmid41156596, year = {2025}, author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH}, title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {41156596}, issn = {2076-0817}, support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology, Vietnam/ ; }, mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; }, abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.}, }
@article {pmid41156619, year = {2025}, author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB}, title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {41156619}, issn = {2076-0817}, mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; }, abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.}, }
@article {pmid41157584, year = {2025}, author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS}, title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, pmid = {41157584}, issn = {1999-4915}, support = {202271250010//Parliamentary Amendment from the S&#xe3;o Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; }, mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; }, abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.}, }
@article {pmid41157605, year = {2025}, author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J}, title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, pmid = {41157605}, issn = {1999-4915}, support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; }, mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genotype ; Genetic Variation ; }, abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.}, }
@article {pmid41157620, year = {2025}, author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ}, title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, pmid = {41157620}, issn = {1999-4915}, support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; }, mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation &amp; purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; }, abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.}, }
@article {pmid41157632, year = {2025}, author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K}, title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.}, journal = {Viruses}, volume = {17}, number = {10}, pages = {}, pmid = {41157632}, issn = {1999-4915}, support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; }, mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; }, abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.}, }
@article {pmid41159034, year = {2025}, author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN}, title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1655428}, pmid = {41159034}, issn = {1664-3224}, mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.<br><br>METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.<br><br>RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.<br><br>DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.}, }
@article {pmid41159664, year = {2025}, author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E}, title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.}, journal = {Molecular nutrition &amp; food research}, volume = {69}, number = {24}, pages = {e70289}, pmid = {41159664}, issn = {1613-4133}, support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; }, mesh = {*Acrolein/metabolism/urine ; Humans ; *Glycerol/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; Male ; Adult ; Female ; Biomarkers/urine ; Diet ; Acetylcysteine/urine/analogs &amp; derivatives ; *Intestines/microbiology ; Middle Aged ; Young Adult ; }, abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.}, }
@article {pmid41160143, year = {2025}, author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM}, title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {12}, pages = {183}, pmid = {41160143}, issn = {1572-9699}, mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.}, }
@article {pmid41160250, year = {2025}, author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y}, title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.}, journal = {Clinical oral investigations}, volume = {29}, number = {11}, pages = {543}, pmid = {41160250}, issn = {1436-3771}, support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; }, mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; }, abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.<br><br>MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.<br><br>RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.<br><br>CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.<br><br>CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.<br><br>TRIAL REGISTRATION: ITMCTR2024000616.}, }
@article {pmid41161274, year = {2025}, author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W}, title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.}, journal = {Journal of environmental management}, volume = {395}, number = {}, pages = {127802}, doi = {10.1016/j.jenvman.2025.127802}, pmid = {41161274}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Carbon Cycle ; Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Microbiota ; }, abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.}, }
@article {pmid41161821, year = {2025}, author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L}, title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {10}, pages = {}, pmid = {41161821}, issn = {2051-1426}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; *Lung/microbiology ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Prospective Studies ; }, abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.<br><br>METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.<br><br>RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).<br><br>CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.}, }
@article {pmid41162178, year = {2025}, author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H}, title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506012}, pmid = {41162178}, issn = {1738-8872}, mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.}, }
@article {pmid41162595, year = {2025}, author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L}, title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37813}, pmid = {41162595}, issn = {2045-2322}, support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation &amp; purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; }, abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.}, }
@article {pmid41163171, year = {2025}, author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z}, title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {24}, number = {1}, pages = {59}, pmid = {41163171}, issn = {1476-0711}, support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&amp;D Program of the China Ministry of Science and Technology/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.<br><br>METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.<br><br>RESULTS: No significant differences were observed in age (62.22&#x2009;&#xb1;&#x2009;5.74 vs. 58.23&#x2009;&#xb1;&#x2009;7.55, p&#x2009;=&#x2009;0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p&#x2009;=&#x2009;0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p&#x2009;<&#x2009;0.05) and distinct beta diversity clustering (p&#x2009;<&#x2009;0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p&#x2009;<&#x2009;0.0001). Neutral modeling indicated stochastic assembly (R&#xb2; >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.<br><br>CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.}, }
@article {pmid41163226, year = {2025}, author = {Huang, S and Chen, Y and Lu, 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 Zhang, W}, title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {350}, pmid = {41163226}, issn = {1743-422X}, support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; }, mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.<br><br>RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n&#x2009;=&#x2009;1), Paramyxoviridae (n&#x2009;=&#x2009;1), Polyomaviridae (n&#x2009;=&#x2009;1), Parvoviridae (n&#x2009;=&#x2009;7), Circoviridae (n&#x2009;=&#x2009;6), and Genomoviridae (n&#x2009;=&#x2009;1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.<br><br>CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.}, }
@article {pmid41163852, year = {2025}, author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H}, title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660970}, pmid = {41163852}, issn = {2235-2988}, mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; }, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.<br><br>METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.<br><br>RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.<br><br>DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.}, }
@article {pmid41164876, year = {2025}, author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K}, title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {45}, number = {12}, pages = {e594-e607}, doi = {10.1161/ATVBAHA.125.322968}, pmid = {41164876}, issn = {1524-4636}, mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Plaque, Atherosclerotic ; *Carotid Artery Diseases/immunology/microbiology/diagnostic imaging/blood/genetics/epidemiology ; Biomarkers/blood ; Prospective Studies ; Aged ; China/epidemiology ; *Complement Pathway, Alternative/genetics ; *Inflammation Mediators/blood ; Mendelian Randomization Analysis ; Risk Factors ; Longitudinal Studies ; Complement C3 ; *Inflammation/blood ; }, abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.<br><br>METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age&#xb1;SD, 57.75&#xb1;5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3&#xd7;. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.<br><br>RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (complement C3; odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.<br><br>CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.}, }
@article {pmid41164885, year = {2025}, author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T}, title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {10}, pages = {e70844}, pmid = {41164885}, issn = {1552-5279}, support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Gen&#xe8;ve/ ; //Fondation Segr&#xe9;, Gen&#xe8;ve/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Gen&#xe8;ve/ ; //Fondation Edmond J. Safra, Gen&#xe8;ve/ ; //Fondation Minkoff, Gen&#xe8;ve/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et Ren&#xe9; Keller, Gen&#xe8;ve/ ; //Fondation AETAS, Gen&#xe8;ve/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //H&#xf4;pitaux Universitaires de Gen&#xe8;ve/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; }, abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.<br><br>METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.<br><br>RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from&#xa0;<&#xa0;2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.<br><br>DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.<br><br>HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.}, }
@article {pmid41165913, year = {2025}, author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM}, title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {11}, pages = {1268}, pmid = {41165913}, issn = {1573-2959}, mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; }, abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.}, }
@article {pmid41166145, year = {2026}, author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K}, title = {A Multiomics Analysis Reveals a Gut Microbiome: LPC Metabolic Axis Driving Postoperative Inflammation in Cardiopulmonary Bypass Patients.}, journal = {Shock (Augusta, Ga.)}, volume = {65}, number = {2}, pages = {188-200}, doi = {10.1097/SHK.0000000000002722}, pmid = {41166145}, issn = {1540-0514}, support = {2023YFA1800900//the National Key R&amp;D Program of China/ ; 2018YFC0910502//the National Key R&amp;D Program of China/ ; 32071465//the National Natural Science Foundation of China/ ; 31871334//the National Natural Science Foundation of China/ ; 31671374//the National Natural Science Foundation of China/ ; 2022-PUMCH-B-115//National High-Level Hospital Clinical Research Founding/ ; 2022-PUMCH-D-005//National High-Level Hospital Clinical Research Founding/ ; 2023&#xe2;&#x20ac;I2M&#xe2;&#x20ac;2&#xe2;&#x20ac;002//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Cardiopulmonary Bypass/adverse effects ; Middle Aged ; Aged ; *Inflammation/metabolism/etiology ; *Postoperative Complications/metabolism/microbiology ; *Lysophosphatidylcholines/metabolism ; Metabolomics ; Metabolome ; Multiomics ; }, abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.<br><br>METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamic pattern of these microbiota and metabolites, as well as their associations with the postoperative risks. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.<br><br>RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50 e-10), and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influences the postoperative risk. The predictive model for intensive care unit stay duration achieved a mean absolute error of 1.27 days and an R&#xb2; of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.<br><br>CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating noninfectious inflammatory responses and host imbalance, offering a multiomics framework for decoding systemic complications beyond classical sepsis paradigms.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates .}, }
@article {pmid41167188, year = {2025}, author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I}, title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {11}, pages = {1977-1994.e8}, doi = {10.1016/j.chom.2025.10.001}, pmid = {41167188}, issn = {1934-6069}, mesh = {Humans ; *Mouth/microbiology ; *Phylogeny ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Periodontitis/microbiology ; Metagenome ; Genomics ; Gastrointestinal Microbiome/genetics ; }, abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.}, }
@article {pmid41168291, year = {2025}, author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM}, title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37987}, pmid = {41168291}, issn = {2045-2322}, mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; }, abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.}, }
@article {pmid41168431, year = {2025}, author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ}, title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2720-2735}, pmid = {41168431}, issn = {2058-5276}, support = {R01 DK101354/DK/NIDDK NIH HHS/United States ; DK120485//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 HL141053/HL/NHLBI NIH HHS/United States ; R01 HL138646/HL/NHLBI NIH HHS/United States ; R01 DK120485/DK/NIDDK NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; R21 HL124712/HL/NHLBI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Uganda ; Alkynes ; Metagenomics ; Benzoxazines/therapeutic use/adverse effects ; Male ; Female ; Feces/microbiology ; Cyclopropanes ; Adult ; Botswana ; *Anti-Retroviral Agents/therapeutic use ; Middle Aged ; United States ; Reverse Transcriptase Inhibitors/therapeutic use ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; }, abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.}, }
@article {pmid41168432, year = {2025}, author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, &#xc2; and Castrillo, G and Wagner, MR}, title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.}, journal = {Nature microbiology}, volume = {10}, number = {11}, pages = {2823-2844}, pmid = {41168432}, issn = {2058-5276}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; IOS-2016351//National Science Foundation (NSF)/ ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; UL1 TR002366/TR/NCATS NIH HHS/United States ; P30 GM145499/GM/NIGMS NIH HHS/United States ; }, mesh = {*Droughts ; *Soil Microbiology ; *Microbiota/genetics ; Zea mays/physiology/genetics/microbiology ; Soil/chemistry ; *Rain ; Kansas ; Plant Roots/microbiology/genetics ; Stress, Physiological ; Metagenome ; Adaptation, Physiological ; Water/metabolism ; *Plants/microbiology/genetics ; Bacteria/classification/genetics ; }, abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.}, }
@article {pmid41168702, year = {2025}, author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML}, title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.}, journal = {Genetics, selection, evolution : GSE}, volume = {57}, number = {1}, pages = {64}, pmid = {41168702}, issn = {1297-9686}, support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.<br><br>RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.<br><br>CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.}, }
@article {pmid41168882, year = {2025}, author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC}, title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {222}, pmid = {41168882}, issn = {2049-2618}, support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//DOE/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; }, abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.}, }
@article {pmid41171125, year = {2026}, author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P}, title = {Metalog: curated and harmonised contextual data for global metagenomics samples.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D826-D834}, pmid = {41171125}, issn = {1362-4962}, support = {668031//Horizon 2020/ ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; ERC-AdG-669830/ERC_/European Research Council/International ; }, mesh = {*Metagenomics/methods ; Animals ; Humans ; *Databases, Genetic ; Metadata ; Metagenome ; Data Curation ; Gastrointestinal Microbiome/genetics ; }, abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.}, }
@article {pmid41172852, year = {2025}, author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S}, title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140283}, doi = {10.1016/j.jhazmat.2025.140283}, pmid = {41172852}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Female ; *Animal Feed ; Rumen/microbiology ; Feces/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.}, }
@article {pmid41173568, year = {2025}, author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I}, title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.}, journal = {Endocrinologia, diabetes y nutricion}, volume = {72}, number = {9}, pages = {501624}, doi = {10.1016/j.endien.2025.501624}, pmid = {41173568}, issn = {2530-0180}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; }, abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.}, }
@article {pmid41173905, year = {2025}, author = {Adhikary, R and Alkhatib, AEA and Hazra, S}, title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38127}, pmid = {41173905}, issn = {2045-2322}, mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; }, abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.}, }
@article {pmid41173910, year = {2025}, author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW}, title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9658}, pmid = {41173910}, issn = {2041-1723}, support = {R01 NS055349/NS/NINDS NIH HHS/United States ; T32 GM148382/GM/NIGMS NIH HHS/United States ; D43 TW010928/TW/FIC NIH HHS/United States ; T32GM148382//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 AI148525/AI/NIAID NIH HHS/United States ; R01NS055349//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; TL1 TR002531/TR/NCATS NIH HHS/United States ; }, mesh = {*Dysbiosis/complications/immunology/microbiology/mortality ; Patient Discharge ; *Gastrointestinal Microbiome/genetics/immunology ; Severity of Illness Index ; Enterobacteriaceae/genetics/immunology/isolation &amp; purification ; Escherichia coli/genetics/immunology/isolation &amp; purification ; Metagenome ; Feces/microbiology ; Host Microbial Interactions/immunology ; Follow-Up Studies ; Uganda/epidemiology ; Malawi/epidemiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/isolation &amp; purification ; Humans ; Male ; Female ; Infant ; Child, Preschool ; Child ; Plasmodium falciparum/immunology/pathogenicity ; *Malaria, Falciparum/complications/diagnosis/immunology/mortality ; Case-Control Studies ; }, abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.}, }
@article {pmid41174397, year = {2025}, author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C}, title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117319}, doi = {10.1016/j.foodres.2025.117319}, pmid = {41174397}, issn = {1873-7145}, mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; }, abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.}, }
@article {pmid41174459, year = {2025}, author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C}, title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 2}, pages = {117386}, doi = {10.1016/j.foodres.2025.117386}, pmid = {41174459}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.}, }
@article {pmid41174518, year = {2025}, author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B}, title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {704}, pmid = {41174518}, issn = {1471-2180}, mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; }, abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.<br><br>RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.<br><br>CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.}, }
@article {pmid41174528, year = {2025}, author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S}, title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {703}, pmid = {41174528}, issn = {1471-2180}, mesh = {Animals ; *Buffaloes/microbiology ; *Milk/microbiology ; Female ; *Microbiota/genetics ; *Mastitis/microbiology/veterinary ; *Acinetobacter/genetics/isolation &amp; purification/classification ; DNA, Bacterial/genetics ; Phylogeny ; Bacteria/classification/genetics/isolation &amp; purification ; Proteobacteria/genetics/isolation &amp; purification/classification ; Metagenome ; }, abstract = {Mastitis has been a major challenge in dairy industry incurring heavy loss to dairy farmers. Although targeted antibiotic regime is successful for culturable microbes, the non-culturable and novel microbes are often overlooked. Hence, the present study employed a whole-metagenome profiling to investigate and compare the microbial diversity among the milk samples of healthy and affected buffaloes. 16 Milk samples were collected from Murrah buffaloes and classified into three groups based on the somatic cell count and California Mastitis Test score, i.e., Clinical (3), Sub-clinical (6), and Healthy (7). DNA extraction from milk was followed by Whole Meta-Genome Shotgun (WGS) sequencing to study microbial diversity. The study revealed that Proteobacteria as the most abundant phylum in the clinical mastitis cases, which could be related to the severity of the disease, whereas Firmicutes were strongly associated with the healthy group of buffaloes. The genus Acinetobacter was most abundant in clinical cases (79%) and least in healthy animals (33%). The present study provides important insights into the microbial population and composition in the milk of mastitis-affected buffaloes. The findings will aid in investigating potential therapeutic ways for reducing antibiotic resistance and treatment costs.}, }
@article {pmid41174950, year = {2025}, author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, M&#xc0; and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G}, title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {12}, pages = {e70418}, pmid = {41174950}, issn = {1478-3231}, support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; }, mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; }, abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.}, }
@article {pmid41175161, year = {2025}, author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV}, title = {Gellan gum-based media recover more diverse microbial communities from soil material.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {338}, pmid = {41175161}, issn = {1432-072X}, support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation &amp; purification/classification/genetics/growth &amp; development ; *Microbiota ; }, abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.}, }
@article {pmid41175752, year = {2025}, author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H}, title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140318}, doi = {10.1016/j.jhazmat.2025.140318}, pmid = {41175752}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Heterocyclic Compounds/toxicity ; *Soil Pollutants/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Virulence Factors/genetics ; }, abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.}, }
@article {pmid41176044, year = {2025}, author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and D'arc, M and Bueno, MG}, title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.}, journal = {Acta tropica}, volume = {272}, number = {}, pages = {107894}, doi = {10.1016/j.actatropica.2025.107894}, pmid = {41176044}, issn = {1873-6254}, mesh = {Animals ; Brazil ; *Feces/virology ; *Forests ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Sigmodontinae/virology ; Zoonoses/virology ; }, abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20 %, 40 %, and 60 %) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.}, }
@article {pmid41177025, year = {2025}, author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S}, title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.}, journal = {Journal of hazardous materials}, volume = {499}, number = {}, pages = {140254}, doi = {10.1016/j.jhazmat.2025.140254}, pmid = {41177025}, issn = {1873-3336}, mesh = {Animals ; *Benzhydryl Compounds/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Phenols/toxicity ; Mice ; Male ; *Cognition/drug effects ; Brain/drug effects/metabolism ; Maze Learning/drug effects ; *Cognitive Dysfunction/chemically induced ; Behavior, Animal/drug effects ; Dysbiosis ; Bisphenol A Compounds ; }, abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.}, }
@article {pmid41177609, year = {2026}, author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W}, title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.}, journal = {Journal of environmental sciences (China)}, volume = {160}, number = {}, pages = {300-307}, doi = {10.1016/j.jes.2025.04.024}, pmid = {41177609}, issn = {1001-0742}, mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; }, abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.}, }
@article {pmid41181319, year = {2025}, author = {Wang, Z and Song, L and Li, D and Jin, Y}, title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1693796}, pmid = {41181319}, issn = {2235-2988}, mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; }, abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.}, }
@article {pmid41181328, year = {2025}, author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS}, title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1660939}, pmid = {41181328}, issn = {2235-2988}, mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation &amp; purification ; Haemophilus influenzae/isolation &amp; purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Infant ; }, abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.<br><br>METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.<br><br>RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.<br><br>DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.}, }
@article {pmid41182235, year = {2025}, author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E}, title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41182235}, issn = {1751-7370}, support = {12T5622N//FWO/ ; G092619N//FWO/ ; }, mesh = {*Daphnia/microbiology/genetics/physiology ; Animals ; *Epigenesis, Genetic ; *Cyanobacteria/physiology ; DNA Methylation ; *Host Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Stress, Physiological ; Daphnia magna ; }, abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or nontoxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed nontoxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on nontoxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.}, }
@article {pmid41182689, year = {2025}, author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ}, title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {21}, pages = {e71207}, pmid = {41182689}, issn = {1530-6860}, mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; }, abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.}, }
@article {pmid41183096, year = {2025}, author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ}, title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.}, journal = {PLoS pathogens}, volume = {21}, number = {11}, pages = {e1013667}, pmid = {41183096}, issn = {1553-7374}, support = {//National Natural Science Foundation of China/ ; //Inter-governmental International Science &amp; Technology Innovation Cooperation/ ; //Guangzhou Science and Technology Plan and the Greater Bay Area Institute of Precision Medicine (Guangzhou)/ ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/virology/immunology ; Immunocompromised Host ; Aged ; Bacteria/isolation &amp; purification/genetics ; Microbiota ; Coinfection/microbiology ; Lung/microbiology/virology ; }, abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.}, }
@article {pmid41183305, year = {2025}, author = {Yang, R and Ma, J and Abebe, H and Tu, Y}, title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {45}, pages = {28711-28723}, doi = {10.1021/acs.jafc.5c08498}, pmid = {41183305}, issn = {1520-5118}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Salinity ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Sodium Chloride/analysis/metabolism ; Sodium/analysis/metabolism ; }, abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.}, }
@article {pmid41183487, year = {2025}, author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y}, title = {Lactobacillus gasseri TF08-1 ameliorates high-fat diet induced nonalcoholic fatty liver disease and regulates gut microbiota in mice.}, journal = {Journal of applied microbiology}, volume = {136}, number = {12}, pages = {}, doi = {10.1093/jambio/lxaf271}, pmid = {41183487}, issn = {1365-2672}, support = {32100009//National Natural Science Foundation of China/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; }, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/therapy/microbiology/etiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Mice ; *Probiotics/administration &amp; dosage ; *Lactobacillus gasseri/genetics/physiology ; Male ; Lipid Metabolism/genetics ; Mice, Inbred C57BL ; Liver/metabolism ; Triglycerides/blood ; Genome, Bacterial ; }, abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.<br><br>METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing L. gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-&#x3b1; level decreased by 42.91%. Meanwhile, the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered proinflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.<br><br>CONCLUSIONS: Lactobacillu gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.}, }
@article {pmid41183495, year = {2025}, author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC}, title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish sauce.}, journal = {Letters in applied microbiology}, volume = {78}, number = {11}, pages = {}, doi = {10.1093/lambio/ovaf128}, pmid = {41183495}, issn = {1472-765X}, support = {112-2313-B-020-017-MY3//National Science and Technology Council of Taiwan/ ; NPUST-KMU-111-P009//National Pingtung University of Science and Technology/ ; }, mesh = {*Biogenic Amines/metabolism/analysis ; Fermentation ; *Enterococcaceae/metabolism/isolation &amp; purification/genetics/classification ; *Fish Products/microbiology/analysis ; *Microbiota ; Animals ; *Fermented Foods/microbiology ; Food Microbiology ; Fishes ; Cadaverine/analysis/metabolism ; }, abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/l) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.}, }
@article {pmid41185061, year = {2025}, author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , }, title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {225}, pmid = {41185061}, issn = {2049-2618}, support = {UL1 TR001427/TR/NCATS NIH HHS/United States ; OPP11755487//Bill and Melinda Gates Foundation/ ; UL1 TR000064/TR/NCATS NIH HHS/United States ; AID-OAA-L-15&#x2013;00003//USAID/ ; }, mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation &amp; purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; }, abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.<br><br>METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.<br><br>RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types&#xa0;and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r&#x2009;=&#x2009;0.76), siblings (r&#x2009;=&#x2009;0.61) and infants (r&#x2009;=&#x2009;0.54), while co-occurrence analysis found a higher likelihood (Pr&#x2009;>&#x2009;0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.<br><br>CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.}, }
@article {pmid41185305, year = {2025}, author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T}, title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117551}, doi = {10.1016/j.foodres.2025.117551}, pmid = {41185305}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; }, abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.}, }
@article {pmid41185359, year = {2025}, author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y}, title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 4}, pages = {117622}, doi = {10.1016/j.foodres.2025.117622}, pmid = {41185359}, issn = {1873-7145}, mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; }, abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.}, }
@article {pmid41186205, year = {2025}, author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W}, title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {94}, number = {5}, pages = {e70178}, doi = {10.1111/aji.70178}, pmid = {41186205}, issn = {1600-0897}, support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; }, abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.<br><br>OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.<br><br>RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.<br><br>CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.}, }
@article {pmid41186403, year = {2025}, author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M}, title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {12}, pages = {e0154725}, pmid = {41186403}, issn = {1098-5336}, support = {20229LEB99//Ministero della Ricerca e dell'Universit&#xe0;/ ; GR-2018-12365988//Italian Ministry of Health/ ; }, mesh = {*Streptococcus thermophilus/physiology/genetics/metabolism ; *Lactococcus lactis/physiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome ; *Adaptation, Physiological ; *Host Microbial Interactions ; Adult ; Gastrointestinal Tract/microbiology ; }, abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.<br><br>IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.}, }
@article {pmid41187758, year = {2025}, author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and ,  and König, B and Sauer, U and Stelling, J and Macpherson, AJ}, title = {A global survey of taxa-metabolic associations across mouse microbiome communities.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {11}, pages = {1960-1976.e10}, doi = {10.1016/j.chom.2025.10.010}, pmid = {41187758}, issn = {1934-6069}, mesh = {Animals ; Mice/microbiology ; *Microbiota/physiology ; Metabolomics ; *Bacteria/classification/metabolism/genetics ; Host Microbial Interactions ; Symbiosis ; }, abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.}, }
@article {pmid41188324, year = {2025}, author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI}, title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38611}, pmid = {41188324}, issn = {2045-2322}, support = {R37 CA249007/CA/NCI NIH HHS/United States ; R37CA249007/CA/NCI NIH HHS/United States ; NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; }, mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; }, abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.}, }
@article {pmid41188334, year = {2025}, author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T}, title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {38587}, pmid = {41188334}, issn = {2045-2322}, mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; }, abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.}, }
@article {pmid41188618, year = {2025}, author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S}, title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {12}, pages = {1295}, pmid = {41188618}, issn = {1573-2959}, support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; }, mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; }, abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.}, }
@article {pmid41188680, year = {2025}, author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA}, title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).}, journal = {Environmental geochemistry and health}, volume = {47}, number = {12}, pages = {547}, pmid = {41188680}, issn = {1573-2983}, support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; }, mesh = {*Geologic Sediments/microbiology ; *Biofilms ; Mining ; *Microbiota ; Metagenomics ; *Water Microbiology ; Western Australia ; Water Pollutants, Chemical/analysis ; Zinc/analysis ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.}, }
@article {pmid41189709, year = {2025}, author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J}, title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1619059}, pmid = {41189709}, issn = {2235-2988}, mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation &amp; purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; }, abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.<br><br>METHODS: We recruited 91 participants, including 31 treatment-na&#xef;ve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.<br><br>RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in &#x3b1;-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.<br><br>DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.}, }
@article {pmid41192043, year = {2026}, author = {Kumar, A and Xu, C and Dakal, TC}, title = {Microbiome based precision medicine through integrated multiomics and machine learning.}, journal = {Microbiological research}, volume = {303}, number = {}, pages = {128384}, doi = {10.1016/j.micres.2025.128384}, pmid = {41192043}, issn = {1618-0623}, mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metabolomics/methods ; Proteomics/methods ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Multiomics ; }, abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.}, }
@article {pmid41192168, year = {2025}, author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA}, title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.}, journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)}, volume = {92}, number = {}, pages = {127787}, doi = {10.1016/j.jtemb.2025.127787}, pmid = {41192168}, issn = {1878-3252}, mesh = {Humans ; *Arthritis, Rheumatoid/blood/microbiology/pathology ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Trace Elements/blood ; *Minerals/blood ; *Cartilage/pathology ; *Gastrointestinal Microbiome ; Adult ; Aged ; }, abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).<br><br>MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.<br><br>RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.<br><br>CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.}, }
@article {pmid41192179, year = {2025}, author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC}, title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140319}, doi = {10.1016/j.jhazmat.2025.140319}, pmid = {41192179}, issn = {1873-3336}, mesh = {*Diethylhexyl Phthalate/toxicity/metabolism ; Biodegradation, Environmental ; *Plasticizers/toxicity/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; *Water Pollutants, Chemical/metabolism/toxicity ; Anaerobiosis ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; }, abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.}, }
@article {pmid41192191, year = {2026}, author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB}, title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {57}, number = {}, pages = {101666}, doi = {10.1016/j.cbd.2025.101666}, pmid = {41192191}, issn = {1878-0407}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Metabolomics ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/classification/metabolism ; Anti-Bacterial Agents/pharmacology ; *Fishes/microbiology/metabolism ; Metagenome ; }, abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.}, }
@article {pmid41192424, year = {2025}, author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z}, title = {Assessment of enzyme diversity in the fermented food microbiome.}, journal = {Cell systems}, volume = {16}, number = {11}, pages = {101430}, doi = {10.1016/j.cels.2025.101430}, pmid = {41192424}, issn = {2405-4720}, mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Fermentation ; Food Microbiology/methods ; Metagenome/genetics ; Machine Learning ; *Enzymes/genetics/metabolism ; }, abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41193635, year = {2025}, author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R}, title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.}, journal = {Nature microbiology}, volume = {10}, number = {12}, pages = {3245-3257}, pmid = {41193635}, issn = {2058-5276}, support = {991222//Simons Foundation/ ; }, mesh = {*Seawater/virology ; *Genome, Viral ; *Genomics/methods ; Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.}, }
@article {pmid41193697, year = {2026}, author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA}, title = {Gut virome dynamics: from commensal to critical player in health and disease.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {23}, number = {2}, pages = {126-144}, pmid = {41193697}, issn = {1759-5053}, support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Virome/physiology ; *Gastrointestinal Microbiome/physiology ; Bacteriophages ; }, abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.}, }
@article {pmid41194562, year = {2025}, author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A}, title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.}, journal = {Environmental microbiology}, volume = {27}, number = {11}, pages = {e70199}, pmid = {41194562}, issn = {1462-2920}, support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Archaea/genetics/metabolism/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.}, }
@article {pmid41195309, year = {2025}, author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F}, title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.}, journal = {Pediatric diabetes}, volume = {2025}, number = {}, pages = {3013063}, pmid = {41195309}, issn = {1399-5448}, mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; }, abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.<br><br>METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included &#x3b1;/&#x3b2;-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.<br><br>RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2]&#x2009;=&#x2009;0.0562, p=0.003 and R [2]&#x2009;=&#x2009;0.0343, p=0.003). HLA-C [&#x2217;] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2]&#x2009;=&#x2009;0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2]&#x2009;=&#x2009;0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [&#x2217;] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19&#x2009;&#xb1;&#x2009;0.14 vs. 0.26&#x2009;&#xb1;&#x2009;0.19&#x2009;&#xb5;g/mL, p=0.029).<br><br>CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [&#x2217;] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.}, }
@article {pmid41196050, year = {2025}, author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N}, title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0095425}, pmid = {41196050}, issn = {2379-5077}, support = {RS-2023-NR077149//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Coronary Artery Disease/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; Female ; Male ; Middle Aged ; *Metabolic Networks and Pathways/genetics ; Aged ; *Bacteria/genetics/classification/metabolism ; Feces/microbiology ; Case-Control Studies ; Metagenomics/methods ; }, abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.}, }
@article {pmid41196055, year = {2025}, author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S}, title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.}, journal = {Microbiology spectrum}, volume = {13}, number = {12}, pages = {e0173225}, pmid = {41196055}, issn = {2165-0497}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; *Skin/microbiology/virology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Viruses/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Forehead/microbiology ; Adult ; DNA, Bacterial/genetics ; Male ; Sequence Analysis, DNA ; Female ; Skin Microbiome ; }, abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.}, }
@article {pmid41196057, year = {2025}, author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU}, title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.}, journal = {Microbiology spectrum}, volume = {13}, number = {12}, pages = {e0094425}, pmid = {41196057}, issn = {2165-0497}, mesh = {Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/microbiology/drug therapy/diagnosis ; *Gastrointestinal Microbiome/drug effects ; *Machine Learning ; Male ; Female ; Aged ; Middle Aged ; Denmark ; Aged, 80 and over ; Adult ; Anti-Bacterial Agents/therapeutic use ; Cohort Studies ; Metagenomics ; }, abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.}, }
@article {pmid41196658, year = {2026}, author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F}, title = {A missense mutation in Muc2 promotes gut microbiome and metabolome-dependent colitis-associated tumorigenesis.}, journal = {The Journal of clinical investigation}, volume = {136}, number = {1}, pages = {}, pmid = {41196658}, issn = {1558-8238}, support = {P30 DK097948/DK/NIDDK NIH HHS/United States ; R37 DK042191/DK/NIDDK NIH HHS/United States ; R56 DK042191/DK/NIDDK NIH HHS/United States ; R01 DK042191/DK/NIDDK NIH HHS/United States ; R56 DK055812/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Mutation, Missense ; Mice ; *Mucin-2/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metabolome ; *Colitis-Associated Neoplasms/genetics/microbiology/metabolism/pathology ; *Colitis, Ulcerative/genetics/microbiology/metabolism/pathology ; *Colitis/genetics/microbiology/metabolism/pathology ; *Carcinogenesis/genetics/metabolism ; Fecal Microbiota Transplantation ; Humans ; Disease Models, Animal ; Female ; }, abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, an ulcerative colitis-like (UC-like) model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie mice showed only mild colitis but no tumorigenesis. By comparison, when re-derived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct proinflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Using either SPF Winnie or WT (Bl/6) donors, fecal microbiota transplantation (FMT) into GF Winnie recipients demonstrated that, while colitis developed regardless of the donor, only FM from SPF Winnie donors resulted in CAC in recipient mice. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thus challenging the concept of colon cancer as a strictly nontransmissible disease.}, }
@article {pmid41197330, year = {2025}, author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE}, title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.}, journal = {Nutrition research (New York, N.Y.)}, volume = {144}, number = {}, pages = {1-15}, doi = {10.1016/j.nutres.2025.10.004}, pmid = {41197330}, issn = {1879-0739}, mesh = {Animals ; Female ; *Probiotics/pharmacology/therapeutic use ; Pregnancy ; *Hypertension ; *Pre-Eclampsia ; Rats ; *Fatty Acids/blood/metabolism ; *Cultured Milk Products ; Gastrointestinal Microbiome ; Blood Pressure/drug effects ; Rats, Sprague-Dawley ; Fermentation ; Esters ; *Milk ; Disease Models, Animal ; Antihypertensive Agents ; }, abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.}, }
@article {pmid41197508, year = {2025}, author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P}, title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140363}, doi = {10.1016/j.jhazmat.2025.140363}, pmid = {41197508}, issn = {1873-3336}, mesh = {*Water Purification ; Biofilms/drug effects ; Bioreactors/microbiology ; *Amoxicillin/pharmacology ; *Bacterial Proteins/biosynthesis ; *Drug Resistance, Bacterial/genetics ; Water Pollutants/isolation &amp; purification ; *Microbial Consortia/drug effects ; Cyanobacteria/drug effects ; *Metagenome/drug effects ; Gene Transfer, Horizontal ; }, abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.}, }
@article {pmid41197616, year = {2025}, author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X}, title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.}, journal = {Cell reports. Medicine}, volume = {6}, number = {11}, pages = {102431}, pmid = {41197616}, issn = {2666-3791}, mesh = {Humans ; *Microbiota/genetics ; *Oral Health ; *Esophageal Squamous Cell Carcinoma/microbiology ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Risk Factors ; *Mouth/microbiology ; Aged ; Saliva/microbiology ; Bacteria/genetics/classification ; }, abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.}, }
@article {pmid41197619, year = {2025}, author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM}, title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.}, journal = {Cell reports methods}, volume = {5}, number = {11}, pages = {101218}, pmid = {41197619}, issn = {2667-2375}, mesh = {Humans ; *Metagenomics/methods ; *Benchmarking/methods ; Microbiota/genetics ; Genome, Human/genetics ; *Viruses/genetics ; Polymorphism, Single Nucleotide/genetics ; Metagenome ; }, abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.}, }
@article {pmid41197631, year = {2026}, author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL}, title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.}, journal = {Cell metabolism}, volume = {38}, number = {1}, pages = {157-173.e9}, pmid = {41197631}, issn = {1932-7420}, support = {F30 DK127846/DK/NIDDK NIH HHS/United States ; U01 AT012990/AT/NCCIH NIH HHS/United States ; R01 AI181021/AI/NIAID NIH HHS/United States ; R01 DK124317/DK/NIDDK NIH HHS/United States ; R01 DK124336/DK/NIDDK NIH HHS/United States ; F32 CA243501/CA/NCI NIH HHS/United States ; R01 AT011423/AT/NCCIH NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; Diet, High-Fat/adverse effects ; Obesity/metabolism/microbiology ; *Dietary Fats/metabolism ; *Lipid Metabolism ; Mice, Inbred C57BL ; Male ; Ceramides/metabolism ; Gastrointestinal Microbiome ; Lipids ; }, abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.}, }
@article {pmid41198823, year = {2025}, author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, &#xd3;}, title = {The association of the rumen virome with methane emissions in dairy cattle.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1534}, pmid = {41198823}, issn = {2399-3642}, mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; }, abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.}, }
@article {pmid41199348, year = {2025}, author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N}, title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {227}, pmid = {41199348}, issn = {2049-2618}, mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; }, abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.<br><br>RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3&#xa0;min for taxonomic analysis and 10&#xa0;min for strain-level analysis against the human microbial gene catalogue when processing 10&#xa0;M paired reads - operating within a modest 5&#xa0;GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.<br><br>CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.}, }
@article {pmid41201223, year = {2025}, author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q}, title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {5}, pages = {37069}, doi = {10.31083/IJVNR37069}, pmid = {41201223}, issn = {0300-9831}, support = {2019YFF0301702//National Key R&amp;D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration &amp; dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; }, abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.<br><br>METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.<br><br>RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 &#xb1; 0.76 kg; LDG: -2.40 &#xb1; 0.67 kg), body fat percentage (HDG: -1.87 &#xb1; 0.69; LDG: -1.49 &#xb1; 0.45), cortisol (HDG: -6.79 &#xb1; 4.26 &#x3bc;g/dL; LDG: -4.5 &#xb1; 4.84 &#x3bc;g/dL), maximum power (HDG: 27.16 &#xb1; 9.77 W; LDG: 14.50 &#xb1; 9.43 W), maximal oxygen uptake (HDG: 8.78 &#xb1; 0.97; LDG: 6.90 &#xb1; 1.37), and half-court triangle run times (HDG: -0.48 &#xb1; 0.36 s; LDG: -0.25 &#xb1; 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 &#xb1; 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.<br><br>CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.}, }
@article {pmid41201496, year = {2026}, author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C}, title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.}, journal = {Journal of advanced research}, volume = {85}, number = {}, pages = {137-154}, pmid = {41201496}, issn = {2090-1224}, mesh = {Animals ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; *Diabetic Retinopathy/drug therapy/metabolism ; Rats ; Proto-Oncogene Proteins c-akt/metabolism ; *Plant Extracts/pharmacology ; *Pomegranate/chemistry ; Vascular Endothelial Growth Factor A/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; *Gastrointestinal Microbiome/drug effects ; Signal Transduction/drug effects ; Male ; Diabetes Mellitus, Experimental/metabolism/complications ; Oxidative Stress/drug effects ; Humans ; Rats, Sprague-Dawley ; Cell Line ; Reactive Oxygen Species/metabolism ; }, abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.<br><br>OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.<br><br>METHODS: PPE was extracted using 50&#xa0;% ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.<br><br>RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.<br><br>CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1&#x3b1;/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.}, }
@article {pmid41201733, year = {2026}, author = {Saleh, RM and Hassan, OM}, title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.}, journal = {Infection}, volume = {54}, number = {1}, pages = {111-126}, pmid = {41201733}, issn = {1439-0973}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Coinfection/microbiology/diagnosis ; *Microbiota ; *Precision Medicine/methods ; }, abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.}, }
@article {pmid41201920, year = {2025}, author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ}, title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.}, journal = {Neoplasia (New York, N.Y.)}, volume = {70}, number = {}, pages = {101245}, pmid = {41201920}, issn = {1476-5586}, support = {P30 CA014089/CA/NCI NIH HHS/United States ; R01 AG069698/AG/NIA NIH HHS/United States ; }, mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; }, abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.}, }
@article {pmid41203618, year = {2025}, author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M}, title = {Development of the preterm infant gut and gastric residuals microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9848}, pmid = {41203618}, issn = {2041-1723}, mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; }, abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.}, }
@article {pmid41204634, year = {2025}, author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q}, title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.}, journal = {Journal of food science}, volume = {90}, number = {11}, pages = {e70654}, doi = {10.1111/1750-3841.70654}, pmid = {41204634}, issn = {1750-3841}, support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactiplantibacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; }, abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.}, }
@article {pmid41205292, year = {2026}, author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA}, title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118904}, doi = {10.1016/j.marpolbul.2025.118904}, pmid = {41205292}, issn = {1879-3363}, mesh = {*Petroleum Pollution ; *Geologic Sediments/microbiology/chemistry ; *Bacteria ; Biodegradation, Environmental ; *Water Pollutants, Chemical/analysis ; *Ecosystem ; Petroleum ; Environmental Monitoring ; Hydrocarbons/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; *Microbiota ; }, abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.}, }
@article {pmid41205408, year = {2026}, author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J}, title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.}, journal = {Journal of neuroradiology = Journal de neuroradiologie}, volume = {53}, number = {1}, pages = {101402}, doi = {10.1016/j.neurad.2025.101402}, pmid = {41205408}, issn = {0150-9861}, mesh = {Humans ; *Colitis, Ulcerative/diagnostic imaging/physiopathology/microbiology/complications ; Male ; Female ; Adult ; Middle Aged ; *Glymphatic System/diagnostic imaging/physiopathology ; Biomarkers ; Gastrointestinal Microbiome ; *Diffusion Magnetic Resonance Imaging/methods ; Case-Control Studies ; *Diffusion Tensor Imaging/methods ; }, abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.<br><br>MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.<br><br>RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (&#x3b2; =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (&#x3b2; =-0.003), CRP (&#x3b2; =-0.035), SII (&#x3b2; =-0.062), INFLA (&#x3b2; =-0.010), and SIRI (&#x3b2; =-0.058). We also observed significant correlations between DKI ALPS index and ESR (&#x3b2; =-0.006), CRP (&#x3b2; =-0.051), SII (&#x3b2; =-0.130), INFLA (&#x3b2; =-0.017), SIRI (&#x3b2; =-0.095), IL-6 (&#x3b2; =-0.081) and NLR (&#x3b2; =-0.108).<br><br>CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.}, }
@article {pmid41206461, year = {2025}, author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H}, title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {32}, number = {6}, pages = {}, pmid = {41206461}, issn = {1756-1663}, support = {//Government of/ ; JPJ009237//Japan/ ; //Bio-oriented Technology Research Advancement Institution/ ; }, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; *Bacteria/genetics/classification ; Metagenome ; *Genomics/methods ; Single-Cell Analysis/methods ; Genome, Bacterial ; }, abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.}, }
@article {pmid41207298, year = {2026}, author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J}, title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D763-D775}, pmid = {41207298}, issn = {1362-4962}, support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; }, abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.}, }
@article {pmid41211947, year = {2025}, author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A}, title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.}, journal = {mSphere}, volume = {10}, number = {12}, pages = {e0054325}, pmid = {41211947}, issn = {2379-5042}, support = {"Une Sant&#xe9;" 2021-2024//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil Regional/ ; Calmette &amp; Yersin postdoctoral fellowship//Institut Pasteur/ ; }, mesh = {Animals ; *Aedes/microbiology/growth &amp; development/physiology ; Female ; *Microbiota ; Mosquito Vectors/growth &amp; development/microbiology ; *Animal Feed/analysis ; Larva/growth &amp; development/microbiology ; *Diet ; *Water ; Metagenomics ; }, abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.}, }
@article {pmid41212311, year = {2025}, author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY}, title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {3}, pages = {42}, pmid = {41212311}, issn = {1433-4909}, mesh = {*Hot Springs/microbiology ; *Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Russia ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.}, }
@article {pmid41214576, year = {2025}, author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W}, title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.}, journal = {BMC neurology}, volume = {25}, number = {1}, pages = {460}, pmid = {41214576}, issn = {1471-2377}, support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Levodopa/pharmacokinetics/therapeutic use/blood ; *Parkinson Disease/drug therapy/blood ; Male ; Female ; *Antiparkinson Agents/pharmacokinetics/therapeutic use/blood ; Middle Aged ; *Tyrosine Decarboxylase/genetics/metabolism ; *Gastrointestinal Microbiome/physiology ; Aged ; Feces/microbiology ; }, abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear. METHODS: The aim of this study was to investigate this relationship in Parkinson’s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography‒tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing. RESULTS: A total of 12 PD patients (age: 58.00 ± 8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0–3.0) and a disease duration of 8.46 ± 4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%±17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics. CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.}, }
@article {pmid41217690, year = {2025}, author = {Nguyen, HN and Kim, OTP and Tran, TT}, title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {11}, pages = {445}, pmid = {41217690}, issn = {1573-0972}, support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; }, mesh = {*Honey/microbiology ; Vietnam ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity/drug effects ; *Virulence Factors/genetics ; *Metagenomics/methods ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Bees/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Genes, Bacterial ; Virulence/genetics ; }, abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.}, }
@article {pmid41218045, year = {2025}, author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N}, title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336700}, pmid = {41218045}, issn = {1932-6203}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Photobacterium/genetics/isolation &amp; purification ; Phylogeny ; Thailand ; Vibrio/genetics/isolation &amp; purification ; }, abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.}, }
@article {pmid41218435, year = {2026}, author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y}, title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124889}, doi = {10.1016/j.watres.2025.124889}, pmid = {41218435}, issn = {1879-2448}, mesh = {RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota ; Metagenomics ; Ecosystem ; Nitrates ; Bacteria/genetics ; }, abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.}, }
@article {pmid41218604, year = {2025}, author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O}, title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.}, journal = {Cell reports. Medicine}, volume = {6}, number = {11}, pages = {102426}, pmid = {41218604}, issn = {2666-3791}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/pharmacology/administration &amp; dosage ; Adult ; Biomarkers/metabolism ; Young Adult ; Prednisolone/pharmacology/administration &amp; dosage ; Healthy Volunteers ; Insulin Resistance ; Methylprednisolone/pharmacology/analogs &amp; derivatives/administration &amp; dosage ; Feces/microbiology ; }, abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).}, }
@article {pmid41220286, year = {2026}, author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK}, title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.}, journal = {Gut and liver}, volume = {20}, number = {2}, pages = {199-212}, pmid = {41220286}, issn = {2005-1212}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Biomarkers/analysis ; Metagenomics/methods ; Machine Learning ; Metabolomics/methods ; Proteomics ; Feces/chemistry/microbiology ; }, abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.}, }
@article {pmid41222144, year = {2025}, author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL}, title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0111225}, pmid = {41222144}, issn = {2379-5077}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Biomedical Research ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Environment ; }, abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.}, }
@article {pmid41222145, year = {2025}, author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE}, title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.}, journal = {mBio}, volume = {16}, number = {12}, pages = {e0234125}, pmid = {41222145}, issn = {2150-7511}, support = {R01 GM147178/GM/NIGMS NIH HHS/United States ; T32 GM156692/GM/NIGMS NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; R00 AI147165/AI/NIAID NIH HHS/United States ; T32 DK120509/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/physiology/isolation &amp; purification/genetics ; *Bacteroides/virology/genetics ; Germ-Free Life ; }, abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.<br><br>IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.}, }
@article {pmid41223471, year = {2025}, author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X}, title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140406}, doi = {10.1016/j.jhazmat.2025.140406}, pmid = {41223471}, issn = {1873-3336}, mesh = {*Sulfamethoxazole/pharmacology/toxicity ; *Microalgae/drug effects/genetics/physiology/metabolism ; *Water Pollutants, Chemical/toxicity ; Adaptation, Physiological ; *Bacteria/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Consortia/drug effects ; Reactive Oxygen Species/metabolism ; Photosynthesis/drug effects ; }, abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.}, }
@article {pmid41224035, year = {2026}, author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F}, title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.}, journal = {Bioresource technology}, volume = {441}, number = {}, pages = {133630}, doi = {10.1016/j.biortech.2025.133630}, pmid = {41224035}, issn = {1873-2976}, mesh = {*Bioreactors/microbiology ; *Methane/biosynthesis ; Anaerobiosis ; *Nitrogen/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonia/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Membranes, Artificial ; Sewage/microbiology ; Biofuels ; }, abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.}, }
@article {pmid41224755, year = {2025}, author = {Gupta, S and Almeida, A}, title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9959}, pmid = {41224755}, issn = {2041-1723}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification/classification/pathogenicity ; Humans ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Klebsiella Infections/microbiology ; *Metagenome/genetics ; Metagenomics/methods ; Virulence Factors/genetics ; Genetic Variation ; }, abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.}, }
@article {pmid41225090, year = {2026}, author = {Ziaei, H and Rezaei, N}, title = {Introduction to Oral Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {3-21}, pmid = {41225090}, issn = {0065-2598}, mesh = {Humans ; *Mouth/immunology/microbiology ; Microbiota/immunology ; Animals ; *Immunity, Innate ; *Immunity, Mucosal ; *Mouth Mucosa/immunology/microbiology ; Adaptive Immunity ; }, abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.}, }
@article {pmid41225104, year = {2026}, author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA}, title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.}, journal = {Advances in experimental medicine and biology}, volume = {1492}, number = {}, pages = {291-313}, pmid = {41225104}, issn = {0065-2598}, mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; }, abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.}, }
@article {pmid41225454, year = {2025}, author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T}, title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.}, journal = {BMC pregnancy and childbirth}, volume = {25}, number = {1}, pages = {1198}, pmid = {41225454}, issn = {1471-2393}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; }, abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).<br><br>METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n&#x2009;=&#x2009;31) and those with normal thyroid function (Control group, n&#x2009;=&#x2009;30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16&#xa0;S rRNA metagenomic sequencing.<br><br>RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p&#x2009;=&#x2009;0.034; Shannon index, p&#x2009;=&#x2009;0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p&#x2009;=&#x2009;0.002, p&#x2009;=&#x2009;0.049, and p&#x2009;=&#x2009;0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.<br><br>CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.}, }
@article {pmid41226502, year = {2025}, author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT}, title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, pmid = {41226502}, issn = {1422-0067}, support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; }, abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.}, }
@article {pmid41226812, year = {2025}, author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T}, title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, pmid = {41226812}, issn = {1422-0067}, support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; }, abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.}, }
@article {pmid41226831, year = {2025}, author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E}, title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.}, journal = {International journal of molecular sciences}, volume = {26}, number = {21}, pages = {}, pmid = {41226831}, issn = {1422-0067}, support = {&#x41a;&#x41f;-06-&#x41d;83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; }, mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; }, abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.}, }
@article {pmid41228409, year = {2025}, author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X}, title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, pmid = {41228409}, issn = {2072-6643}, support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; }, mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; }, abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.}, }
@article {pmid41228422, year = {2025}, author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S}, title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.}, journal = {Nutrients}, volume = {17}, number = {21}, pages = {}, pmid = {41228422}, issn = {2072-6643}, support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; }, abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.}, }
@article {pmid41229166, year = {2025}, author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K}, title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70128}, pmid = {41229166}, issn = {2045-8827}, support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, P&#xe4;ivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Waist-Hip Ratio ; }, abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.}, }
@article {pmid41231233, year = {2025}, author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE}, title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.}, journal = {Microbial genomics}, volume = {11}, number = {11}, pages = {}, pmid = {41231233}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; }, abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.}, }
@article {pmid41231970, year = {2025}, author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO}, title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {12}, pages = {e0148025}, pmid = {41231970}, issn = {1098-5336}, support = {2020.07928//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.00194.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.02027.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.13872//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/01061/2014/CP1223/CT000//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0087/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/148270/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04612/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Lactate Dehydrogenases/genetics/metabolism/chemistry ; Metagenomics ; *Flavin-Adenine Dinucleotide/metabolism ; Metagenome ; Molecular Docking Simulation ; Crystallography, X-Ray ; Catalytic Domain ; Lactic Acid/metabolism ; }, abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.<br><br>IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.}, }
@article {pmid41232227, year = {2026}, author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M}, title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110783}, doi = {10.1016/j.vetmic.2025.110783}, pmid = {41232227}, issn = {1873-2542}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; India ; Metagenomics ; *Rhipicephalus/microbiology ; *Coxiella/genetics/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Microbiota ; DNA, Bacterial/genetics ; }, abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.}, }
@article {pmid41232906, year = {2026}, author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M}, title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.}, journal = {Environmental research}, volume = {288}, number = {Pt 2}, pages = {123287}, doi = {10.1016/j.envres.2025.123287}, pmid = {41232906}, issn = {1096-0953}, mesh = {*Wastewater/microbiology ; India ; Metagenomics ; *Microbiota ; *Drug Resistance, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13 % of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49 %), macrolide-lincosamide-streptogramin (15.84 %), beta-lactam (7.95 %), and tetracycline (6.52 %). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.}, }
@article {pmid41233306, year = {2025}, author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X}, title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9980}, pmid = {41233306}, issn = {2041-1723}, support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; }, abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.}, }
@article {pmid41233350, year = {2025}, author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW}, title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1782}, pmid = {41233350}, issn = {2052-4463}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; }, mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; }, abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.}, }
@article {pmid41233799, year = {2025}, author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA}, title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1276}, pmid = {41233799}, issn = {1479-5876}, mesh = {*Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Skin/microbiology ; Metagenomics ; *Dermatology/methods ; }, abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.<br><br>METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.<br><br>RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.<br><br>CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.}, }
@article {pmid41233936, year = {2025}, author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS}, title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {234}, pmid = {41233936}, issn = {2049-2618}, mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; }, abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.}, }
@article {pmid41233937, year = {2025}, author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M}, title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {231}, pmid = {41233937}, issn = {2049-2618}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.}, }
@article {pmid41235136, year = {2025}, author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y}, title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {9993-10010}, pmid = {41235136}, issn = {1177-8881}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; }, abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.<br><br>METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.<br><br>RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.<br><br>CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.}, }
@article {pmid41236031, year = {2025}, author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ}, title = {Altered oral microbiome diversity in patients with oral candidiasis.}, journal = {Archives of oral biology}, volume = {180}, number = {}, pages = {106430}, doi = {10.1016/j.archoralbio.2025.106430}, pmid = {41236031}, issn = {1879-1506}, mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; }, abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.<br><br>DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.<br><br>RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.<br><br>CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.}, }
@article {pmid41236788, year = {2025}, author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C}, title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e72950}, pmid = {41236788}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists &amp; inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; }, abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.<br><br>OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.<br><br>METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.<br><br>RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.<br><br>CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.<br><br>TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.<br><br>DERR1-10.2196/72950.}, }
@article {pmid41236809, year = {2025}, author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY}, title = {Characterization of Gut Microbiota of Honey Bees in Korea.}, journal = {Polish journal of microbiology}, volume = {74}, number = {4}, pages = {428-445}, pmid = {41236809}, issn = {2544-4646}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; Republic of Korea ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Phylogeny ; }, abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.}, }
@article {pmid41237622, year = {2025}, author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J}, title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140425}, doi = {10.1016/j.jhazmat.2025.140425}, pmid = {41237622}, issn = {1873-3336}, mesh = {*Pisum sativum/microbiology/growth &amp; development/drug effects/metabolism ; *Rhizosphere ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Metabolomics ; *Polyethylene/toxicity ; Soil Microbiology ; *Microbiota/drug effects ; *Microplastics/toxicity ; *Soil Pollutants/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; }, abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.}, }
@article {pmid41237630, year = {2025}, author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L}, title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140469}, doi = {10.1016/j.jhazmat.2025.140469}, pmid = {41237630}, issn = {1873-3336}, mesh = {*Wetlands ; *Soil Microbiology ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics ; Metagenome ; Microbiota ; }, abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.}, }
@article {pmid41237940, year = {2026}, author = {Borroni, D and Lo Monaco, F and Ferraro, S and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C}, title = {Ocular surface microbiota in primary open angle glaucoma.}, journal = {Experimental eye research}, volume = {262}, number = {}, pages = {110734}, doi = {10.1016/j.exer.2025.110734}, pmid = {41237940}, issn = {1096-0007}, mesh = {Humans ; *Glaucoma, Open-Angle/complications/microbiology ; *Eye/microbiology ; *Microbiota ; Cross-Sectional Studies ; Italy ; Case-Control Studies ; Bacteria/classification ; Dysbiosis/complications ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1 × 10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.}, }
@article {pmid41238729, year = {2025}, author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY}, title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {39988}, pmid = {41238729}, issn = {2045-2322}, support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; }, mesh = {*Premature Birth/epidemiology/microbiology/physiopathology/prevention &amp; control ; *Vagina/microbiology ; *Cervix Uteri/microbiology/physiopathology ; Humans ; Female ; Microbiota/genetics ; *Metagenomics ; Cervical Length Measurement ; Risk Factors ; East Asian People/statistics &amp; numerical data ; Risk Assessment/methods ; Prospective Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Pregnancy ; Adult ; }, abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.}, }
@article {pmid41238915, year = {2025}, author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA}, title = {Microbial signals in primary and metastatic brain tumors.}, journal = {Nature medicine}, volume = {31}, number = {11}, pages = {3675-3688}, pmid = {41238915}, issn = {1546-170X}, support = {F32 CA260769/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA256006/CA/NCI NIH HHS/United States ; R01 CA227156/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; S10 OD021685/OD/NIH HHS/United States ; P50 CA221703/CA/NCI NIH HHS/United States ; R21 NS130323/NS/NINDS NIH HHS/United States ; P50 CA127001/CA/NCI NIH HHS/United States ; R21 CA283514/CA/NCI NIH HHS/United States ; S10 RR029552/RR/NCRR NIH HHS/United States ; }, mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; }, abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.}, }
@article {pmid41239026, year = {2025}, author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H}, title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {211}, pmid = {41239026}, issn = {1896-1851}, support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.}, }
@article {pmid41239201, year = {2025}, author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A}, title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {86}, pmid = {41239201}, issn = {2730-6844}, support = {SRUG2204254606//National Research Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration &amp; dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; }, abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.<br><br>DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.}, }
@article {pmid41239203, year = {2025}, author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D}, title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1578}, pmid = {41239203}, issn = {1471-2229}, mesh = {*Mycorrhizae/physiology ; *Rhizosphere ; *Nicotiana/growth &amp; development/microbiology ; *Seedlings/growth &amp; development/microbiology ; Soil Microbiology ; Plant Roots/microbiology/growth &amp; development ; Microbiota ; }, abstract = {BACKGROUND: Numerous studies have demonstrated significant variations in the plant growth-promoting effects among different species of arbuscular mycorrhizal fungi (AMF). However, the underlying mechanisms remain incompletely understood, particularly regarding how distinct AMF species regulate the rhizosphere microbiome. RESULTS: Five AMF species (Funneliformis mosseae, Diversispora versiformis, Clariodeoglous etunicatum, Rhizophagus intraradices, and Acaulospora delicate) were inoculated to investigate their effects on tobacco seedling growth and rhizosphere microecological regulation. The results showed that all AMF inoculations significantly increased shoot and root biomass, N/P/K uptake, morphological traits (height, stem diameter, leaf area), chlorophyll content (SPAD), and root architecture (length, surface area, volume, diameter) of tobacco seedlings. Among them, the treatment inoculated with R. intraradices showed the most outstanding growth-promoting effect in all growth indicators. Metagenomic analysis indicated that AMF inoculation significantly altered the diversity and community structure of rhizosphere substrate microorganisms. Among them, R. intraradices inoculation yielded the highest microbial diversity, with an associated network exhibiting enhanced complexity. KEGG functional annotation revealed metabolic pathways (IAA biosynthesis, iron-siderophore transport regulation, exopolysaccharide production, and nutrient cycling) consistently associated with tobacco growth promotion in all AMF inoculations. However, species-specific mechanisms were observed: F. mosseae promotes tobacco seedling growth by enhancing IAA synthesis through the recruitment of beneficial microorganisms such as Nostoc, Flavisolibacter, Frateuria, and Sphingomonas. D. versiformis enhanced carbon fixation via the hydroxypropionate-hydroxybutyrate cycle, driven by the proliferation of Glaciecola, Pedococcus, Phycicoccus, and Hephaestia. C. etunicatum facilitated phosphorus/iron accumulation through organic phosphorus mineralization, phosphate transport, and iron acquisition accompanied by the recruitment of, Hartmannibacter, Lysobacter, Moheibacter, and Pseudolabrys. R. intraradices improved nitrogen assimilation through augmented nitrogen transport and assimilatory nitrate reduction (ANRA), correlated with the recruitment of Azospirillum, Sphingobium, Mesorhizobium, Paracoccus, and Parafilimonas. A. delicate stimulated plant growth via polyphosphate degradation and exopolysaccharide biosynthesis, associated with the enrichment of Segetibacter, Ferruginibacter, Hyphomicrobium and Pseudomonas. Notably, this study revealed that functional divergence in rhizosphere microbiomes associated with the five tested fungal species was primarily reflected in the abundance rather than the composition of functional genes. CONCLUSION: In summary, AMF inoculation significantly enhanced tobacco seedling biomass and agronomic traits by improving mineral nutrient assimilation efficiency and restructuring the rhizosphere microbial community. Different AMF species exhibited distinct microecological regulation patterns. This study elucidated the growth-promoting mechanisms of AMF from a microbial interaction perspective, providing a theoretical basis for establishing a sustainable tobacco cultivation system.}, }
@article {pmid41239457, year = {2025}, author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K}, title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {1287}, pmid = {41239457}, issn = {1479-5876}, mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; }, abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.<br><br>METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16&#xa0;S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).<br><br>RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.<br><br>CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.}, }
@article {pmid41240707, year = {2025}, author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E}, title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.}, journal = {Poultry science}, volume = {104}, number = {12}, pages = {106092}, pmid = {41240707}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; Animal Feed/analysis ; *Mycobiome/drug effects ; Diet/veterinary ; *Fungi/physiology/classification/drug effects ; *Gastrointestinal Microbiome/drug effects ; Bacteria/classification/drug effects ; Random Allocation ; Probiotics/administration &amp; dosage ; Feces/microbiology ; Dietary Supplements/analysis ; Oils, Volatile/administration &amp; dosage/metabolism ; Anti-Bacterial Agents/administration &amp; dosage ; Male ; Bacitracin ; Salicylates ; }, abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.}, }
@article {pmid41241073, year = {2026}, author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W}, title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.}, journal = {Journal of affective disorders}, volume = {394}, number = {Pt B}, pages = {120709}, doi = {10.1016/j.jad.2025.120709}, pmid = {41241073}, issn = {1573-2517}, mesh = {Humans ; Male ; *Major Depressive Disorder/drug therapy/microbiology ; *Gastrointestinal Microbiome/genetics/drug effects ; Female ; Adult ; Prospective Studies ; Middle Aged ; *Selective Serotonin Reuptake Inhibitors/therapeutic use ; Metagenomics ; *Antidepressive Agents/therapeutic use ; Feces/microbiology ; *Serotonin and Noradrenaline Reuptake Inhibitors/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.<br><br>METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12&#xa0;&#xb1;&#xa0;15.79&#xa0;years, 8 males), while 14 were non-responders (40.14&#xa0;&#xb1;&#xa0;17.28&#xa0;years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).<br><br>RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.<br><br>CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.}, }
@article {pmid41243436, year = {2025}, author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A}, title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2576657}, pmid = {41243436}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; }, abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.}, }
@article {pmid41243980, year = {2026}, author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N}, title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D1743-D1752}, pmid = {41243980}, issn = {1362-4962}, support = {320237//Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; //Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Rhizosphere ; *Crops, Agricultural/microbiology ; *Microbiota/genetics ; Soil Microbiology ; *Metagenomics/methods ; Metagenome ; Software ; }, abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.}, }
@article {pmid41247052, year = {2026}, author = {Huang, X and Zeng, J and Yang, F and Liu, Y and Chen, J and Wang, H and Li, S and Li, C and Zhang, S}, title = {Microbial succession in human tissues postmortem: insights from 2bRAD-M sequencing.}, journal = {Microbiology spectrum}, volume = {14}, number = {1}, pages = {e0266624}, pmid = {41247052}, issn = {2165-0497}, mesh = {Humans ; *Postmortem Changes ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Liver/microbiology ; Spleen/microbiology ; Lung/microbiology ; Cadaver ; Male ; Kidney/microbiology ; Metagenomics/methods ; Female ; }, abstract = {Microbial communities play a crucial role in decomposition, yet their patterns in human tissues remain underexplored. Most previous research has often focused on animal models such as mice and swine, with limited studies on human samples, primarily targeting specific environments like the gut and skin. Consequently, gaps persist in understanding postmortem microbial dynamics within internal human organs. The 2bRAD-M sequencing technology offers a powerful approach for human thanatomicrobiome research, overcoming key limitations of 16S rRNA and metagenomic sequencing methods. In this study, we used 2bRAD-M to profile microbial succession across seven human tissues-heart, liver, spleen, lung, kidney, calf muscle, and gut-at various postmortem intervals (PMIs). Significant variations in microbial community composition were observed across organs and decomposition stages, with Proteobacteria dominating early and Firmicutes later. A comparison of frozen and unfrozen cadavers (PMI 1-7 days) revealed divergent microbial shifts in the liver and spleen, while other tissues exhibited limited variation. These findings highlight complex, organ-specific microbial trajectories and suggest that microbial signatures could serve as biomarkers for PMI estimation. This research deepens our understanding of the microbial succession within internal human organs postmortem and contributes to elucidating the identity and role of microorganisms in human decomposition.IMPORTANCEHumans host a diverse array of microbial communities that play a crucial role in the decomposition process after death. Understanding these postmortem microbial dynamics is essential, as they offer valuable insights into the progression of decomposition with significant implications for forensic science. The role of microorganisms in corpse decomposition has gained increasing attention in both forensic and ecological research, but studies in this area remain in their early stages, requiring further in-depth exploration. This work pioneers the use of 2bRAD-M sequencing to investigate microbial changes across various human organs over increasing postmortem intervals. By enhancing knowledge of postmortem microbiota dynamics, the study contributes to refining and improving the accuracy of forensic methodologies.}, }
@article {pmid41249223, year = {2025}, author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL}, title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40115}, pmid = {41249223}, issn = {2045-2322}, support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; }, mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth &amp; development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; }, abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.}, }
@article {pmid41250628, year = {2026}, author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL}, title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.}, journal = {Journal of basic and clinical physiology and pharmacology}, volume = {37}, number = {1}, pages = {9-24}, pmid = {41250628}, issn = {2191-0286}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/physiology ; Probiotics/therapeutic use/administration &amp; dosage ; *Urinary Tract Infections/microbiology ; Dysbiosis/microbiology ; Prebiotics/administration &amp; dosage ; Animals ; *Urinary Tract/microbiology ; Female ; }, abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.}, }
@article {pmid41252249, year = {2025}, author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS}, title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.}, journal = {Cell reports}, volume = {44}, number = {11}, pages = {116573}, doi = {10.1016/j.celrep.2025.116573}, pmid = {41252249}, issn = {2211-1247}, mesh = {Humans ; Indonesia ; *Rural Population ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; *Urban Population ; Metagenome ; *Microbiota ; Male ; Female ; }, abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.}, }
@article {pmid41252442, year = {2026}, author = {Zentgraf, J and Schmitz, JE and Rahmann, S}, title = {Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {1}, pages = {}, pmid = {41252442}, issn = {1367-4811}, mesh = {Humans ; *Software ; *Metagenomics/methods ; *Microbiota/genetics ; *DNA Contamination ; Sequence Analysis, DNA/methods ; Algorithms ; *Metagenome ; }, abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.<br><br>RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.<br><br>Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/), and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).}, }
@article {pmid41252568, year = {2025}, author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G}, title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {19}, number = {12}, pages = {1285-1298}, doi = {10.1080/17474124.2025.2592078}, pmid = {41252568}, issn = {1747-4132}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Biomarkers, Tumor ; Predictive Value of Tests ; Feces/microbiology ; Occult Blood ; }, abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.<br><br>AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.<br><br>EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.}, }
@article {pmid41253025, year = {2025}, author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP}, title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {149}, number = {}, pages = {157550}, doi = {10.1016/j.phymed.2025.157550}, pmid = {41253025}, issn = {1618-095X}, mesh = {*Rheum/chemistry/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/metabolism ; *Diarrhea/chemically induced/therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; Male ; *Lactobacillus ; Wine ; Mice ; }, abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.<br><br>PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.<br><br>METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-&#x3ba;B), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.<br><br>RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-&#x3b1;, IL-17, and IFN-&#x3b3;), inhibit the expression of TLR4/NF-&#x3ba;B, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.<br><br>CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-&#x3ba;B and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.}, }
@article {pmid41254331, year = {2025}, author = {Bersch-Ferreira, &#xc2;C and Fonseca, DC and Tramujas, L and Schiavon, CA and Nakagawa Santos, RH and V Machado, RH and Biasi Cavalcanti, A and Marcadenti, A}, title = {Gut Microbiota Composition and Arterial Hypertension Improvement Post-Roux-en-Y Gastric Bypass: GATEWAY Trial Sub-Analysis After 5 Years.}, journal = {Obesity surgery}, volume = {35}, number = {12}, pages = {5346-5356}, pmid = {41254331}, issn = {1708-0428}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastric Bypass ; *Hypertension/microbiology/surgery/complications/physiopathology ; Female ; Male ; Adult ; Cross-Sectional Studies ; Middle Aged ; *Obesity, Morbid/surgery/microbiology/complications ; Feces/microbiology ; Treatment Outcome ; Remission Induction ; }, abstract = {INTRODUCTION: The aim of this study was to explore the relationship between gut microbiota composition and hypertension remission in individuals with obesity and hypertension who underwent Roux-en-Y gastric bypass (RYGB) surgery five years prior.<br><br>METHODS: This is a sub-analysis of the GATEWAY trial using cross-sectional data from participants five years post-surgery. Three groups were included: patients who underwent RYGB and achieved hypertension remission (Group 1, n&#x2009;=&#x2009;12), patients who underwent RYGB but did not achieve remission (Group 2, n&#x2009;=&#x2009;12), and a control group of individuals with obesity and hypertension who did not undergo surgery (Group 3, n&#x2009;=&#x2009;15). Gut microbiota composition was evaluated using metagenomic sequencing of fecal samples, with taxonomic classification at the phylum, class, and order levels.<br><br>RESULTS: No statistically significant differences were found in overall microbiota composition between the groups. However, microbial richness was higher in both surgical groups compared to the control group, suggesting a potential link between bariatric surgery and increased gut microbial diversity.<br><br>CONCLUSION: While gut microbiota composition did not significantly differ between individuals with and without hypertension remission, the observed increase in microbial richness among those undergoing bariatric surgery underscores the complex interplay between obesity treatment, gut microbiota, and blood pressure regulation. Further research is needed to elucidate these long-term relationships.}, }
@article {pmid41255157, year = {2026}, author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H}, title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {38}, number = {9}, pages = {e14484}, doi = {10.1002/adma.202514484}, pmid = {41255157}, issn = {1521-4095}, support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Lipopolysaccharides/chemistry/metabolism ; *Hydrogels/chemistry/pharmacology ; Mice ; *Toll-Like Receptor 4/metabolism ; Polymyxin B/chemistry/pharmacology ; *Microbiota/drug effects ; Humans ; Mice, Inbred C57BL ; Wound Healing/drug effects ; Polyethyleneimine/chemistry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.}, }
@article {pmid41255529, year = {2025}, author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L}, title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1710868}, pmid = {41255529}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; }, abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.}, }
@article {pmid41258495, year = {2025}, author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A}, title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {136}, pmid = {41258495}, issn = {1432-184X}, support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; }, mesh = {Animals ; *Microbiota ; *Symbiosis ; *Gastropoda/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Bacteriophages/isolation &amp; purification/genetics/classification ; Phylogeny ; }, abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.}, }
@article {pmid41258716, year = {2025}, author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME}, title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.}, journal = {mSphere}, volume = {10}, number = {12}, pages = {e0068325}, pmid = {41258716}, issn = {2379-5042}, support = {K43 TW012302/TW/FIC NIH HHS/United States ; K43TW012302/NH/NIH HHS/United States ; KIC240402211772//National Research Foundation/ ; }, mesh = {Humans ; Africa ; Biomedical Research ; *Microbiota ; South Africa ; Translational Research, Biomedical ; }, abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.}, }
@article {pmid41259558, year = {2025}, author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A}, title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.}, journal = {Journal of applied oral science : revista FOB}, volume = {33}, number = {}, pages = {e20250476}, pmid = {41259558}, issn = {1678-7765}, mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; }, abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.<br><br>METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.<br><br>RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p&#x2264;0.05, LDA&#x2265;2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.<br><br>CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.}, }
@article {pmid41260011, year = {2026}, author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J}, title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.}, journal = {Marine pollution bulletin}, volume = {223}, number = {}, pages = {119004}, doi = {10.1016/j.marpolbul.2025.119004}, pmid = {41260011}, issn = {1879-3363}, mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Freezing ; *Bacteria/classification ; Seasons ; Ecosystem ; *Microbiota ; Ice Cover ; Geologic Sediments/microbiology ; Nitrogen ; }, abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.}, }
@article {pmid41260114, year = {2025}, author = {Ahmad, W and Ray, R and Khan, AL}, title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.}, journal = {The Science of the total environment}, volume = {1007}, number = {}, pages = {180812}, doi = {10.1016/j.scitotenv.2025.180812}, pmid = {41260114}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Silicates ; *Heat-Shock Response ; *Soil Microbiology ; *Glycine max/physiology/microbiology ; Hot Temperature ; }, abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.}, }
@article {pmid41260397, year = {2026}, author = {Abbasi, E}, title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.}, journal = {Journal of virological methods}, volume = {340}, number = {}, pages = {115301}, doi = {10.1016/j.jviromet.2025.115301}, pmid = {41260397}, issn = {1879-0984}, mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation &amp; purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; }, abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.}, }
@article {pmid41261182, year = {2025}, author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S}, title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {464}, pmid = {41261182}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; }, abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.}, }
@article {pmid41261745, year = {2026}, author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z}, title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D925-D931}, pmid = {41261745}, issn = {1362-4962}, support = {2022FY100905//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; }, mesh = {*Virome/genetics ; Animals ; *Metagenomics/methods ; *Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Chiroptera/virology ; *Software ; Ticks/virology ; Zoonoses/virology ; Humans ; Culicidae/virology ; Animals, Wild/virology ; Rodentia/virology ; Metagenome ; Genome, Viral ; }, abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.}, }
@article {pmid41263098, year = {2026}, author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y}, title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D555-D563}, pmid = {41263098}, issn = {1362-4962}, support = {R03OD039979/NH/NIH HHS/United States ; R01 GM140370/GM/NIGMS NIH HHS/United States ; R01GM140370/NH/NIH HHS/United States ; R03 OD039979/OD/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multigene Family ; Metagenome ; *Databases, Genetic ; Polysaccharides/metabolism ; Metagenomics/methods ; *Glycoside Hydrolases/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; Genome, Bacterial ; }, abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.}, }
@article {pmid41264852, year = {2025}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.}, journal = {Biochemistry}, volume = {64}, number = {24}, pages = {4609-4627}, pmid = {41264852}, issn = {1520-4995}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Viruses/genetics/metabolism ; *Viral Proteins/genetics/metabolism ; Microbiota ; *Biotechnology/methods ; Metagenomics/methods ; Ecosystem ; Ecology ; }, abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.}, }
@article {pmid41266326, year = {2025}, author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC}, title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10223}, pmid = {41266326}, issn = {2041-1723}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 DK120870/DK/NIDDK NIH HHS/United States ; N01 HC065236/HL/NHLBI NIH HHS/United States ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R61 HL157069/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; N01 HC065237/HL/NHLBI NIH HHS/United States ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R33 HL157069/HL/NHLBI NIH HHS/United States ; N01 HC065233/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01 HC065235/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; OT3 HL147154/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01 HC065234/HL/NHLBI NIH HHS/United States ; R01 AI152504/AI/NIAID NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; R01 AG085320/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; }, abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.}, }
@article {pmid41266356, year = {2025}, author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C}, title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {215}, pmid = {41266356}, issn = {2055-5008}, support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; }, mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; }, abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.}, }
@article {pmid41266796, year = {2025}, author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R}, title = {Calculating fast differential genome coverages among metagenomic sources using micov.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1624}, pmid = {41266796}, issn = {2399-3642}, support = {R24 AI118629/AI/NIAID NIH HHS/United States ; R01 CA241728/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; }, abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.}, }
@article {pmid41266970, year = {2025}, author = {Jin, L and Xu, Q and Miao, C and Zhan, J and Zhang, Y and Li, M and Cheng, J and Liu, P and Yang, Y and Zhou, H and Hu, Z and Li, F and Wu, C}, title = {Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1745}, pmid = {41266970}, issn = {1471-2229}, support = {110202102033//the Key Grant of China National Tobacco Corporation, China/ ; }, mesh = {Multiomics ; *Plant Leaves/microbiology/physiology/metabolism ; *Nicotiana/microbiology/physiology/metabolism ; *Symbiosis ; *Odorants/analysis ; *Volatile Organic Compounds/metabolism ; Gas Chromatography-Mass Spectrometry ; *Plant Senescence ; Proteomics ; *Microbiota ; }, abstract = {Aging in crops like tea and tobacco involves the production of secondary metabolites, with symbiotic microbes playing a key role. However, their dynamic changes and correlation with metabolites during aging remain poorly understood. This study investigates changes in microbial communities, aroma compounds, and protein expression during tobacco leaf aging using artificial accelerated aging techniques, which combine GC-MS, metagenomics, and metaproteomics methods. We identified 62 aroma compounds with distinct change patterns and observed significant changes in the structure of symbiotic bacteria. Type one, represented by Wolbachia_endosymbiont_of_Diaphorina_citri, increased in abundance from the fourth month, correlating with compounds like 2-Furaldehyde. Type two, represented by Sphingomonas_sp_LK11, showed a bimodal abundance pattern, correlating with compounds like Tabanone. Metaproteomics revealed that protein functions were initially limited to cytoskeleton organization but diversified from the fourth month. Fungi also displayed two distinct clustering patterns, Rhizopus and Mortierella elongata were abundant early on, while Colletotrichum asianum and Trichophyton violaceum appeared later. Rhizopus and other fungi exhibited a significant positive correlation with 24 aroma compounds, including 5-Methylfuran-2(5 H)-one. Linderina pennispora and other fungi showed a significant positive correlation with 28 aroma compounds, including 2-Furaldehyde. The dynamic changes in microbial community structure during aging are closely related to the generation of aroma compounds. Overall, temporal shifts in microbial communities were closely linked to aroma formation. One set of microorganisms, such as Wolbachia_endosymbiont_of_Diaphorina_citri and Linderina pennispora, is positively correlated with 2-Furaldehyde, Isophorone, and 2-Methylbenzofuran. Another set, including Sphingomonas_sp_LK11 and Rhizopus, exhibits a positive correlation with 5-Methylfuran-2(5 H)-one and 1,2-Cyclohexanedione. These findings provide new insights into the biological mechanisms of tobacco leaf aging, and offer new research directions for the development and innovation of future tobacco products.}, }
@article {pmid41267035, year = {2025}, author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z}, title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {236}, pmid = {41267035}, issn = {2049-2618}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; }, abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.<br><br>RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.<br><br>CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.}, }
@article {pmid41267624, year = {2025}, author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J}, title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70234}, pmid = {41267624}, issn = {1758-2229}, support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; }, mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; }, abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.}, }
@article {pmid41268133, year = {2025}, author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C}, title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.}, journal = {Topics in spinal cord injury rehabilitation}, volume = {31}, number = {4}, pages = {111-129}, pmid = {41268133}, issn = {1945-5763}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; }, abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.<br><br>OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).<br><br>METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).<br><br>RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.<br><br>CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.}, }
@article {pmid41269405, year = {2025}, author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q}, title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {102}, pmid = {41269405}, issn = {1559-0267}, support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; }, mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; }, abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.}, }
@article {pmid41270667, year = {2025}, author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T}, title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.}, journal = {Chemosphere}, volume = {393}, number = {}, pages = {144767}, doi = {10.1016/j.chemosphere.2025.144767}, pmid = {41270667}, issn = {1879-1298}, mesh = {*Methylmercury Compounds/analysis ; *Oryza/chemistry ; *Mercury/analysis ; *Soil Pollutants/analysis ; *Soil Microbiology ; Soil/chemistry ; Microbiota ; Environmental Monitoring ; }, abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.}, }
@article {pmid41270835, year = {2025}, author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L}, title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.}, journal = {Virus research}, volume = {362}, number = {}, pages = {199666}, pmid = {41270835}, issn = {1872-7492}, mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; }, abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.}, }
@article {pmid41270896, year = {2026}, author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M}, title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.}, journal = {Gene}, volume = {978}, number = {}, pages = {149913}, pmid = {41270896}, issn = {1879-0038}, support = {D43 CA260658/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology ; Case-Control Studies ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Pilot Projects ; Neoplasm Staging ; Adult ; Bacteria/genetics/classification ; }, abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.<br><br>METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n&#xa0;=&#xa0;23) prior to any treatment initiation, and unrelated healthy controls (n&#xa0;=&#xa0;24) to elucidate their microbial diversity and relative abundance.<br><br>RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2]&#xa0;=&#xa0;0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY: aerobactin biosynthesis.<br><br>CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.}, }
@article {pmid41273973, year = {2025}, author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z}, title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140564}, doi = {10.1016/j.jhazmat.2025.140564}, pmid = {41273973}, issn = {1873-3336}, mesh = {*Rivers/virology ; China ; *Bacteriophages/genetics/physiology ; *Ecosystem ; Fresh Water/virology ; Virome ; Geologic Sediments ; }, abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.}, }
@article {pmid41274873, year = {2025}, author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J}, title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11543}, pmid = {41274873}, issn = {2041-1723}, mesh = {*Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Humans ; Feces/microbiology ; Metagenome/genetics ; *Bacteria/genetics/classification ; Longitudinal Studies ; Metagenomics/methods ; Male ; Female ; Adult ; }, abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.}, }
@article {pmid41274878, year = {2025}, author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R}, title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11536}, pmid = {41274878}, issn = {2041-1723}, support = {R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; R01HD080444//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; K99 HD113834/HD/NICHD NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; R21 HD099473/HD/NICHD NIH HHS/United States ; F32HD105364//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32 HD105364/HD/NICHD NIH HHS/United States ; R01HD109830//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; }, mesh = {Humans ; *Milk, Human/microbiology ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Adult ; Feces/microbiology ; Infant, Newborn ; Bifidobacterium/genetics/isolation &amp; purification ; Male ; Metagenomics ; Breast Feeding ; }, abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.}, }
@article {pmid41275070, year = {2025}, author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G}, title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11541}, pmid = {41275070}, issn = {2041-1723}, support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Prophages/genetics/physiology ; Animals ; Humans ; *Colitis/chemically induced/microbiology/virology ; Fucosyltransferases/genetics/metabolism ; Mice ; *Trisaccharides/metabolism/biosynthesis ; Female ; *Gastrointestinal Microbiome ; Male ; Galactoside 2-alpha-L-fucosyltransferase ; Mice, Inbred C57BL ; Lysogeny ; Metagenome ; Dextran Sulfate ; Adult ; Middle Aged ; }, abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.}, }
@article {pmid41275679, year = {2026}, author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J}, title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.}, journal = {Water research}, volume = {289}, number = {Pt B}, pages = {124956}, doi = {10.1016/j.watres.2025.124956}, pmid = {41275679}, issn = {1879-2448}, mesh = {*Biodegradation, Environmental ; *Mining ; *Microbial Consortia ; Bioreactors ; }, abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.}, }
@article {pmid41275986, year = {2026}, author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , }, title = {Prebiotic Administration to Chronic Kidney Disease Patients Modifies Their Fecal Microbiome and Host Metabolism.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {36}, number = {3}, pages = {419-429}, doi = {10.1053/j.jrn.2025.10.015}, pmid = {41275986}, issn = {1532-8503}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Amino Acids ; Dysbiosis/diet therapy/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Inulin/administration &amp; dosage ; Oligosaccharides/administration &amp; dosage ; Pilot Projects ; *Prebiotics/administration &amp; dosage ; *Renal Insufficiency, Chronic/diet therapy/metabolism/microbiology ; }, abstract = {OBJECTIVE(S): Prebiotics are believed to improve gut microbial dysbiosis and dysmetabolism in chronic kidney disease (CKD) patients. However, impact of prebiotics on gut microbial metagenome and dynamic changes in metabolome has not been clearly defined.<br><br>METHODS: We conducted a nonrandomized, open-label, three-phase pilot trial to investigate the effect of daily oral prebiotic, oligofructose-enriched inulin (p-inulin), on stool functional metagenome and changes in plasma, urine, and stool metabolites in 13 CKD patients. The study comprised a pretreatment phase (8 weeks), p-inulin treatment phase (12 weeks), and post-treatment phase (8 weeks).<br><br>RESULTS: During treatment phase, there was a significant increase in the abundance of Bifidobacterium adolescentis, Bifidobacterium longum, and Lachnospiraceae species. Microbial pathways related to carbohydrate degradation and amino acid biosynthesis were enriched during the treatment phase, but urea biosynthetic pathway was attenuated. In plasma, metabolic biosynthetic pathways for valine, leucine, and isoleucine were activated during the treatment phase. Microbial genes related to lipid metabolism were enriched during post-treatment. Abundance of several polar and nonpolar lipids were altered in plasma and stool samples during treatment and post-treatment phases. Pathway analysis for lipids indicated suppression of triglyceride biosynthesis in plasma and enhanced triglyceride degradation in stool during the treatment phase. Secondary bile acid levels in plasma, urine, and stool were significantly reduced during p-inulin consumption. Urine levels of indoxyl sulfate and p-cresol sulfate were reduced during treatment phase.<br><br>CONCLUSION(S): P-inulin administration to CKD patients resulted in a distinct shift in toxin-generating proteolysis to amino acid biosynthesis and favorable changes in lipid metabolism.}, }
@article {pmid41277537, year = {2026}, author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH}, title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D734-D742}, pmid = {41277537}, issn = {1362-4962}, support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Disease/genetics ; Phenotype ; Software ; }, abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.}, }
@article {pmid41278154, year = {2025}, author = {Zheng, L and Duan, SL and Wang, K}, title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.}, journal = {World journal of gastroenterology}, volume = {31}, number = {42}, pages = {113170}, pmid = {41278154}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; }, abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.}, }
@article {pmid41278541, year = {2025}, author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T}, title = {MeTAline: enabling reproducible and scalable metagenomic analyses.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf158}, pmid = {41278541}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; }, abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.}, }
@article {pmid41282978, year = {2025}, author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J}, title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20348}, pmid = {41282978}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; }, abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.}, }
@article {pmid41282988, year = {2025}, author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y}, title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20199}, pmid = {41282988}, issn = {2167-8359}, mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; Archaea/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.<br><br>METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.<br><br>RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P&#xa0;=&#xa0;0.038 at the family, P&#xa0;=&#xa0;0.019 at the genus and P&#xa0;=&#xa0;0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P&#xa0;<&#xa0;0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P&#xa0;=&#xa0;0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.<br><br>CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.}, }
@article {pmid41283667, year = {2025}, author = {Zhang, J and Meng, F and Sun, Y and Xu, W and Wu, S and Su, X}, title = {Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0145325}, pmid = {41283667}, issn = {2379-5077}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; //Taishan Scholar Project of Shandong Province/ ; //Shandong Talents Team Cultivation Plan of University Preponderant Discipline/ ; }, mesh = {*Deep Learning ; *Phylogeny ; Humans ; *Microbiota/genetics ; Algorithms ; }, abstract = {The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning (DL) models, which typically focus on microbial distribution patterns, neglecting the underlying relationships between microbes. As a result, model performance can be significantly affected by data sparsity, misclassified features, or incomplete microbial profiles. To overcome these challenges, we introduce Phylo-Spec, a phylogeny-driven deep learning algorithm that integrates multi-aspect microbial information for improved status recognition. Phylo-Spec fuses convolutional features of microbes within a phylogenetic hierarchy via a bottom-up iteration and significantly alleviates the challenges due to sparse data and inaccurate profiling. Additionally, the model dynamically assigns unclassified species to virtual nodes on the phylogenetic tree based on higher-level taxonomy, minimizing interferences from unclassified species. Phylo-Spec also captures the feature importance via an information gain-based mechanism through the phylogenetic structure propagation, enhancing the interpretability of classification decisions. Phylo-Spec demonstrated superior efficacy in microbiome status classification across two in silico synthetic data sets that simulate the aforementioned cases, outperforming existing ML and DL methods. Validation with real-world metagenomic and amplicon data further confirmed the model's performance in multiple status classification, establishing a powerful framework for microbiome-based health state identification and microbe-disease association. The source code is available at https://github.com/qdu-bioinfo/Phylo-Spec.IMPORTANCEThe human microbiome profoundly influences health and disease, but current computational tools often overlook the evolutionary relationships among microbes, leading to incomplete or inaccurate interpretations of complex microbial data. Phylo-Spec provides a new way to understand the microbiome by combining microbial abundance, taxonomy, and phylogeny within a unified deep learning framework. This model not only improves the accuracy of health status classification but also highlights key microbial contributors linked to disease. By capturing both microbial diversity and evolutionary context, Phylo-Spec bridges the gap between bioinformatics and biological insight, offering a powerful and interpretable approach for advancing microbiome-based diagnostics and precision medicine.}, }
@article {pmid41285255, year = {2026}, author = {Wang, S and Ma, G and Qi, C and Cheng, S and Lai, H and Zhou, L and Wu, G and Chen, Z and Mao, X and Jing, T and He, Y and Zhou, H}, title = {Trimethylamine-N-oxide disrupts spermatogenesis by inducing mitochondrial oxidative stress injury through Hippo signaling.}, journal = {Free radical biology &amp; medicine}, volume = {243}, number = {}, pages = {452-465}, doi = {10.1016/j.freeradbiomed.2025.11.052}, pmid = {41285255}, issn = {1873-4596}, mesh = {Male ; Animals ; *Mitochondria/metabolism/drug effects/pathology ; *Oxidative Stress/drug effects ; Humans ; Mice ; *Methylamines/metabolism/blood ; *Spermatogenesis/drug effects ; Hippo Signaling Pathway ; Signal Transduction/drug effects ; Testis/metabolism/drug effects/pathology ; Leydig Cells/metabolism/drug effects ; *Protein Serine-Threonine Kinases/metabolism/genetics ; Adult ; Spermatozoa/drug effects/metabolism/pathology ; Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: The gut-testis axis is increasingly recognized as a regulator of male reproductive health; however, the key microbial contributors, metabolites, and underlying mechanisms remain unclear.<br><br>METHODS: We performed fecal metagenomic sequencing in 107 participants to identify microbial taxa associated with abnormal semen parameters. Serum trimethylamine-N-oxide (TMAO) levels were measured and correlated with semen quality. In mouse models, including fecal microbiota transplantation, dietary choline supplementation, mono-colonization, and direct TMAO administration, we assessed sperm morphology, testicular androgen synthesis, and testicular histology. Testicular transcriptomics, in vitro Leydig cell assays, and mitochondrial function analyses were conducted to investigate the effects of TMAO on Hippo signaling, oxidative phosphorylation, mitochondrial membrane damage, and steroidogenesis.<br><br>RESULTS: Choline-to-trimethylamine converting bacteria, including Phocaeicola massiliensis, Veillonella spp., and Klebsiella pneumoniae, were enriched in men with abnormal semen parameters. Circulating TMAO levels were inversely associated with semen volume, total sperm count, and motile sperm count. In mouse models, elevated TMAO induced testicular dysfunction characterized by impaired sperm morphology, reduced testicular androgen synthesis, and histological abnormalities. Consistently, gene set enrichment analysis (GSEA) of testicular transcriptomes revealed significant suppression of mitochondrial translation, membrane integrity, oxidative phosphorylation, and adenosine triphosphate (ATP) metabolism. TMAO also suppressed steroidogenesis by reducing the expression of steroidogenic acute regulatory protein (StAR). Mechanistic studies in TM3 Leydig cells further demonstrated that TMAO, by promoting Yap phosphorylation, disrupted mitochondrial structure and morphology, decreased mitochondrial membrane potential, increased mitochondrial reactive oxygen species (ROS) levels, impaired ATP synthesis, and promoted mitochondrial fragmentation with upregulation of the mitochondrial fission molecule (Fis1).<br><br>CONCLUSIONS: Our findings demonstrate that TMAO activates Hippo signaling to induce mitochondrial dysfunction and suppress testosterone synthesis, thereby impairing spermatogenesis. These results highlight TMAO biosynthesis and its downstream signaling as potential therapeutic targets for improving male fertility.}, }
@article {pmid41285454, year = {2026}, author = {Safika, S and Nisa', C and Supratikno,  and Cahyadi, DD}, title = {Gut microbiota profiling of Javan pangolin (Manis javanica).}, journal = {The Journal of veterinary medical science}, volume = {88}, number = {1}, pages = {191-195}, pmid = {41285454}, issn = {1347-7439}, mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Pangolins/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; }, abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.}, }
@article {pmid41285752, year = {2025}, author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T}, title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10336}, pmid = {41285752}, issn = {2041-1723}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; }, abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.}, }
@article {pmid41285810, year = {2025}, author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ}, title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {216}, pmid = {41285810}, issn = {2055-5008}, support = {F32 DK128975/DK/NIDDK NIH HHS/United States ; R01 DK131267/DK/NIDDK NIH HHS/United States ; F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; }, mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; }, abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.}, }
@article {pmid41286799, year = {2025}, author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K}, title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.}, journal = {BMC psychiatry}, volume = {25}, number = {1}, pages = {1117}, pmid = {41286799}, issn = {1471-244X}, mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; }, abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.<br><br>METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13&#x2009;years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.<br><br>RESULTS: Fifty-three participants (mean age&#x2009;=&#x2009;10.2&#x2009;years, SD&#x2009;=&#x2009;1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M&#x2009;=&#x2009;2.03, SE&#x2009;=&#x2009;0.33 vs. 2.86, SE&#x2009;=&#x2009;0.34), p&#x2009;=&#x2009;0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M&#x2009;=&#x2009;70.10, SE&#x2009;=&#x2009;0.09) than the placebo group (M&#x2009;=&#x2009;89.72, SE&#x2009;=&#x2009;0.07), p&#x2009;=&#x2009;0.04. However, the kefir group self-reported more sleep problems post-intervention (M&#x2009;=&#x2009;39.81, SE&#x2009;=&#x2009;0.75 vs. 37.40, SE&#x2009;=&#x2009;0.65), p&#x2009;=&#x2009;0.02. For Go/NoGo RT variance, a non-significant interaction (p&#x2009;=&#x2009;0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.<br><br>CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.<br><br>ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.<br><br>TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.}, }
@article {pmid41286929, year = {2025}, author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM}, title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {401}, pmid = {41286929}, issn = {1474-760X}, support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; }, abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.}, }
@article {pmid41288100, year = {2026}, author = {van Dam, F and Westmeijer, G and Rezaei Somee, M and Ketzer, M and Kietäväinen, R and Ono, S and Bertilsson, S and McIntosh, JC and Dopson, M and Drake, H}, title = {Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.}, journal = {mBio}, volume = {17}, number = {1}, pages = {e0301725}, pmid = {41288100}, issn = {2150-7511}, support = {EAR 2120733//NSF FRES SMRFS grant/ ; DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Meteoroids ; Sweden ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics ; Metagenomics ; Phylogeny ; Archaea/metabolism/genetics ; }, abstract = {Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a δ[13]Cmethanol-methane isotope enrichment of up to 98.6‰. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.}, }
@article {pmid41289310, year = {2025}, author = {Zhao, JX and Zheng, WB and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Yang, MT and Nan, FL and Jiang, J and Elsheikha, HM and Zhang, XX}, title = {Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {11}, pages = {e0013768}, pmid = {41289310}, issn = {1935-2735}, support = {//NSFC-Yunnan Joint Fund/ ; //National Key Research and Development Program of China/ ; //Shandong Provincial Natural Science Foundation/ ; //Key Laboratory of Veterinary Parasitology of Gansu Province Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; Rats ; *Toxoplasma/physiology ; Disease Models, Animal ; Male ; Metabolomics ; *Toxoplasmosis/metabolism/parasitology/microbiology ; *Toxoplasmosis, Animal/metabolism/microbiology/parasitology ; }, abstract = {Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.}, }
@article {pmid41289388, year = {2025}, author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI}, title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {48}, pages = {e2523178122}, pmid = {41289388}, issn = {1091-6490}, support = {K01DK134840/GF/NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; DK30292//HHS | NIH (NIH)/ ; INV-016367/GATES/Gates Foundation/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; }, abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.}, }
@article {pmid41290652, year = {2025}, author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN}, title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10492}, pmid = {41290652}, issn = {2041-1723}, mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; }, abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.}, }
@article {pmid41290716, year = {2025}, author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I}, title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11620}, pmid = {41290716}, issn = {2041-1723}, support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; }, mesh = {Bees/microbiology/physiology ; Animals ; *Microbiota/genetics/physiology ; Symbiosis ; Pollination ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; Hydrogen-Ion Concentration ; Fungi/genetics/classification ; }, abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.}, }
@article {pmid41290836, year = {2025}, author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS}, title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41935}, pmid = {41290836}, issn = {2045-2322}, mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.}, }
@article {pmid41291018, year = {2025}, author = {Angwong, C and Pientong, C and Ekalaksananan, T and Burassakarn, A and Tongchai, P and Overgaard, HJ and Aromseree, S}, title = {Systematic review and meta-analysis of virome profiles and quantification of Torque teno virus load in blood of acute febrile illness patients.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45340}, pmid = {41291018}, issn = {2045-2322}, support = {IN66039//Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand/ ; }, mesh = {Humans ; *Torque teno virus/genetics/isolation &amp; purification ; *Viral Load ; *DNA Virus Infections/virology/epidemiology/blood ; *Fever/virology/blood ; *Virome ; Anelloviridae/genetics ; Thailand/epidemiology ; }, abstract = {Acute febrile illness (AFI) is a sudden fever which can be caused by various viruses such as dengue, Zika, and chikungunya viruses. This study aimed to identify viruses present in AFI patients via metagenomic next-generation sequencing (mNGS) through meta-analysis, and to compare the prevalence and viral load of the common viruses between AFI patients and healthy blood donors in northeastern Thailand. Our meta-analysis revealed that human anelloviruses-including torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV)-were the most prevalent viruses detected. We confirmed their presence in peripheral blood mononuclear cells from 203 AFI patients and 100 healthy blood donors using real-time PCR. TTV was the most identified anellovirus, detected in 84% of healthy donors and 61.08% of AFI patients. The mean TTV load was significantly lower in AFI patients compared to healthy donors. In AFI patients, TTV load increased in those with higher total white blood cell and neutrophil counts but decreased in those with higher lymphocyte counts. Our findings demonstrate high prevalence of anelloviruses, particularly TTV, in both AFI patients and healthy donors, and highlight the potential value of the TTV load in blood as an immune status biomarker in AFI patients.}, }
@article {pmid41291200, year = {2025}, author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H}, title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45351}, pmid = {41291200}, issn = {2045-2322}, support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; }, mesh = {Animals ; *Diterpenes/pharmacology/therapeutic use ; *Acute Lung Injury/drug therapy/chemically induced/metabolism/pathology ; *Phenanthrenes/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Epoxy Compounds/pharmacology/therapeutic use ; *Bile Acids and Salts/metabolism ; Mice ; Lipopolysaccharides/toxicity ; *Lung/metabolism/drug effects/pathology ; Mice, Inbred BALB C ; Male ; Disease Models, Animal ; Metabolomics ; Cytokines/metabolism ; }, abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.}, }
@article {pmid41291216, year = {2025}, author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F}, title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {8}, pmid = {41291216}, issn = {1432-184X}, mesh = {Biodegradation, Environmental ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Bioreactors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Sulfates/metabolism ; Coal Mining ; Water Pollutants, Chemical/metabolism ; }, abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.}, }
@article {pmid41291881, year = {2025}, author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A}, title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.}, journal = {Biology of sex differences}, volume = {16}, number = {1}, pages = {101}, pmid = {41291881}, issn = {2042-6410}, support = {R01 MD015904/GF/NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; R01 MD015904/MD/NIMHD NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; U54 DK123755/DK/NIDDK NIH HHS/United States ; T32DK007180/GF/NIH HHS/United States ; }, mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; }, abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.<br><br>AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.<br><br>METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as &#x2265;2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.<br><br>RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.<br><br>CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.}, }
@article {pmid41294355, year = {2025}, author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C}, title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0118525}, pmid = {41294355}, issn = {2379-5077}, support = {T15 LM009451/NH/NIH HHS/United States ; R01DK108366,R01DK131581/NH/NIH HHS/United States ; R01 DK131581/DK/NIDDK NIH HHS/United States ; UM1 TR004399/TR/NCATS NIH HHS/United States ; R01 DK108366/DK/NIDDK NIH HHS/United States ; P30 DK048520/DK/NIDDK NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; Male ; *Prevotella/isolation &amp; purification ; *HIV Infections/microbiology/metabolism ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; Feces/microbiology ; Homosexuality, Male ; }, abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.<br><br>IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.}, }
@article {pmid41297027, year = {2026}, author = {Palanisamy, H and Vidyalakshmi, S}, title = {Deciphering the interrelation of gut microbiota and BMI in atherosclerosis: a metagenomic approach.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-12}, doi = {10.1139/cjm-2025-0075}, pmid = {41297027}, issn = {1480-3275}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Atherosclerosis/microbiology ; *Body Mass Index ; Metagenomics ; Obesity/microbiology/complications ; Male ; Female ; Middle Aged ; Aged ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; Overweight/microbiology ; }, abstract = {Atherosclerotic cardiovascular disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However, the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome-based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups, respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modify the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.}, }
@article {pmid41297254, year = {2025}, author = {Hatwar, N and Qureshi, A}, title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140589}, doi = {10.1016/j.jhazmat.2025.140589}, pmid = {41297254}, issn = {1873-3336}, mesh = {*Polyvinyl Chloride/metabolism ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation &amp; purification ; *Microbial Consortia ; Solid Waste ; Soil Microbiology ; Refuse Disposal ; }, abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.}, }
@article {pmid41297255, year = {2025}, author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y}, title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140566}, doi = {10.1016/j.jhazmat.2025.140566}, pmid = {41297255}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; Humans ; Norway ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; }, abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.}, }
@article {pmid41297400, year = {2025}, author = {Chen, S and Liu, Q and Li, D}, title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128088}, doi = {10.1016/j.jenvman.2025.128088}, pmid = {41297400}, issn = {1095-8630}, mesh = {*Lignin/metabolism ; *Composting ; *Microbiota ; Manure ; Cattle ; Animals ; Bacteria ; }, abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.}, }
@article {pmid41297516, year = {2026}, author = {Xu, L and Zhang, J and Xiao, Y and Jin, P and Zhang, J}, title = {High-fat diet promotes colorectal tumorigenesis through gut microbiota-mediated metabolic reprogramming and M2 macrophage polarization.}, journal = {Biochemical and biophysical research communications}, volume = {794}, number = {}, pages = {153014}, doi = {10.1016/j.bbrc.2025.153014}, pmid = {41297516}, issn = {1090-2104}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Diet, High-Fat/adverse effects ; *Macrophages/pathology/metabolism/immunology ; *Colorectal Neoplasms/pathology/metabolism/microbiology/etiology ; Mice ; Mice, Inbred C57BL ; *Carcinogenesis/pathology/metabolism ; Male ; Metabolic Reprogramming ; }, abstract = {BACKGROUND: High-fat diet (HFD) drives colorectal cancer (CRC) progression through gut microbiota dysbiosis and M2 macrophage polarization, yet the microbiota-immunity crosstalk remains mechanistically unresolved.<br><br>METHODS: APC[min/+] (CRC model, n&#xa0;=&#xa0;8) and wild-type controls (n&#xa0;=&#xa0;7) received 12-weeks HFD. We employed integrated metagenomic sequencing (Illumina NovaSeq) and immunohistochemistry (targeting CD206+ M2 macrophages) to investigate the linkages between the gut microbiota and the host.<br><br>RESULTS: CRC mice exhibited colonic adenocarcinoma with increased M2 macrophages. Gut microbiota in CRC mice showed enrichment of pro-inflammatory taxa (e.g., Bacteroides massiliensis, Vampirovibrion) and upregulated pathways (carbohydrate metabolism, mucin degradation). Strikingly, the relative abundances of Bacteroides massiliensis and Vampirovibrion showed significant positive correlations with CD206+ M2 macrophage infiltration levels.<br><br>CONCLUSION: HFD induces microbiota-directed metabolic reprogramming and M2 polarization, synergistically accelerating CRC. Notably, targeting key pro-inflammatory taxa (e.g., B. massiliensis) or glycan hydrolysis pathways (e.g. GH95 enzyme) may provide mechanism-guided anti-CRC strategies.}, }
@article {pmid41297753, year = {2026}, author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S}, title = {Phosphate-iron modified Enteromorpha Prolifera hydrochar enhances dry anaerobic digestion of food waste: Synergistic mechanisms of electron transfer network, microbial consortia remodeling, and metagenomic insights.}, journal = {Environmental research}, volume = {289}, number = {}, pages = {123385}, doi = {10.1016/j.envres.2025.123385}, pmid = {41297753}, issn = {1096-0953}, mesh = {Anaerobiosis ; Iron/chemistry ; *Microbial Consortia ; Phosphates/chemistry ; *Ulva ; *Refuse Disposal/methods ; Electron Transport ; Metagenomics ; Solid Waste ; Food Loss and Waste ; Edible Seaweeds ; }, abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6 % improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32 %. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9 %) and hydrogenotrophic methanogens Methanoculleus (+17.7 %); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255 %), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.}, }
@article {pmid41298102, year = {2026}, author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A}, title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.}, journal = {Gut}, volume = {75}, number = {2}, pages = {316-325}, pmid = {41298102}, issn = {1468-3288}, mesh = {Humans ; *Pancreatitis/complications/microbiology/mortality ; Male ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; *Diabetes Mellitus/microbiology/etiology ; Prospective Studies ; Follow-Up Studies ; Aged ; Adult ; Acute Disease ; Disease Progression ; }, abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.<br><br>OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.<br><br>DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.<br><br>RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for &#x3b2;-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.<br><br>CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.<br><br>TRIAL REGISTRATION NUMBER: NCT04777812.}, }
@article {pmid41298327, year = {2025}, author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ}, title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70229}, pmid = {41298327}, issn = {1758-2229}, support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; }, mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; }, abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.}, }
@article {pmid41298355, year = {2025}, author = {Holcik, L and von Haeseler, A and Pflug, FG}, title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10523}, pmid = {41298355}, issn = {2041-1723}, mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; }, abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.}, }
@article {pmid41298564, year = {2025}, author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP}, title = {Laser-assisted microbial culturomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10614}, pmid = {41298564}, issn = {2041-1723}, support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Biofilms/growth &amp; development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/growth &amp; development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; }, abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.}, }
@article {pmid41299176, year = {2026}, author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS}, title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.}, journal = {Nature}, volume = {649}, number = {8098}, pages = {982-990}, pmid = {41299176}, issn = {1476-4687}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; S10 RR026780/RR/NCRR NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; Prophages/genetics/physiology/isolation &amp; purification ; Feces/microbiology/virology ; *Bacteria/virology/genetics/classification ; Virus Integration ; Gene Transfer, Horizontal ; Male ; Female ; }, abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.}, }
@article {pmid41299512, year = {2025}, author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B}, title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.}, journal = {Reproductive biology and endocrinology : RB&amp;E}, volume = {23}, number = {1}, pages = {154}, pmid = {41299512}, issn = {1477-7827}, mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation &amp; purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; }, abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.<br><br>METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n&#x2009;=&#x2009;15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n&#x2009;=&#x2009;13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.<br><br>RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p&#x2009;=&#x2009;0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.<br><br>CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.}, }
@article {pmid41299624, year = {2025}, author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W}, title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {242}, pmid = {41299624}, issn = {2049-2618}, mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.<br><br>RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.<br><br>CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.}, }
@article {pmid41299634, year = {2025}, author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V}, title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {241}, pmid = {41299634}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; }, abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.<br><br>RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.<br><br>CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.}, }
@article {pmid41299763, year = {2025}, author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N}, title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {243}, pmid = {41299763}, issn = {2049-2618}, mesh = {*Gene Transfer, Horizontal ; Animals ; Antarctic Regions ; *Microbiota/genetics ; *Porifera/microbiology/physiology ; Cold Temperature ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; *Adaptation, Physiological/genetics ; Seawater/microbiology ; Phylogeny ; Acclimatization ; }, abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.<br><br>RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.<br><br>CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.}, }
@article {pmid41305529, year = {2025}, author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W}, title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.}, journal = {Viruses}, volume = {17}, number = {11}, pages = {}, pmid = {41305529}, issn = {1999-4915}, support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; }, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; }, abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.}, }
@article {pmid41305578, year = {2025}, author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium,  and Molano, LG and Keller, V}, title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.}, journal = {Nutrients}, volume = {17}, number = {22}, pages = {}, pmid = {41305578}, issn = {2072-6643}, support = {469073465//DFG/ ; }, mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Metagenome ; }, abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.}, }
@article {pmid41306589, year = {2025}, author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H}, title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1708266}, pmid = {41306589}, issn = {2235-2988}, mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation &amp; purification ; *Murinae/microbiology ; }, abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.<br><br>METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.<br><br>RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.<br><br>CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.}, }
@article {pmid41307322, year = {2025}, author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M}, title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.}, journal = {Journal of periodontal research}, volume = {60}, number = {12}, pages = {1237-1253}, pmid = {41307322}, issn = {1600-0765}, support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Saliva/microbiology ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Feces/microbiology ; Female ; Metabolomics ; Adult ; Middle Aged ; *Mouth/microbiology ; Multiomics ; }, abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.}, }
@article {pmid41308447, year = {2025}, author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H}, title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.}, journal = {Journal of hazardous materials}, volume = {500}, number = {}, pages = {140613}, doi = {10.1016/j.jhazmat.2025.140613}, pmid = {41308447}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Drug Resistance, Microbial/drug effects/genetics ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/pharmacology ; *Anti-Inflammatory Agents/pharmacology ; Lipopolysaccharides ; Male ; }, abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.}, }
@article {pmid41308739, year = {2026}, author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S}, title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.}, journal = {Journal of advanced research}, volume = {86}, number = {}, pages = {1035-1047}, pmid = {41308739}, issn = {2090-1224}, mesh = {Animals ; *Anthraquinones/pharmacology ; *Pancreatitis/drug therapy/metabolism/pathology/chemically induced ; Mice ; *Signal Transduction/drug effects ; *Acinar Cells/drug effects/metabolism/pathology ; *Methylamines/metabolism ; Male ; Gastrointestinal Microbiome/drug effects ; Inflammation/metabolism/drug therapy ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Disease Models, Animal ; NF-kappa B/metabolism ; Acute Disease ; }, abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.<br><br>OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.<br><br>METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography&#x2012;mass spectrometry (LC&#x2012;MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.<br><br>RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.<br><br>CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-&#x3ba;B/NLRP3 signaling pathway and inhibiting acinar cell inflammation.}, }
@article {pmid41309379, year = {2025}, author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH}, title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2506014}, pmid = {41309379}, issn = {1738-8872}, mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Streptococcus/metabolism ; }, abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.}, }
@article {pmid41309890, year = {2025}, author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E}, title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42423}, pmid = {41309890}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; 100217/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; }, abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.}, }
@article {pmid41310063, year = {2025}, author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM}, title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45469}, pmid = {41310063}, issn = {2045-2322}, support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Feces/microbiology ; Female ; Male ; Adult ; Middle Aged ; Health Status ; }, abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.}, }
@article {pmid41310455, year = {2025}, author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X}, title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {3}, pmid = {41310455}, issn = {1471-2180}, support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Animal Feed/analysis ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; *Poaceae ; *Edible Grain ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; United States ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.}, }
@article {pmid41310797, year = {2025}, author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X}, title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.}, journal = {Radiation oncology (London, England)}, volume = {20}, number = {1}, pages = {179}, pmid = {41310797}, issn = {1748-717X}, support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; }, mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; }, abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.<br><br>METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72&#xa0;h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.<br><br>RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p&#x2009;<&#x2009;0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4&#x2009;+&#x2009;T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5&#x207a; intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.<br><br>CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.}, }
@article {pmid41310806, year = {2025}, author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J}, title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {248}, pmid = {41310806}, issn = {2049-2618}, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; }, abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.<br><br>RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.<br><br>CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.}, }
@article {pmid41312195, year = {2025}, author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W}, title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {5191656}, pmid = {41312195}, issn = {1865-1682}, mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; }, abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.}, }
@article {pmid41312680, year = {2026}, author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H}, title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.}, journal = {The Journal of dermatology}, volume = {53}, number = {3}, pages = {430-436}, pmid = {41312680}, issn = {1346-8138}, support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/immunology ; *Cyclosporine/therapeutic use/pharmacology ; Male ; Female ; Adult ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Skin/microbiology/drug effects/immunology ; Middle Aged ; *Mycobiome/drug effects ; Malassezia/isolation &amp; purification ; Young Adult ; Calcineurin Inhibitors/therapeutic use/pharmacology ; DNA, Fungal/isolation &amp; purification ; Treatment Outcome ; }, abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.}, }
@article {pmid41313018, year = {2025}, author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0086225}, pmid = {41313018}, issn = {2379-5077}, support = {2022YFD2100700//National Key Research and Development Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; BR221203//Fundamental Research Funds of Inner Mongolia Agricultural University/ ; }, mesh = {Humans ; Female ; *Osteoarthritis, Knee/drug therapy/microbiology/therapy ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Postmenopause ; Middle Aged ; *Bifidobacterium animalis ; Aged ; *Chondroitin Sulfates/therapeutic use ; Treatment Outcome ; *Chondroitin/therapeutic use ; }, abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.<br><br>IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.}, }
@article {pmid41313537, year = {2026}, author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS}, title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.}, journal = {Probiotics and antimicrobial proteins}, volume = {18}, number = {4}, pages = {5223-5245}, pmid = {41313537}, issn = {1867-1314}, mesh = {Humans ; *Obesity/microbiology/metabolism/therapy ; *Gastrointestinal Microbiome ; Probiotics/administration &amp; dosage ; Animals ; Prebiotics/administration &amp; dosage ; Dysbiosis/microbiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.}, }
@article {pmid41313993, year = {2025}, author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y}, title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128135}, doi = {10.1016/j.jenvman.2025.128135}, pmid = {41313993}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Carbon Dioxide ; Fermentation ; *Microbiota ; Soil/chemistry ; }, abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.}, }
@article {pmid41314069, year = {2025}, author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK}, title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181062}, doi = {10.1016/j.scitotenv.2025.181062}, pmid = {41314069}, issn = {1879-1026}, mesh = {India ; Seasons ; *Microbiota ; *Railroads ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Bacteria/classification ; }, abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.}, }
@article {pmid41315190, year = {2025}, author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and ,  and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M}, title = {Unveiling the global urban virome through wastewater metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10707}, pmid = {41315190}, issn = {2041-1723}, support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; }, mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; Cities ; Animals ; Metagenome ; }, abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.}, }
@article {pmid41315266, year = {2025}, author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P}, title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10777}, pmid = {41315266}, issn = {2041-1723}, support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Zea mays/microbiology/genetics/growth &amp; development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; }, abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.}, }
@article {pmid41315331, year = {2025}, author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S}, title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {223}, pmid = {41315331}, issn = {2055-5008}, support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; }, mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; }, abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.}, }
@article {pmid41315430, year = {2025}, author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D}, title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42704}, pmid = {41315430}, issn = {2045-2322}, support = {R01 DK124581/DK/NIDDK NIH HHS/United States ; R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; }, mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; }, abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).}, }
@article {pmid41316248, year = {2025}, author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N}, title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {6}, pmid = {41316248}, issn = {1479-5876}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/virology/blood ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; Metabolomics ; Case-Control Studies ; }, abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent metabolic disorder with complex gut microbiome involvement. While bacterial dysbiosis in NAFLD has been widely studied, the role of the gut virome remains largely unexplored. METHODS: We profiled gut viral communities from 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene repertoires were analyzed. Serum metabolomic data were integrated to assess virus–metabolite interactions, and random forest models were constructed to evaluate the diagnostic potential of viral signatures. RESULTS: Overall viral diversity showed no significant differences between NAFLD and controls, but subtle compositional shifts were detected at the vOTU level, with 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched phages primarily targeted Bacteroides, whereas non-NAFLD-enriched phages were associated with beneficial genera such as Faecalibacterium, Oscillibacter, and Prevotella. Functional annotation revealed a reorganization of viral gene repertoires: genes involved in DNA recombination and horizontal transfer (e.g. int, recD) were depleted, while those related to host interaction and stress response (e.g. xerD, dnaK, hipB) were enriched in NAFLD, indicating enhanced viral persistence and host communication. Serum metabolomic profiling identified 8 differential metabolites, and correlation analysis linked specific vOTUs with altered metabolic pathways. A random forest model based on viral features achieved an AUC of 0.758, outperforming the bacterial model, while integration of viral and bacterial features further improved prediction (AUC = 0.837). CONCLUSION: The gut virome in NAFLD undergoes compositional and functional remodeling characterized by a shift toward host-adaptive, metabolically interactive viral communities. These viral alterations are closely associated with host metabolic changes and demonstrate strong diagnostic potential. Our findings highlight the virome as an overlooked yet critical component of the gut ecosystem in NAFLD pathogenesis and as a promising source of noninvasive biomarkers for disease prediction and monitoring.}, }
@article {pmid41316344, year = {2025}, author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J}, title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {6}, pmid = {41316344}, issn = {2049-2618}, support = {82171317//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Female ; Male ; Mice ; Bacteria/metabolism ; *Brain-Gut Axis/drug effects ; *Butyrates/metabolism ; Cell Line ; *Cognitive Dysfunction/drug therapy/microbiology ; Gastrointestinal Microbiome ; Glucuronates/metabolism ; *Infarction, Middle Cerebral Artery/complications/microbiology ; *Mannose/analogs &amp; derivatives/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Neurogenesis/drug effects ; *Oligosaccharides/pharmacology/therapeutic use ; Disease Models, Animal ; }, abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.<br><br>RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation.&#xa0;Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects.&#xa0;In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.<br><br>CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.}, }
@article {pmid41316726, year = {2026}, author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P}, title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D902-D911}, pmid = {41316726}, issn = {1362-4962}, support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; }, mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; }, abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.}, }
@article {pmid41317994, year = {2026}, author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM}, title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {2}, pages = {101129}, pmid = {41317994}, issn = {1938-3207}, support = {R01 AG055948/AG/NIA NIH HHS/United States ; R01 AR072741/AR/NIAMS NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Bone Density ; Aged ; *Gastrointestinal Microbiome/physiology ; *Dietary Approaches To Stop Hypertension ; Middle Aged ; Puerto Rico/ethnology ; Diet ; *Bone and Bones/physiology ; Absorptiometry, Photon ; Osteoporosis ; }, abstract = {BACKGROUND: Bone mineral density (BMD) explains fractures incompletely; studies relating lifestyle to bone quality are lacking.<br><br>OBJECTIVES: This study aims to examine associations of diet quality with bone measures [bone material strength index (BMSi), trabecular bone score (TBS), BMD], evaluate moderation by inflammation, identify gut microbiome features linked to diet quality, and quantify diet-microbiome-bone relationships.<br><br>METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored food frequency questionnairew, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with microbiome multivariate association with linear models regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).<br><br>RESULTS: DASH score was not associated with BMSi [&#x3b2; = -0.10; 95% confidence interval (CI): -0.46, 0.27; P = 0.60], TBS (&#x3b2; = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (&#x3b2; = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (&#x3b2; = 0.002; 95% CI: -0.003, 0.006, P = 0.52) but was at total hip (&#x3b2; = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (&#x3b2; = -0.0001, P = 0.89). Lachnospira eligens was 1 of 4 taxa positively associated with DASH score and BMD. No microbial pathways were associated with the DASH score.<br><br>CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.}, }
@article {pmid41318497, year = {2025}, author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X}, title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {24}, pmid = {41318497}, issn = {1479-5876}, support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; }, mesh = {*Lupus Erythematosus, Systemic/microbiology ; Humans ; *Mycobiome ; *Microbial Interactions ; *Fungi/genetics ; Bacteria ; *Gastrointestinal Microbiome ; Case-Control Studies ; Feces/microbiology ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a complex autoimmune disorder shaped by host genetics and environmental exposures, including the gut microbiota. While bacterial dysbiosis in SLE is well characterized, the role of the gut mycobiome and its cross-kingdom interactions remains largely unexplored. METHODS: Using fecal metagenomic sequencing from 117 SLE patients and 115 healthy controls (HCs), we established a non-redundant fungal genome catalog and revealed significant alterations in fungal composition, function, and cross-kingdom ecology. RESULTS: Fungal diversity was increased in SLE, with enrichment of potentially pathogenic taxa such as Candida, Malassezia, and Trichophyton, and depletion of commensal genera such as Pichia. Functional analysis showed expanded biosynthetic and redox capacities in SLE-associated fungi, including enrichment of RiPP- and terpene-related biosynthetic gene clusters and oxidative stress–related Pfam domains. Several predicted metabolites—such as kynurenine, phenylacetic acid, secondary bile acids, and acylcarnitines—were linked to immune activation and inflammation, suggesting that fungal metabolism may contribute to immune dysregulation. Network analysis revealed sparser and less centralized fungal–bacterial interactions in SLE, indicating disrupted ecological stability and the emergence of fungal taxa as key structural drivers. Integrating fungal and bacterial profiles markedly improved diagnostic performance (AUC = 0.934), underscoring the complementary predictive value of the gut mycobiome. In contrast, post-treatment samples showed reduced fungal richness but no major compositional shifts. CONCLUSIONS: This study provides a comprehensive, multi-dimensional view of the gut mycobiome in SLE, demonstrating its taxonomic, functional, and ecological remodeling. Our findings highlight the potential contribution of fungal metabolic and redox activities to SLE pathogenesis and support the inclusion of fungi in multi-kingdom microbiome frameworks for disease diagnosis and therapeutic development.}, }
@article {pmid41318814, year = {2026}, author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C}, title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.}, journal = {British journal of cancer}, volume = {134}, number = {3}, pages = {439-446}, pmid = {41318814}, issn = {1532-1827}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Adrenal Cortex Hormones/administration &amp; dosage/therapeutic use ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Antibodies, Monoclonal, Humanized/administration &amp; dosage/therapeutic use ; *Claudins/immunology ; Gastrointestinal Microbiome/drug effects ; Granulocyte Colony-Stimulating Factor/administration &amp; dosage/therapeutic use ; *Immunotherapy, Adoptive/methods ; Retrospective Studies ; *Stomach Neoplasms/therapy/immunology/pathology/drug therapy ; Treatment Outcome ; }, abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.<br><br>METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.<br><br>RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P&#x2009;<&#x2009;0.001) and overall survival (OS) (3.9 vs. 9.5 months; P&#x2009;<&#x2009;0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.<br><br>CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.<br><br>TRIAL REGISTRATION: NCT03874897.}, }
@article {pmid41319383, year = {2026}, author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L}, title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.}, journal = {Water research}, volume = {290}, number = {}, pages = {125031}, doi = {10.1016/j.watres.2025.125031}, pmid = {41319383}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Bioreactors/microbiology ; Waste Disposal, Fluid ; Anaerobiosis ; Microbiota ; Wastewater ; }, abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.}, }
@article {pmid41319542, year = {2026}, author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W}, title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.}, journal = {Food chemistry}, volume = {499}, number = {}, pages = {147314}, doi = {10.1016/j.foodchem.2025.147314}, pmid = {41319542}, issn = {1873-7072}, mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation &amp; purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; }, abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.}, }
@article {pmid41320324, year = {2026}, author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P}, title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.}, journal = {Gut}, volume = {75}, number = {5}, pages = {968-983}, pmid = {41320324}, issn = {1468-3288}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Oleic Acid/metabolism ; Humans ; Mice ; *Colorectal Neoplasms/pathology/microbiology/metabolism ; *Stress, Psychological/complications/microbiology ; Neoplasm Metastasis ; *Dysbiosis/microbiology ; Male ; Female ; }, abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.<br><br>OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.<br><br>DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.<br><br>RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.<br><br>CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.}, }
@article {pmid41324463, year = {2025}, author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I}, title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41324463}, issn = {1751-7370}, support = {101000213//Horizon2020/ ; ERC 866530/ERC_/European Research Council/International ; ISF 979/25//Israel Science Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology/growth &amp; development ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; }, abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes, including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.}, }
@article {pmid41326129, year = {2026}, author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S}, title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.}, journal = {Pesticide biochemistry and physiology}, volume = {216}, number = {Pt 1}, pages = {106807}, doi = {10.1016/j.pestbp.2025.106807}, pmid = {41326129}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; }, abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.}, }
@article {pmid41327018, year = {2025}, author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D}, title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {28}, pmid = {41327018}, issn = {1471-2229}, support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; }, mesh = {*Soil Microbiology ; *Curcuma/growth &amp; development ; *Soil/chemistry ; Metagenomics ; Agriculture/methods ; *Microbiota ; Nutrients/analysis ; Bacteria/genetics ; Nitrogen/analysis ; }, abstract = {BACKGROUND: Turmeric (Curcuma longa L.) is a key spice, medicinal and industrially important crop that is increasingly being cultivated under sustainable practices such as natural farming system (NFS). This study compares NFS and conventional/chemical farming system (CFS) in terms of soil physicochemical properties, enzyme activities, microbial diversity, and yield parameters, providing a comprehensive understanding of their ecological and agronomic impacts. RESULTS: Field experiments evaluated nine NFS treatments alongside CFS for high throughput amplicon (16S rRNA and ITS) metagenomics, soil physicochemical properties, enzyme activities, and yield parameters. NFS treatments with ≥ 5 t/ha mulching and 4 t/ha Ghanjeevamrit (i.e. NFS-T6 and NFS-T9) significantly enhanced soil organic carbon (~ 0.25%), nitrogen (~ 239.9 kg/ha), and phosphorus (~ 38.16 kg/ha), alongside elevated enzyme activities like alkaline phosphatase (ALP; ~112.11 µg PNP/g/hr) and protease (PR; ~16.22 µg Tyrosine/g/hr). These treatments also exhibited significantly higher microbial richness and evenness (Shannon index: ~5.09; Simpson index: ~0.981). NFS enriched beneficial bacterial (e.g., Priestia, unclassified Acidobacteria, etc.) and saprophytic fungal genera (e.g., Humicola, Mortierella, etc.), enhancing soil nutrient cycling and soil health. Conversely, CFS enriched chemical-resilient and pathogenic taxa (e.g., Alternaria, Curvularia, etc.). NFS-T5 (40.66 t/ha) and NFS-T9 (40.47 t/ha) yielded over twice the fresh rhizome compared to CFS. NFS treatments recorded higher net returns and Benefit-Cost Ratios (BCRs) of 7.51 to 10.57. Microbial profiling of natural farming (NF) inputs (Beejamrit, Jeevamrit, and Ghanjeevamrit) showed distinct bacterial and fungal communities influencing soil microbiome structure. Co-occurrence network analysis of NF soils revealed that microbial taxa introduced via NF inputs had limited integration into native soil communities, indicating selective incorporation governed by competitive ecological interactions. CONCLUSIONS: Natural farming practices significantly enhanced soil fertility, microbial community structure, enzymatic activity (ALP and PR), and turmeric productivity with superior BCRs. These findings provide scientific evidence supporting natural farming as a viable and sustainable agricultural approach, contributing to improved soil health and crop performance in turmeric cultivation.}, }
@article {pmid41327304, year = {2025}, author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S}, title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {13}, pmid = {41327304}, issn = {2049-2618}, support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Animals ; *Genistein/pharmacology/administration &amp; dosage ; *Nitrogen/metabolism ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Female ; Dietary Supplements ; Milk/chemistry ; Feces/microbiology ; Metabolomics ; Bacteria/classification/metabolism/genetics ; }, abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.<br><br>RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.<br><br>CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.}, }
@article {pmid41327409, year = {2025}, author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L}, title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {10}, pmid = {41327409}, issn = {2049-2618}, support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&amp;D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; }, mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Disease Resistance/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Plant Leaves/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; }, abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.<br><br>RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.<br><br>CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.}, }
@article {pmid41327428, year = {2025}, author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I}, title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {11}, pmid = {41327428}, issn = {2049-2618}, support = {ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; }, mesh = {*Plasmids/genetics ; *In Situ Hybridization, Fluorescence/methods ; *Single-Cell Analysis/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; *Microbiota/genetics ; Gene Transfer, Horizontal ; Humans ; }, abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.<br><br>RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy&#xa0;number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.<br><br>CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.}, }
@article {pmid41328016, year = {2025}, author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O}, title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587968}, pmid = {41328016}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; }, abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).}, }
@article {pmid41328030, year = {2025}, author = {Hickman, B and Korpela, K}, title = {Impact of data compositionality on the detection of microbiota responses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2590841}, pmid = {41328030}, issn = {1949-0984}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; }, abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.}, }
@article {pmid41328492, year = {2025}, author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C}, title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592423}, pmid = {41328492}, issn = {1949-0984}, mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics/growth &amp; development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; }, abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.<br><br>METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at&#x2009;<&#x2009;33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.<br><br>RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).<br><br>CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.}, }
@article {pmid41330099, year = {2025}, author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R}, title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181101}, doi = {10.1016/j.scitotenv.2025.181101}, pmid = {41330099}, issn = {1879-1026}, mesh = {Animals ; *Oligochaeta/physiology/virology/microbiology ; *Gastrointestinal Microbiome ; Soil Pollutants/metabolism ; Inactivation, Metabolic ; RNA, Ribosomal, 16S ; Biodegradation, Environmental ; Bacteria ; Metagenome ; }, abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.}, }
@article {pmid41330199, year = {2026}, author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ}, title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128411}, doi = {10.1016/j.micres.2025.128411}, pmid = {41330199}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; Desert Climate ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Temperature ; Rhizosphere ; Metagenome ; Microbiota/genetics ; Genome, Bacterial ; Soil/chemistry ; Phylogeny ; Ecosystem ; }, abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.}, }
@article {pmid41330454, year = {2026}, author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, JX and Su, KP and Wang, B}, title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.}, journal = {Brain, behavior, and immunity}, volume = {132}, number = {}, pages = {106203}, doi = {10.1016/j.bbi.2025.106203}, pmid = {41330454}, issn = {1090-2139}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy ; *Dysbiosis/physiopathology/microbiology ; Animals ; Brain/physiopathology ; Probiotics/therapeutic use ; Sleep/physiology ; *Brain-Gut Axis/physiology ; }, abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.}, }
@article {pmid41332430, year = {2025}, author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML}, title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593076}, pmid = {41332430}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; }, abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.}, }
@article {pmid41333806, year = {2025}, author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M}, title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1634631}, pmid = {41333806}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.<br><br>RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.<br><br>CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.}, }
@article {pmid41334589, year = {2025}, author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H}, title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593119}, pmid = {41334589}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; }, abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.}, }
@article {pmid41335477, year = {2025}, author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H}, title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, pmid = {41335477}, issn = {2057-5858}, mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation &amp; purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; }, abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.}, }
@article {pmid41338072, year = {2025}, author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S}, title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181092}, doi = {10.1016/j.scitotenv.2025.181092}, pmid = {41338072}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Microalgae/physiology ; *Soil Microbiology ; Fertilizers ; *Cyanobacteria/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Metabolomics ; Agriculture ; }, abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.}, }
@article {pmid41338123, year = {2026}, author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y}, title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.}, journal = {Journal of psychiatric research}, volume = {193}, number = {}, pages = {223-235}, doi = {10.1016/j.jpsychires.2025.11.029}, pmid = {41338123}, issn = {1879-1379}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Schizophrenia/microbiology/metabolism ; Male ; Female ; Adult ; *Proline/metabolism ; *Metabolome/physiology ; *Metagenome ; Middle Aged ; }, abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.}, }
@article {pmid41338426, year = {2026}, author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y}, title = {Decoding microbial-mediated sulfur transformation pathways in mangrove wetland: Metagenomic and hydrogeochemical insights.}, journal = {Environmental research}, volume = {290}, number = {}, pages = {123472}, doi = {10.1016/j.envres.2025.123472}, pmid = {41338426}, issn = {1096-0953}, mesh = {*Wetlands ; *Sulfur/metabolism ; China ; Metagenomics ; *Microbiota ; Geologic Sediments/microbiology ; Bacteria/metabolism/genetics ; Metagenome ; }, abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07 %) and Salmonella prevailing in mudflat sediments (23.87-60.98 %). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.}, }
@article {pmid41339319, year = {2025}, author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , }, title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9904}, pmid = {41339319}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; }, abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age <one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants had greater alpha diversity and significant differences in bacterial beta diversity, with 114 species and 38 genera differing in abundance. Indigenous infants almost exclusively had higher carriage of Megaspaera, Streptococcus, Caecibacter, Parolsenella and Prevotella species, and markedly higher numbers of gut viruses and fungi. Bifidobacteria ssp. were dominant in Indigenous infants. Despite encroaching Westernisation, the gut microbiome of Indigenous infants retains key features of traditional societies worldwide, attesting to the dominant influence of remote environment and traditional lifestyle in maintaining microbiome diversity.}, }
@article {pmid41339392, year = {2025}, author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R}, title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43082}, pmid = {41339392}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.}, }
@article {pmid41339745, year = {2026}, author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G}, title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.}, journal = {Nature microbiology}, volume = {11}, number = {1}, pages = {94-110}, pmid = {41339745}, issn = {2058-5276}, support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Mice ; *Phytochemicals/metabolism ; *Diet ; Biotransformation ; *Bacteria/metabolism/genetics/classification/enzymology ; Plants, Edible/metabolism/chemistry ; Metagenomics ; }, abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.}, }
@article {pmid41339801, year = {2025}, author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H}, title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {15}, pmid = {41339801}, issn = {1471-2180}, support = {7222026//Natural Science Foundation of Beijing Municipality/ ; }, mesh = {Humans ; Male ; Female ; Metagenomics/methods ; Adult ; *Microbiota/genetics ; Middle Aged ; *Haemophilus influenzae/genetics/isolation &amp; purification/classification ; Fungi/genetics/classification/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; *Mycoses/microbiology ; Aspergillus flavus/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.<br><br>METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.<br><br>RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score&#x2009;>&#x2009;5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r&#x2009;=&#x2009;-0.46, P&#x2009;=&#x2009;0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P&#x2009;<&#x2009;0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.<br><br>CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.}, }
@article {pmid41340070, year = {2025}, author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM}, title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {249}, pmid = {41340070}, issn = {2049-2618}, mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.<br><br>RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.<br><br>CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.}, }
@article {pmid41340071, year = {2025}, author = {Peng, J and Liu, X and Wang, J and Meng, N and Cai, R and Peng, Y and Han, Y and Liao, J and Li, C and Rubin-Blum, M and Ma, Q and Dong, X}, title = {Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {16}, pmid = {41340071}, issn = {2049-2618}, support = {1359/23//Israel Science Foundation/ ; 32170121//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; 3502Z202373076//Natural Science Foundation Project of Xiamen City/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; }, mesh = {*Quorum Sensing/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism ; Metagenome ; *Seawater/microbiology ; Phylogeny ; *Microbiota/genetics ; Ecosystem ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. However, its contribution in deep-sea cold seep ecosystems, where diverse microbial communities and frequent communication occur, remains poorly understood. In this study, we aimed to elucidate the occurrence and potential ecological roles of quorum sensing in cold seeps.<br><br>RESULTS: We analyzed 170 metagenomes and 33 metatranscriptomes from 17 global cold seep sites, identifying 299,355 quorum sensing genes from the cold seep non-redundant gene catalog. These genes represent 34 types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. A total of 32,500 quorum sensing genes were identified in 3576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs, and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles in cold seeps. Phylogenetic analysis and protein domain identification highlighted the involvement of key quorum sensing-related proteins (e.g., PDE, RpfC/G, CahR, and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression further confirmed the activity of representative LuxI-R pairs, and metabolomic profiling suggested the presence of putative quorum sensing inhibitors in cold seep sediments.<br><br>CONCLUSIONS: Overall, these findings highlight the complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere. Video Abstract.}, }
@article {pmid41340151, year = {2025}, author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE}, title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.}, journal = {Biology of sex differences}, volume = {17}, number = {1}, pages = {2}, pmid = {41340151}, issn = {2042-6410}, support = {R01 MH105447/MH/NIMH NIH HHS/United States ; R01MH105447-01/NH/NIH HHS/United States ; }, mesh = {Animals ; *Citalopram/pharmacology ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Pregnancy ; *Selective Serotonin Reuptake Inhibitors/pharmacology ; *Prenatal Exposure Delayed Effects/microbiology ; Rats ; Sex Characteristics ; *Metabolome/drug effects ; Animals, Newborn ; }, abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.<br><br>METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.<br><br>RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.<br><br>CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.}, }
@article {pmid41340249, year = {2025}, author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER}, title = {Molecular insights into the gut-thyroid axis: microbiota-driven biomarkers and diagnostic applications.}, journal = {Expert review of molecular diagnostics}, volume = {25}, number = {12}, pages = {915-928}, doi = {10.1080/14737159.2025.2599225}, pmid = {41340249}, issn = {1744-8352}, support = {451&#x2013;03-136/2025&#x2013;03/200017//Ministry of Science, Technological Development, and Innovation of the Republic of Serbia/ ; }, mesh = {Humans ; *Biomarkers/metabolism ; *Gastrointestinal Microbiome ; *Thyroid Gland/metabolism ; *Thyroid Diseases/diagnosis/metabolism/microbiology/etiology ; Metabolomics/methods ; Metagenomics/methods ; }, abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.<br><br>AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.<br><br>EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.}, }
@article {pmid41340567, year = {2025}, author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M}, title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593050}, pmid = {41340567}, issn = {1949-0984}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Cross-Sectional Studies ; Czech Republic ; *Diet, Vegan ; *Gastrointestinal Microbiome ; Italy ; *Metabolome ; Metagenome ; Multiomics ; Vegans ; }, abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.}, }
@article {pmid41342600, year = {2025}, author = {Bauchinger, F and Berry, D}, title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {1}, pages = {}, pmid = {41342600}, issn = {1574-6941}, support = {10.55776/COE7//Austrian Science Fund/ ; }, mesh = {Humans ; *Polysaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/metabolism/classification ; *Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; *Transcriptome ; Metagenomics ; Mucins/metabolism ; }, abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.}, }
@article {pmid41344333, year = {2026}, author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B}, title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.}, journal = {Current biology : CB}, volume = {36}, number = {1}, pages = {16-27.e4}, doi = {10.1016/j.cub.2025.10.087}, pmid = {41344333}, issn = {1879-0445}, mesh = {China ; *Microbiota ; Humans ; *Soil Microbiology ; Bacteria/classification/genetics ; *Fungi/classification/isolation &amp; purification ; }, abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.}, }
@article {pmid41344778, year = {2026}, author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S}, title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.}, journal = {Food microbiology}, volume = {135}, number = {}, pages = {104986}, doi = {10.1016/j.fm.2025.104986}, pmid = {41344778}, issn = {1095-9998}, mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteriophages/genetics/classification/isolation &amp; purification ; *Microbiota ; Food Microbiology ; }, abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.}, }
@article {pmid41345102, year = {2025}, author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M}, title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10051}, pmid = {41345102}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 27/2023//Chronic Disease Research Foundation (CDRF)/ ; }, mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; }, abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.}, }
@article {pmid41345261, year = {2026}, author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I}, title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.}, journal = {Nature microbiology}, volume = {11}, number = {1}, pages = {317-334}, pmid = {41345261}, issn = {2058-5276}, support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Archaea/classification/genetics ; *Bacteria/classification/genetics/metabolism ; Colorectal Neoplasms/microbiology ; Crohn Disease/microbiology ; Datasets as Topic ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Molecular Sequence Annotation ; Phylogeny ; Reference Values ; Genes, Bacterial ; }, abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.}, }
@article {pmid41345617, year = {2025}, author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN}, title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {1915}, pmid = {41345617}, issn = {1472-6831}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Mouth/microbiology ; Secondary Data Analysis ; *Microbiota ; }, abstract = {With an astounding global prevalence, both diabetes mellitus and gum disease pose significant health concerns. Gum disease has been identified as a risk factor for diabetes mellitus, and its treatment has shown improvements in markers of glucose management. We hypothesised that bacteria commonly associated with the oral microbiome could be disproportionately present in the gut of individuals with type 2 diabetes mellitus (T2DM) compared to healthy controls, suggesting a possible association between oral-associated bacteria and metabolic dysregulation. This hypothesis is supported by known interactions between the oral microbiome and systemic health, particularly the role of inflammation in both conditions. Therefore, we aimed to conduct a secondary analysis of whole-genomic sequencing data of studies published over the last twenty years (2004–2024) related to the gut microbiome of patients with T2DM to identify oral-associated bacteria in their gut compared to healthy individuals. We searched for studies related to the gut microbiome, whole metagenomics, and T2DM in Ovid Medline, EMBASE, and Web of Science databases. Studies that included whole metagenomic data from adult populations of all genders with T2DM were selected, resulting in the reanalysis of metagenomic sequencing data from a total of 9 studies (n = 1,224 metagenomes) for bacterial species data. From the 41,689 gut microbial species identified across the selected studies, 497 were classified as of oral-associated bacteria, corresponding with entries in the Human Oral Microbiome Database (HOMD). These oral bacteria comprised 1.19% of the gut microbiome. Notably, twenty oral-associated bacterial species were statistically significant in their presence among patients with diabetes compared to healthy individuals, irrespective of their abundance. Key oral pathogens included Corynebacterium striatum, Staphylococcus capitis, Kingella kingae, Corynebacterium propinquum, Prevotella sp. oral taxon 820, Prevotella scopos, Selenomonas artemidis, Bordetella pertussis, Selenomonas sp. oral taxon 137, and Staphylococcus hominis. Specifically, periodontal pathogens such as, Porphyromonas gingivalis, Tannerella forsythia, and Capnocytophaga sp. oral taxon 332 were found to be significantly higher in patients with T2DM. These bacteria are associated with conditions like endocarditis, bacteremia, and inflammatory responses, which are prevalent in both diabetes and periodontitis. Although causal relationships cannot be directly established, our findings suggest that bacteria typically originating from the oral cavity may be more prevalent in the gut microbiome of patients with T2DM, supporting the potential role of oral-gut microbial interactions in metabolic dysregulation.}, }
@article {pmid41345737, year = {2025}, author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H}, title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {18}, pmid = {41345737}, issn = {2049-2618}, support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; }, mesh = {Animals ; *Rumen/microbiology/virology/metabolism/drug effects ; *Goats/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Aflatoxin B1/toxicity/administration &amp; dosage ; Animal Feed/analysis ; *Metabolome/drug effects ; Bacteria/classification/genetics/drug effects/isolation &amp; purification/metabolism ; Fermentation ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; }, abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.<br><br>RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.<br><br>CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.}, }
@article {pmid41345831, year = {2025}, author = {Bu, Y and Sun, F and Liu, L and He, X and Wang, H and Chen, Z and He, T and Xu, S and Zhao, X and Meng, X}, title = {Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {20}, pmid = {41345831}, issn = {1471-2164}, support = {CX23YQ31//Heilongjiang Agricultural Science and Technology Innovation Leapfrog Project/ ; CARS-37//Supported by China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Understanding the rumen microbiota's development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.<br><br>METHODS: Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).<br><br>RESULTS: The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P&#x2009;<&#x2009;0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P&#x2009;<&#x2009;0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41345979, year = {2025}, author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M}, title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {48}, pmid = {41345979}, issn = {2049-2618}, support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Saliva/metabolism/chemistry/microbiology ; Female ; Male ; Dental Caries/microbiology ; *Microbiota ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood/complications ; *Glucose/metabolism ; Middle Aged ; *Fructose/metabolism/blood ; Adult ; Biofilms/growth &amp; development ; Metabolomics/methods ; Aged ; *Gingiva/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.<br><br>RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.<br><br>CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.}, }
@article {pmid41345980, year = {2025}, author = {Jiang, Y and Che, L and Li, SC}, title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {17}, pmid = {41345980}, issn = {2049-2618}, support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Non-alcoholic Fatty Liver Disease/microbiology ; Metabolic Networks and Pathways ; Cohort Studies ; }, abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.<br><br>RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.<br><br>CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.}, }
@article {pmid41346331, year = {2025}, author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M}, title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.}, journal = {Journal of food science}, volume = {90}, number = {12}, pages = {e70751}, doi = {10.1111/1750-3841.70751}, pmid = {41346331}, issn = {1750-3841}, support = {BT/PR46349/AAQ/3/1063/2022//&#x2003;Department of Biotechnology/ ; //&#x2003;Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; }, abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.}, }
@article {pmid41347789, year = {2025}, author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS}, title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {12}, pages = {e0098825}, pmid = {41347789}, issn = {1098-5336}, support = {S10 OD034282/OD/NIH HHS/United States ; 1-106223-01-01//Electric Power Research Institute/ ; }, mesh = {*Molybdenum/metabolism ; *Groundwater/microbiology/chemistry ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Microbiota ; }, abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.}, }
@article {pmid41348443, year = {2025}, author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM}, title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, pmid = {41348443}, issn = {2057-5858}, mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; }, abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.}, }
@article {pmid41348596, year = {2025}, author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA}, title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {6}, pages = {}, pmid = {41348596}, issn = {1477-4054}, support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; }, mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; }, abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.}, }
@article {pmid41348832, year = {2025}, author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A}, title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337760}, pmid = {41348832}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.}, }
@article {pmid41349311, year = {2026}, author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A}, title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110820}, doi = {10.1016/j.vetmic.2025.110820}, pmid = {41349311}, issn = {1873-2542}, mesh = {Animals ; *Abattoirs ; Swine/microbiology ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *Meat/microbiology ; Food Microbiology ; }, abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.}, }
@article {pmid41350118, year = {2026}, author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T}, title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.}, journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {55}, number = {3}, pages = {368-380}, pmid = {41350118}, issn = {1600-0714}, mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; Male ; *Microbiota/genetics ; *Mouth Neoplasms/microbiology/pathology ; Female ; Middle Aged ; Aged ; Saliva/microbiology ; Case-Control Studies ; Adult ; *Mouth/microbiology ; DNA, Bacterial ; }, abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.}, }
@article {pmid41350329, year = {2025}, author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T}, title = {Differences in prokaryotic and viral community between rumen and feces.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43232}, pmid = {41350329}, issn = {2045-2322}, mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; }, abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.}, }
@article {pmid41350543, year = {2025}, author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL}, title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43215}, pmid = {41350543}, issn = {2045-2322}, support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; }, mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; }, abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.}, }
@article {pmid41350554, year = {2025}, author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M}, title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {560}, pmid = {41350554}, issn = {2045-2322}, mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Fragile X Syndrome/microbiology/psychology ; Pilot Projects ; Male ; Child ; Female ; *Gastrointestinal Microbiome/drug effects ; }, abstract = {The gut microbiome (GM) is increasingly recognized as a key modulator of neurodevelopment via the microbiome-gut-brain axis. Fragile X syndrome (FXS), the most common inherited monogenic cause of intellectual disability, shares behavioural and molecular features with other neurodevelopmental disorders (NDDs), yet the role of the GM in FXS remains largely unexplored. In this open-label, single-arm trial, 15 children with genetically confirmed FXS received a daily probiotic formulation containing Lactobacillus casei, Lactobacillus salivarius, and Bifidobacterium breve for 12 weeks. Behavioural analysis and metagenomic sequencing with network and pathway analyses were performed before and after probiotic supplementation. Significant improvements were observed in irritability (-3.9, SD: ± 5.2; p = 0.027), communication (+ 1.7, SD: ± 2.5; p = 0.022), socialization (+ 1.4, SD: ± 2.1; p = 0.033), and adaptive behaviour (+ 1.3, SD: ± 1.4; p = 0.004). While overall microbial diversity remained stable, SparCC network analysis revealed increases in connectivity measures such as edge count and clustering coefficient, indicating denser microbial interactions and greater community coordination after probiotic supplementation. Functional profiling showed trends toward increased microbial activity in fatty acid biosynthesis, NAD salvage, and starch degradation pathways. This pilot study provides initial evidence that probiotics may modulate structural and functional properties of the GM, with potential links to improved behavioural outcomes in children with FXS. Larger, controlled trials are needed to validate the therapeutic potential of GM-targeted interventions in FXS and related NDDs.}, }
@article {pmid41350579, year = {2025}, author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M}, title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {4}, pmid = {41350579}, issn = {2055-5008}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Infant ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; Metagenomics/methods ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.}, }
@article {pmid41351056, year = {2025}, author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ}, title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {253}, pmid = {41351056}, issn = {2049-2618}, support = {DE-AC02-05CH11231//DOE/ ; DE-AC05-76RL01830//DOE/ ; }, mesh = {*Microbiota/genetics ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; North America ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Adaptation, Physiological ; Metagenomics/methods ; }, abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.<br><br>RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.<br><br>CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.}, }
@article {pmid41351708, year = {2025}, author = {Campbell, KL and Armitage, AR and Labonté, JM}, title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {21}, pmid = {41351708}, issn = {1432-184X}, mesh = {*Wetlands ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Geologic Sediments/microbiology/virology ; Nitrogen/metabolism ; Poaceae/microbiology ; Carbon/metabolism ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Sulfur/metabolism ; Ecosystem ; }, abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.}, }
@article {pmid41351981, year = {2026}, author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X}, title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {150}, number = {}, pages = {157610}, doi = {10.1016/j.phymed.2025.157610}, pmid = {41351981}, issn = {1618-095X}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Male ; Mice ; *Reactive Oxygen Species/metabolism ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; }, abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.<br><br>PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.<br><br>METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.<br><br>RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.<br><br>CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.}, }
@article {pmid41352011, year = {2026}, author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X}, title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140640}, doi = {10.1016/j.jhazmat.2025.140640}, pmid = {41352011}, issn = {1873-3336}, mesh = {*Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Hydrocarbons, Chlorinated/metabolism ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Microbiota ; }, abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.}, }
@article {pmid41352476, year = {2026}, author = {Su, J and Zhao, K and Zhou, X and Pan, Z and Xia, C}, title = {Early-life exposure to linezolid caused gut microbiota dysbiosis can be inherited from parents to offspring.}, journal = {Chemico-biological interactions}, volume = {424}, number = {}, pages = {111863}, doi = {10.1016/j.cbi.2025.111863}, pmid = {41352476}, issn = {1872-7786}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Linezolid/adverse effects/pharmacology ; Male ; *Dysbiosis/chemically induced/microbiology ; Female ; Mice ; *Anti-Bacterial Agents/adverse effects ; }, abstract = {BACKGROUND AND OBJECTIVES: Linezolid is a broad-spectrum antibiotic against Gram-positive bacterial infections. Widespread use of linezolid has brought about significant adverse effects and potential reproductive toxicity, but there is not yet any study regarding to the transgenerational impact.<br><br>METHODS: Gut microbiota and metabolites from the 12-weeks old male mice who were treated with one-week linezolid at 4 weeks of age, as well as those from their offsprings, were analyzed by metagenomics and metabolomics, respectively. Reproductivity of the male parents were monitored, including fertility, litter size, survival and weight gain of offsprings.<br><br>RESULTS: Offsprings survival from the linezolid-treated male parents was obviously decreased, although fertilities, litter size, or weight gain was not affected. The linezolid-induced gut microbiota perturbation in male parents was manifested as lower alpha diversity, distinguishing beta diversity, and the dramatically altered profiles of function genes and metabolites. Especially, linezolid exposure reversed the relationship between Dysosmobacter and butyrogenic species, and that between Dysosmobacter and inflammation-associated species. Interestingly, gut microbiota dysbiosis also existed in both female and male offsprings from the treated male parents. Moreover, it was found that the differential metabolites enriched in ABC transporter pathway were found male parents and offsprings, while those enriched in sphingolipid signaling pathway were only found in offsprings of both sexes.<br><br>CONCLUSIONS: The early-life short-term exposure to linezolid make long-term gut microbiota dysregulation, which was even inherited from parents to offsprings. These findings raised critical concern about the ecological consequences of early-life antibiotic exposure and clinical safety evaluations.}, }
@article {pmid41353361, year = {2025}, author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J}, title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {449}, pmid = {41353361}, issn = {2041-1723}, support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; INV048982//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; U19 AI084044/AI/NIAID NIH HHS/United States ; INV048956//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; R01 NR014784/NR/NINR NIH HHS/United States ; UH2AI083264//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI116799/AI/NIAID NIH HHS/United States ; T32AI162579//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Female ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Humans ; *Bacteria/genetics/classification ; Metagenome/genetics ; Metagenomics/methods ; Mycobiome/genetics ; Genome, Bacterial ; }, abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.}, }
@article {pmid41354223, year = {2026}, author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S}, title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.}, journal = {Diabetes research and clinical practice}, volume = {231}, number = {}, pages = {113043}, doi = {10.1016/j.diabres.2025.113043}, pmid = {41354223}, issn = {1872-8227}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Retinopathy/microbiology ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Diabetes Mellitus, Type 2/microbiology/complications ; }, abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.}, }
@article {pmid41354462, year = {2026}, author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C}, title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {7}, pages = {e12020}, pmid = {41354462}, issn = {2198-3844}, support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; }, mesh = {Humans ; China ; *Synovitis/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; *Osteoarthritis, Knee/metabolism/microbiology ; Middle Aged ; Proteomics/methods ; *Knee Joint/metabolism/pathology ; Aged ; Metabolomics/methods ; Dysbiosis/metabolism ; Synovial Fluid/metabolism ; Multiomics ; }, abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.}, }
@article {pmid41354674, year = {2025}, author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L}, title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {13}, pmid = {41354674}, issn = {2055-5008}, support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; }, mesh = {*Tryptophan/metabolism/biosynthesis ; Animals ; *Gastrointestinal Microbiome ; *Ursidae/microbiology ; Mice ; *Streptococcus/genetics/metabolism/isolation &amp; purification/classification ; Feces/microbiology/chemistry ; Metagenomics ; Whole Genome Sequencing ; Humans ; Male ; }, abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.}, }
@article {pmid41354765, year = {2025}, author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J}, title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {40}, pmid = {41354765}, issn = {2399-3642}, mesh = {Animals ; *Phascolarctidae/microbiology/virology ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/pathogenicity ; Age Factors ; *Drug Resistance, Microbial/genetics ; Male ; *Bacteria/genetics/pathogenicity/drug effects ; Female ; }, abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.}, }
@article {pmid41354993, year = {2025}, author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D}, title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {43425}, pmid = {41354993}, issn = {2045-2322}, support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ursidae/microbiology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage/therapeutic use ; *Antibiotic Prophylaxis ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Cefotaxime/pharmacology/administration &amp; dosage ; Feces/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/classification ; }, abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.}, }
@article {pmid41355553, year = {2025}, author = {Kim, MJ and Park, JH and Eom, YB}, title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.}, journal = {MicrobiologyOpen}, volume = {14}, number = {6}, pages = {e70197}, pmid = {41355553}, issn = {2045-8827}, support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; }, mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; }, abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.}, }
@article {pmid41358839, year = {2026}, author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q}, title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {1}, pages = {e0189025}, pmid = {41358839}, issn = {1098-5336}, mesh = {Animals ; *Chickens/microbiology/metabolism/growth &amp; development ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Animal Feed/analysis ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metabolomics ; Metagenomics ; Fermentation ; }, abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.<br><br>IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (&#x2264;20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.}, }
@article {pmid41360540, year = {2026}, author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J}, title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {223}, number = {Pt 2}, pages = {117842}, doi = {10.1016/j.foodres.2025.117842}, pmid = {41360540}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; }, abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.}, }
@article {pmid41360901, year = {2025}, author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R}, title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1067}, pmid = {41360901}, issn = {2045-2322}, support = {10045515//Innovate UK/ ; BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cattle ; *Ostertagia/immunology ; *Rumen/microbiology/parasitology ; *Ostertagiasis/veterinary/prevention &amp; control/parasitology/immunology ; *Vaccination/veterinary ; *Cattle Diseases/parasitology/prevention &amp; control/microbiology/immunology ; Abomasum/parasitology ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/parasitology ; }, abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.}, }
@article {pmid41361265, year = {2025}, author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J}, title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {33}, pmid = {41361265}, issn = {1471-2180}, support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Metagenome ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Phylogeny ; Genome, Bacterial ; }, abstract = {Antibiotic resistance poses a significant threat to human health, and the human gut microbiota serves as a major reservoir of antibiotic resistance genes (ARGs). In this study, we analyzed 149,515 metagenome-assembled genomes (MAGs) from human gut microbiomes and revealed marked geographic variations in the global distribution of gut-associated ARGs. Asia exhibits the highest diversity of ARGs. At the phylum level, Pseudomonadota was identified as the predominant ARG host among pathogenic bacteria, with its pathogenic strains frequently exhibiting high levels of multidrug resistant strains harboring ≥ 5 ARGs accounting for up to 88.5% and 79.1% in Africa and South America, respectively. Campylobacterota was also recognized as a potential high-risk ARG host phylum. Horizontal gene transfer (HGT) analysis revealed that ARG transmission predominantly occurred within the same phylum, with Bacillota being the most active donor, which was likely influenced by antibiotic selection pressure. Actinomycetota and Bacteroidota were identified as major recipients of interphylum HGT, indicating their greater capacity to acquire exogenous ARGs. Through the integration of deep learning and structural calculation, we also identified a potentially novel class of β-lactam resistance genes. This study provides a comprehensive global landscape of gut-associated resistomes, underscores the critical roles of public health infrastructure, antibiotic misuse, and HGT in shaping antimicrobial resistance (AMR), and offers methodological insights for the discovery of novel ARGs. Our findings highlight urgent challenges and provide a scientific basis for developing global AMR mitigation strategies.}, }
@article {pmid41361579, year = {2025}, author = {Anunobi, OO and Abiola, RB and Ogah, CF}, title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {1}, pages = {6}, pmid = {41361579}, issn = {1572-9699}, mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation &amp; purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.}, }
@article {pmid41363534, year = {2026}, author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y}, title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.}, journal = {mSphere}, volume = {11}, number = {1}, pages = {e0053925}, pmid = {41363534}, issn = {2379-5042}, mesh = {Animals ; China ; *Virome/genetics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Culicidae/virology ; Metagenomics ; *Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; *Genetic Variation ; Culex/virology ; }, abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.}, }
@article {pmid41364878, year = {2026}, author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ}, title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma.}, journal = {Blood advances}, volume = {10}, number = {5}, pages = {1634-1645}, pmid = {41364878}, issn = {2473-9537}, mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Immunotherapy, Adoptive/adverse effects/methods ; Aged ; Biomarkers ; Treatment Outcome ; Adult ; Recurrence ; }, abstract = {CD19 chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (R/R-DLBCL), but challenges such as posttreatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from patients with R/R-DLBCL were analyzed at apheresis (47 samples) and 1 month after infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly-diagnosed DLBCL, R/R-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders had higher levels of Bacteroides fragilis, whereas nonresponders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in R/R-DLBCL.}, }
@article {pmid41365051, year = {2026}, author = {Wang, H and Congzhu,  and Wang, J and Lin, X and Guo, Y and Kiani, FA and Zhou, X and Ding, Y}, title = {Clostridium perfringens can promote the formation of fatty liver in cows.}, journal = {Veterinary microbiology}, volume = {312}, number = {}, pages = {110826}, doi = {10.1016/j.vetmic.2025.110826}, pmid = {41365051}, issn = {1873-2542}, mesh = {Animals ; Cattle ; *Clostridium perfringens/pathogenicity/physiology ; *Fatty Liver/microbiology/veterinary ; *Cattle Diseases/microbiology ; Female ; *Clostridium Infections/veterinary/microbiology ; Cytokines/metabolism/genetics ; Gastrointestinal Microbiome ; Mice ; Liver/microbiology/pathology ; Dysbiosis/microbiology/veterinary ; Ileum/microbiology ; }, abstract = {During the periparturient period, reduced feed intake often causes negative energy balance in dairy cows, leading to fat mobilization, hepatic lipid accumulation, and fatty liver disease (FLD), ultimately compromising health and milk production. This study investigated the association between FLD and gut microbiota dysbiosis, with a particular focus on the role of Clostridium perfringens within the gut-liver axis. Metagenomic sequencing of ileal contents revealed a marked decrease in microbial diversity in cows with FLD, along with increased abundances of potential pathogens such as C. perfringens, Enterobacter cloacae, and Vibrio alginolyticus. Functional annotation indicated elevated expression of virulence factors (e.g., Hsp60, flagella, mu-toxin), antibiotic resistance genes (e.g., otrA, lsaC), and pathways related to lipopolysaccharide (LPS) biosynthesis and mitogen-activated protein kinase (MAPK) signaling pathways, suggesting enhanced pro-inflammatory potential. qPCR analysis of ileal tissue demonstrated reduced expression of tight junction proteins (zona occludens 1 (ZO-1), Claudin-1, and Occludin) and increased levels of pro-inflammatory cytokines (Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumour necrosis factor-alpha (TNF-α)), alongside a decrease in the anti-inflammatory cytokine interleukin-10 (IL-10), indicating compromised intestinal barrier function and local inflammation. Given the significant enrichment of C. perfringens in the ileum of FLD cows, we hypothesized its involvement in disease pathogenesis. To test this, C. perfringens was isolated and orally administered to antibiotic-pretreated mice fed a high-fat diet. These mice developed exacerbated hepatic steatosis, metabolic disturbances, and heightened inflammatory responses. Moreover, Western blot analysis revealed reduced expression of intestinal tight junction proteins (ZO-1, Claudin-1, Occludin), indicating increased intestinal permeability. Quantitative PCR confirmed upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and downregulation of IL-10 in both intestinal and hepatic tissues. These findings indicate that C. perfringens may promote FLD by impairing gut barrier integrity and enhancing inflammatory responses. In conclusion, our findings suggest that C. perfringens may contribute to the development of FLD in dairy cows by impairing intestinal barrier integrity and promoting systemic inflammation.}, }
@article {pmid41365368, year = {2026}, author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X}, title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.}, journal = {Bioresource technology}, volume = {442}, number = {}, pages = {133782}, doi = {10.1016/j.biortech.2025.133782}, pmid = {41365368}, issn = {1873-2976}, mesh = {*Phenanthrenes/metabolism ; *Cadmium/toxicity ; Biodegradation, Environmental/drug effects ; *Microbial Consortia/drug effects ; Arthrobacter/metabolism ; Klebsiella/metabolism ; Minerals/metabolism ; }, abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.}, }
@article {pmid41365917, year = {2025}, author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D}, title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {227}, pmid = {41365917}, issn = {2055-5008}, support = {314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; }, mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.}, }
@article {pmid41366061, year = {2026}, author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY}, title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.}, journal = {British journal of cancer}, volume = {134}, number = {3}, pages = {469-476}, pmid = {41366061}, issn = {1532-1827}, support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology ; *Life Style ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Diet ; Adult ; Aged ; Cohort Studies ; Age of Onset ; }, abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.<br><br>METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.<br><br>RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC&#x2009;=&#x2009;0.95, 95% CI&#x2009;=&#x2009;0.92-0.98).<br><br>CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.}, }
@article {pmid41366428, year = {2025}, author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW}, title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.}, journal = {Journal of neuroinflammation}, volume = {22}, number = {1}, pages = {285}, pmid = {41366428}, issn = {1742-2094}, support = {R01 NS127372/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; }, mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; }, abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.<br><br>METHODS: C57BL6/J mice were randomized to CCI (6&#xa0;m/s, 2&#xa0;mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16&#xa0;S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.<br><br>RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.<br><br>CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.}, }
@article {pmid41368641, year = {2025}, author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L}, title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1696701}, pmid = {41368641}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs &amp; derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; }, abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.<br><br>METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.<br><br>RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/I&#x3ba;B&#x3b1;/NF-&#x3ba;B pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.<br><br>CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-&#x3ba;B signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.}, }
@article {pmid41369293, year = {2025}, author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L}, title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41369293}, issn = {1751-7370}, support = {//ocean negative carbon emissions program (ONCE)/ ; //Shanghai Frontiers Research Fund of the Hadal Biosphere, the deep ocean microbiome and ecosystem program (DOME)/ ; 42276149//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Bacteria/metabolism/genetics/classification ; Microbiota ; *Hydrocarbons, Halogenated/analysis/metabolism ; Halogenation ; Carbon/analysis/metabolism ; *Organic Chemicals/metabolism/analysis ; Biodegradation, Environmental ; Metagenomics ; }, abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.}, }
@article {pmid41369685, year = {2025}, author = {Mohammadi, R and Morovati, H and Safari, F}, title = {The human mycobiome: a critical yet understudied component of health and disease.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {12}, pages = {}, pmid = {41369685}, issn = {1465-2080}, mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; }, abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.}, }
@article {pmid41370178, year = {2025}, author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS}, title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {41370178}, issn = {2050-084X}, support = {NIHR200915//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; }, abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.}, }
@article {pmid41370957, year = {2026}, author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G}, title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.}, journal = {Environment international}, volume = {207}, number = {}, pages = {109971}, doi = {10.1016/j.envint.2025.109971}, pmid = {41370957}, issn = {1873-6750}, mesh = {*Wastewater/microbiology ; *Gene Transfer, Horizontal ; *Microplastics/analysis ; *Microbiota ; Virulence Factors/genetics ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; }, abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.}, }
@article {pmid41371128, year = {2026}, author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH}, title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140758}, doi = {10.1016/j.jhazmat.2025.140758}, pmid = {41371128}, issn = {1873-3336}, mesh = {*Gene Transfer, Horizontal/drug effects ; Aquaculture ; *Gastrointestinal Microbiome/drug effects ; *Enrofloxacin/pharmacology ; Animals ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Fatty Acids, Volatile/metabolism ; Bacteriophages/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; }, abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.}, }
@article {pmid41371144, year = {2026}, author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y}, title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140716}, doi = {10.1016/j.jhazmat.2025.140716}, pmid = {41371144}, issn = {1873-3336}, mesh = {*Microbial Consortia ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Trichloroethanes/metabolism ; Chloroflexi/metabolism/genetics ; Halogenation ; Bacteria/metabolism/genetics ; }, abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.}, }
@article {pmid41372407, year = {2026}, author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N}, title = {Gut micro-organisms associated with health, nutrition and dietary interventions.}, journal = {Nature}, volume = {650}, number = {8101}, pages = {450-458}, pmid = {41372407}, issn = {1476-4687}, support = {/WT_/Wellcome Trust/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Diet ; Male ; Female ; United Kingdom ; Body Mass Index ; Risk Factors ; United States ; *Health ; Middle Aged ; *Nutritional Status ; Adult ; Metagenomics ; }, abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.}, }
@article {pmid41372637, year = {2026}, author = {Kosmopoulos, JC and Pallier, W and Malik, AA and Anantharaman, K}, title = {Ecosystem health shapes viral ecology in peatland soils.}, journal = {Nature microbiology}, volume = {11}, number = {1}, pages = {142-154}, pmid = {41372637}, issn = {2058-5276}, support = {DBI2047598//National Science Foundation (NSF)/ ; 2137424//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; *Viruses/genetics/classification/isolation &amp; purification ; United Kingdom ; Metagenome ; Microbiota ; Carbon ; Phylogeny ; }, abstract = {Peatlands hold up to one-third of Earth's soil carbon but are increasingly turning from being carbon sinks to becoming carbon sources due to human impacts. Restoration efforts aim to reverse this trend, but viral influences on peatland recovery remain unclear, despite viruses being potent regulators of microbiomes and ecosystem function. Here we sequenced soil metagenomes to study viral communities across seven UK peatlands, each encompassing areas representing three peatland ecosystem health statuses: natural, damaged and restored. We found that viral diversity and community structure were shaped by both geography and ecosystem health. Viruses were geographically widespread, yet exhibited ecosystem health-specific endemism and functional adaptation, highlighting their sensitivity to restoration. Virus-host dynamics ranged from stable 'piggyback-the-winner' relationships to decoupled dynamics in those infecting keystone aerobes, sulfate reducers, carbohydrate degraders and fermenters. These findings position viruses as dynamic drivers of peatland ecosystem recovery and could unlock pathways to bolster carbon retention and accelerate climate mitigation.}, }
@article {pmid41372750, year = {2025}, author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J}, title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {26}, pmid = {41372750}, issn = {1471-2180}, mesh = {*Wastewater/microbiology/chemistry ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Agricultural Irrigation ; Metals, Heavy/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Cities ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; }, abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.<br><br>METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.<br><br>RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37&#xa0;&#xb5;g/L), chromium (1.89&#xa0;&#xb5;g/L), and nickel (4.93&#xa0;&#xb5;g/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P&#x2009;<&#x2009;0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P&#x2009;<&#x2009;0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P&#x2009;<&#x2009;0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.<br><br>CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.}, }
@article {pmid41372802, year = {2025}, author = {Almas, S and Carpenter, RE and Tamrakar, VK and Singh, A and Sharma, A and Sharma, R}, title = {Precision metagenomics reveals microbial landscape in acute upper respiratory infections: a comprehensive dataset.}, journal = {BMC research notes}, volume = {19}, number = {1}, pages = {18}, pmid = {41372802}, issn = {1756-0500}, mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Acute Disease ; Male ; Female ; Middle Aged ; Adult ; }, abstract = {OBJECTIVES: The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina[®]/IDbyDNA Respiratory Pathogen ID/AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance.<br><br>DATA DESCRIPTION: This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial resistance detection, and therapeutic interventions. Its potential for reuse and integration with other omics datasets enhances its significance. The comprehensive nature of the data facilitates research into relationships between the respiratory microbiota and host factors, including clinical outcomes, immune responses, or genetic predispositions. Moreover, the article underscores the interdisciplinary potential by advocating for the integration of this dataset with other relevant datasets such as transcriptomics or metabolomics, enabling a deeper understanding of the intricate interactions in acute upper respiratory infections. The presented dataset contributes to the expanding knowledge in precision metagenomics and holds the promise to propel research and clinical practices in the field of respiratory diseases.}, }
@article {pmid41373768, year = {2025}, author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A}, title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, pmid = {41373768}, issn = {1422-0067}, support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; }, mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation &amp; purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; }, abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.}, }
@article {pmid41373884, year = {2025}, author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L}, title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.}, journal = {International journal of molecular sciences}, volume = {26}, number = {23}, pages = {}, pmid = {41373884}, issn = {1422-0067}, support = {LF-ST-21-500002//LEO Foundation/ ; }, mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; }, abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.}, }
@article {pmid41378778, year = {2025}, author = {Zhou, Y and Ren, X and Li, B and Tang, H and Guo, Y and Yang, L and Han, J and Zhou, B}, title = {Bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate Triggers IBD-like Pathology through the Gut Microbiota-Arachidonic Acid Axis: Protective Role of Akkermansia muciniphila.}, journal = {Environmental science &amp; technology}, volume = {59}, number = {50}, pages = {27156-27172}, doi = {10.1021/acs.est.5c12302}, pmid = {41378778}, issn = {1520-5851}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Inflammatory Bowel Diseases/chemically induced ; Arachidonic Acid/metabolism ; Akkermansia ; Phthalic Acids ; }, abstract = {Environmental pollutants are increasingly recognized as modulators of gut microbiota and metabolic pathways, contributing to the rising global incidence of inflammatory bowel disease (IBD). The novel brominated flame retardant bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH) is increasingly detected in ecosystems and human tissues, yet its impact on intestinal health remains unclear. Here, we combined shotgun metagenomics, untargeted metabolomics, and targeted biochemical assays in a murine model to reveal how TBPH drives IBD-like pathology. TBPH exposure resulted in shortened colons, disrupted epithelial barriers, and elevated systemic pro-inflammatory cytokines, accompanied by gut microbiota dysbiosis marked by depletion of Akkermansia muciniphila (AKK). Decreased abundance of AKK correlated with arachidonic acid (AA) accumulation and hyperactivation of the phospholipase A2 (PLA2)-cyclooxygenase 2 (COX2)-prostaglandin E2 (PGE2) inflammatory cascade, leading to NF-κB activation and mucosal injury. Supplementation with viable AKK restored AA homeostasis, suppressed inflammatory signaling, and preserved the barrier integrity. These results demonstrate a microbiota-dependent mechanism linking TBPH exposure to AA-driven intestinal inflammation and identify AKK as a critical protective species, which highlights the gut microbiota-AA metabolic axis as a potential mechanism for pollutant-induced intestinal disorders.}, }
@article {pmid41378921, year = {2026}, author = {Montini, A and Pellegrini, C and Loddo, G and Ravaioli, F and Baldelli, L and Mainieri, G and Pirazzini, C and Mazzotta, E and Carano, F and Sala, C and De Fanti, S and Bacalini, MG and Provini, F}, title = {Analysis of gut microbiota in Restless Legs Syndrome: searching for a metagenomic signature.}, journal = {Sleep}, volume = {49}, number = {4}, pages = {}, pmid = {41378921}, issn = {1550-9109}, support = {//Pan-European RLS Association/ ; }, mesh = {Humans ; *Restless Legs Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Metagenomics ; Feces/microbiology ; Sleep Initiation and Maintenance Disorders/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Surveys and Questionnaires ; }, abstract = {STUDY OBJECTIVES: We aim to analyze the microbiota composition in Restless Legs Syndrome (RLS) patients and its relationship with the different RLS phenotypes.<br><br>METHODS: We recruited idiopathic RLS (RLS) and insomnia (INS) patients and healthy subjects (CTRL). Validated questionnaires (Pittsburg Sleep Quality Index, International Restless Legs Syndrome Study Group Rating Scale, Insomnia Severity Index, Beck Depression Inventory-II) were administered in the RLS and INS. Fecal microbiota was analyzed by 16S rRNA gene sequencing according to Illumina metagenomics standard procedure on MiSeq Platform. Dada2 pipeline was used to process sequencing data, while DESeq2 and Aldex2 tools were used to calculate differential abundance taxa, correcting for age, sex, body mass index, sequencing run, and presence of mood disorders.<br><br>RESULTS: The sample included 37 RLS (28 females, mean age 64.78&#xa0;years), 31 INS (22 females, mean age 60.64&#xa0;years), and 33 CTRL (24 females, mean age 62.54&#xa0;years). Differential abundance analysis revealed a statistically significant decrease in the abundance of Lachnoclostridium and Flavonifractor genera in RLS compared to CTRL and INS, but not in the INS compared to CTRL. Lachnoclostridium abundance tended to decrease with long disease duration and a predominant motor phenotype. In the RLS group, several genera were identified as significantly associated with International Restless Legs Syndrome Study Group Rating Scale and Pittsburg Sleep Quality Index scores.<br><br>CONCLUSIONS: Although only a few previous studies have reported the presence of small intestinal bacterial overgrowth in RLS, to the best of our knowledge this is the first study to highlight significant differences in the gut microbiota composition of RLS compared to both CTRL and INS, identifying a specific RLS metagenomic signature. Statement of Significance This is the first study to comprehensively characterize the gut microbiota in patients with Restless Legs Syndrome (RLS), identifying a distinct microbial signature compared to insomnia patients and healthy controls. We observed alterations alpha and beta diversity and specific changes in bacterial families and genera, some of which significantly correlated with RLS clinical features. In particular, Lachnoclostridium genus was significantly reduced in RLS and tended to be less abundant in patients with longer disease duration and without sensory symptoms. This genus is known to modulate systemic inflammation through the production of short-chain fatty acids, suggesting a potential link between gut dysbiosis, inflammation, and dopaminergic dysfunction. These findings support a role for gut microbiota alterations in RLS pathogenesis and open new avenues for microbiota-based diagnostic and therapeutic strategies.}, }
@article {pmid41379027, year = {2025}, author = {Esvap, E and Ulgen, KO}, title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.}, journal = {Biotechnology journal}, volume = {20}, number = {12}, pages = {e70164}, doi = {10.1002/biot.70164}, pmid = {41379027}, issn = {1860-7314}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; }, abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.}, }
@article {pmid41379245, year = {2025}, author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S}, title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {12}, pages = {504}, pmid = {41379245}, issn = {1573-0972}, support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; }, mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation &amp; purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.}, }
@article {pmid41379255, year = {2025}, author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D}, title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.}, journal = {Archives of microbiology}, volume = {208}, number = {1}, pages = {65}, pmid = {41379255}, issn = {1432-072X}, mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; }, abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.}, }
@article {pmid41379797, year = {2025}, author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D}, title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0337322}, pmid = {41379797}, issn = {1932-6203}, mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation &amp; purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; }, abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.<br><br>METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n&#x2009;=&#x2009;37; 66.1%), IBD-Unclassified (n&#x2009;=&#x2009;9; 16.1%), ulcerative proctitis (n&#x2009;=&#x2009;7; 12.5%), and Crohn's disease (n&#x2009;=&#x2009;3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.<br><br>RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).<br><br>CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.}, }
@article {pmid41380611, year = {2026}, author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X}, title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119550}, doi = {10.1016/j.ecoenv.2025.119550}, pmid = {41380611}, issn = {1090-2414}, mesh = {*Mining ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; China ; *Lead/analysis/toxicity ; *Microbiota/drug effects ; *Zinc/analysis/toxicity ; Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Bacteria/genetics/drug effects/classification ; Agriculture ; Soil/chemistry ; Cadmium/analysis/toxicity ; Stress, Physiological ; }, abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.}, }
@article {pmid41380668, year = {2025}, author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and ,  and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM}, title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {12}, pages = {2148-2166.e8}, pmid = {41380668}, issn = {1934-6069}, support = {P01 HL154998/HL/NHLBI NIH HHS/United States ; R01 HL149883/HL/NHLBI NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; }, abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.}, }
@article {pmid41381025, year = {2026}, author = {Zabaleta, WDB and Gomez, JDR and Santofimio Villa, LF and Angarita, NB and Alzate, JF and Garzón, YEG and Cantillo-Barraza, O and Triana-Chavez, O and Vargas, PAO and Urrea, DA}, title = {Metatranscriptomic insights into feeding preferences, bacterial diversity, and insect-specific viruses genomics in Aedes aegypti populations from Ibagué, Colombia.}, journal = {Acta tropica}, volume = {273}, number = {}, pages = {107941}, doi = {10.1016/j.actatropica.2025.107941}, pmid = {41381025}, issn = {1873-6254}, mesh = {Animals ; *Aedes/virology/microbiology/physiology ; Colombia ; Female ; *Mosquito Vectors/virology/microbiology ; *Feeding Behavior ; *Bacteria/classification/genetics/isolation &amp; purification ; *Insect Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; Genome, Viral ; }, abstract = {Aedes aegypti is not only the primary vector of medically important arboviruses worldwide, but also a host of a wide range of arthropod-specific viruses (ISVs), whose genomic and biological diversity remains largely unknown across most regions of Colombia. Investigating its associated microbiota including viruses and bacteria is essential, as these interactions can influence vector competence. Metatranscriptomic analysis of this vector provides quantitative insights into the presence of such microorganisms and their potential links to blood meal sources. In this study, we analyzed 320 blood-fed female A. aegypti mosquitoes collected from urban areas of Ibagué, Colombia, using RNA-Seq to identify eukaryotic, prokaryotic, and viral sequences, with particular emphasis on insect-specific viruses (ISVs). This approach allowed us to assess the diversity and relative abundance of microorganisms across four mosquito populations, infer potential feeding sources, identify and recover complete viral genomes, and detect parasite families. Despite inherent limitations related to taxonomic classification based on databases, our findings contribute to a better understanding of the ecological and epidemiological characteristics of A. aegypti populations circulating in Ibagué, Colombia, and their vector-pathogen-host interactions.}, }
@article {pmid41381092, year = {2025}, author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM}, title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.}, journal = {Environmental microbiology reports}, volume = {17}, number = {6}, pages = {e70261}, pmid = {41381092}, issn = {1758-2229}, support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; }, mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; }, abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.}, }
@article {pmid41381437, year = {2025}, author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J}, title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11067}, pmid = {41381437}, issn = {2041-1723}, mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth &amp; development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; }, abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.}, }
@article {pmid41381751, year = {2025}, author = {Tabe, C and Motooka, D and Fujita, T and Makiguchi, T and Taima, K and Tanaka, H and Itoga, M and Ishioka, Y and Akita, T and Ishidoya, M and Chubachi, K and Fukushima, T and Tanaka, Y and Odagiri, H and Kameyama, Y and Kobori, Y and Tasaka, S and Fujii, H}, title = {The gut microbiota as a potential biomarker in patients with EGFR-mutant lung cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1672}, pmid = {41381751}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; ErbB Receptors/genetics/antagonists &amp; inhibitors ; Female ; Male ; *Lung Neoplasms/drug therapy/genetics/microbiology ; Middle Aged ; Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics/microbiology ; *Mutation ; Protein Kinase Inhibitors/therapeutic use/adverse effects ; RNA, Ribosomal, 16S/genetics ; Diarrhea/microbiology/chemically induced ; Biomarkers, Tumor/genetics ; Feces/microbiology ; }, abstract = {Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are highly effective against EGFR-mutant non-small cell lung cancer (NSCLC); however, identifying biomarkers that predict prognosis and adverse events is necessary. Although the gut microbiota is considered to be a biomarker for NSCLC without mutations, no studies have examined its potential as a biomarker for EGFR-mutant NSCLC. Here, we investigated the association between gut microbiota composition and diarrhea, a common side effect caused by EGFR-TKIs. In addition, we examined the association between the efficacy of EGFR-TKIs and the gut microbiota. A total of 21 NSCLC patients with EGFR mutations were enrolled. Fecal samples were collected prior to EGFR-TKI treatment and 16S rRNA metagenome sequencing was performed to evaluate the microbiota profile. In addition, α-diversity, β-diversity, and Linear discriminant analysis Effect Size (LEfSe) analyses were performed. The α-diversity of the gut microbiota was higher in patients with grade 0-1 diarrhea than in those with grade 2-3 diarrhea (Shannon, p = 0.0367). In terms of β-diversity, there was a significant difference in the best overall response between patients with a partial response (PR) to EGFR-TKIs and those with stable disease (SD)/progressive disease (PD) (weighted p = 0.041). Analysis of microbial composition revealed an increased abundance of Ruminococcus in the PR group. In patients taking EGFR-TKIs, a higher α-diversity may be associated with less severe diarrhea. In addition, a high abundance of Ruminococcus may be a potential biomarker for predicting favorable efficacy of EGFR-TKIs.}, }
@article {pmid41382117, year = {2025}, author = {Wang, Y and Bai, Z and Sun, J and Gong, Q and Miao, W and Niu, Z and Li, X and Xu, J and Lai, Z}, title = {Intestinal congestion-driven gut dysbiosis: a cross-disease hemodynamic mechanism in liver cirrhosis and heart failure.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {79}, pmid = {41382117}, issn = {1479-5876}, support = {SYYYRC-2022006//First Hospital of Shanxi Medical University/ ; 202103021224408//Natural Science Foundation of Shanxi Province/ ; 202203021221248//Natural Science Foundation of Shanxi Province/ ; 202204010931008//Shanxi Provincial Science and Technology Department/ ; YDZJSX2021B012//Shanxi Provincial Science and Technology Department/ ; 82470693//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2023065//Health Commission of Shanxi Province/ ; }, mesh = {Humans ; *Liver Cirrhosis/physiopathology/microbiology/complications ; *Heart Failure/physiopathology/complications/microbiology ; *Dysbiosis/physiopathology/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Intestines/pathology/microbiology/physiopathology ; *Hemodynamics ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; }, abstract = {BACKGROUND: Intestinal congestion is a common pathophysiological feature of both liver cirrhosis and heart failure (HF). This study aimed to investigate whether intestinal congestion induces similar gut microbiota and metabolite alterations under both conditions, and to identify key microbial and metabolic signatures. METHODS: We analyzed 117 cirrhosis patients (uncomplicated cirrhosis, cirrhosis with hepatocellular carcinoma, transjugular intrahepatic portosystemic shunt, and liver transplantation), 75 HF patients, and 31 healthy controls (CG). We performed 16S rRNA sequencing on all samples to assess gut microbial diversity, and subjected six representative samples per group to metagenomic sequencing. We conducted untargeted metabolomics on 30 fecal samples each from the uncomplicated cirrhosis, HF with reduced ejection fraction (HFrEF), and CG groups to profile intestinal metabolites, followed by correlation analyses among representative taxa, clinical characteristics, and key metabolites. RESULTS: Intestinal congestion of different etiologies exhibits similar alterations in the gut microbiota, particularly in patients with uncomplicated cirrhosis and HFrEF. Alterations in Bacteroides were closely associated with the severity of congestion. Veillonella and Lactobacillales were enriched in cirrhotic patients, whereas Coprococcus was uniquely abundant in HFs. Metabolomic analysis revealed significant reductions in tripeptides, anti-inflammatory compounds, and prostaglandin analogs in patients with intestinal congestion. Musacin D and neopterin may serve as potential noninvasive biomarkers for HF and cirrhosis, respectively. CONCLUSION: Intestinal congestion is associated with gut microbiota dysbiosis and metabolic disturbances in cirrhosis and HFs, with specific microbes and metabolites showing potential predictive value for distinguishing underlying diseases.}, }
@article {pmid41382244, year = {2025}, author = {Bae, IH and Kim, H and Kim, SM and Lee, YH}, title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {23}, pmid = {41382244}, issn = {2049-2618}, support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; }, mesh = {*Mycorrhizae/physiology/genetics ; *Symbiosis ; *Soil Microbiology ; *Microbiota ; *Tricholoma/physiology ; Soil/chemistry ; Nitrogen/metabolism ; Plant Roots/microbiology ; Ecosystem ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.<br><br>RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.<br><br>CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.}, }
@article {pmid41384736, year = {2026}, author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A}, title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.}, journal = {mSystems}, volume = {11}, number = {1}, pages = {e0136425}, pmid = {41384736}, issn = {2379-5077}, mesh = {Fermentation ; *Coffea/microbiology/metabolism/chemistry ; Metabolomics/methods ; Humans ; Metagenomics/methods ; Taste ; Metabolome ; Microbiota ; Coffee/microbiology ; }, abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.<br><br>IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.}, }
@article {pmid41384994, year = {2025}, author = {Zhang, J and Liu, J and Bayani, A}, title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.}, journal = {Journal of cancer research and clinical oncology}, volume = {152}, number = {1}, pages = {8}, pmid = {41384994}, issn = {1432-1335}, mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.}, }
@article {pmid41385764, year = {2025}, author = {Yang, H and Yu, Y and Cui, R and Zhang, Q and Chen, B and Zhang, Z and Xu, N and Sun, L and Lu, T and Qian, H}, title = {Environmental and Microbial Drivers of Global Rhizosphere Resistome Assembly.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {51}, pages = {32568-32576}, doi = {10.1021/acs.jafc.5c11060}, pmid = {41385764}, issn = {1520-5118}, mesh = {Soil Microbiology ; Rhizosphere ; *Bacteria/genetics/isolation &amp; purification/drug effects/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Vegetables/microbiology ; Microbiota ; }, abstract = {Soil serves as a critical reservoir for antibiotic resistance genes (ARGs); however, the ecological mechanisms driving ARG assembly at the plant-soil interface remain poorly understood. In this study, we analyzed 383 metagenomic samples and identified 4803 predicted ARGs, which were classified into two distinct clusters. The ARG-abundant cluster exhibited higher rhizospheric ARG abundance and diversity but posed a relatively lower health risk compared to the ARG-scarce cluster. Warm and nutrient-rich soils promote diverse resistomes shaped by complex microbial interactions, whereas humid environments promote more homogeneously predicted ARG compositions. Environmental variables such as the temperature and nitrogen were found to indirectly influence resistome composition by modulating microbial diversity. Notably, relatively high proportions of high-risk predicted ARGs were detected in grains and raw-eat vegetables, highlighting a potential threat to public health. Our findings underscore the importance of incorporating both environmental and microbial perspectives into agricultural practices to mitigate ARG dissemination in soil.}, }
@article {pmid41385957, year = {2026}, author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L}, title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.}, journal = {Poultry science}, volume = {105}, number = {1}, pages = {106177}, pmid = {41385957}, issn = {1525-3171}, mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; }, abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.}, }
@article {pmid41386031, year = {2026}, author = {Shu, M and Xue, H and Yang, Y and Zhang, X and Li, S and Bian, T and Yuan, K and Xu, C}, title = {Microbial-enzyme co-fermentation of low-grade tobacco: Metagenomics and metabolomic insights into flavor formation.}, journal = {Enzyme and microbial technology}, volume = {194}, number = {}, pages = {110803}, doi = {10.1016/j.enzmictec.2025.110803}, pmid = {41386031}, issn = {1879-0909}, mesh = {Fermentation ; *Nicotiana/microbiology/metabolism/chemistry ; Plant Leaves/microbiology/metabolism/chemistry ; Metagenomics ; Volatile Organic Compounds/analysis/metabolism ; Metabolomics ; Gas Chromatography-Mass Spectrometry ; Odorants/analysis ; Flavoring Agents/metabolism ; Taste ; Microbiota ; Bacteria/metabolism/genetics/classification ; }, abstract = {Microbial-enzyme co-fermentation effectively enhances the quality of low-grade tobacco leaves quality, but the underlying mechanisms of flavor formation remain unclear. This study investigated the dynamics and relationships of microbial communities and volatile aroma metabolites during low-grade tobacco leaves fermentation through metagenomics and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that during microbial-enzyme co-fermentation, the tobacco leaves fermented for four days (D4) exhibited the highest levels of total sugars and reducing sugars, the peak total content of aroma metabolites, and the best sensory quality. Pseudomonadota, Bacillota, and Ascomycota were dominant microorganisms during fermentation. During the initial stage (D1-D4), Saccharomyces was the dominant genus, which was subsequently displaced by Pantoea at D5. This microbial succession coincided with a decline in sensory quality, indicating its crucial role in shaping flavor evolution during co-fermentation. During microbial-enzyme co-fermentation process, a total of 46 volatile metabolites were detected in low-grade tobacco leaves. Among them, seven esters with high variable important in projection values and strong microbial correlations were identified as characteristic aroma metabolites, including ethyl phenylacetate, benzyl acetate, phenylethyl acetate, ethyl myristate, ethyl palmitate, ethyl oleate, and methyl linolenate. Gene function annotation revealed carbohydrate metabolism was the most abundant, followed by amino acid metabolism. Spearman correlation analysis elucidated the formation mechanism of characteristic ester metabolites. Specifically, short-chain esters correlated with glycerolipid and amino acid metabolism, while long-chain esters linked to glycolysis and fatty-acid biosynthetic pathways.}, }
@article {pmid41387308, year = {2026}, author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R}, title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {12}, pages = {e17747}, pmid = {41387308}, issn = {2198-3844}, support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; }, mesh = {*Aspirin/adverse effects/toxicity/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Mice ; Male ; Intestines/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; *Carboxylesterase/metabolism ; *Carboxylic Ester Hydrolases/metabolism ; *Intestinal Diseases/chemically induced/microbiology ; }, abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.}, }
@article {pmid41387551, year = {2026}, author = {Kelsey, C and Moulder, R and Yancey, H and Prescott, S and McCulloch, JA and Trinchieri, G and Dreisbach, C and Alhusen, J and Grossmann, T}, title = {Bidirectional relations between the maternal and infant gut microbiome and behavior.}, journal = {Pediatric research}, volume = {99}, number = {6}, pages = {2335-2344}, pmid = {41387551}, issn = {1530-0447}, support = {K99 HD115830/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; Infant ; *Gastrointestinal Microbiome ; *Infant Behavior ; *Mothers ; Adult ; Feces/microbiology ; Male ; Infant, Newborn ; *Mother-Child Relations ; Temperament ; Surveys and Questionnaires ; Metagenomics ; }, abstract = {BACKGROUND: An infant's mother is one of the first sources of neonatal microbial colonization, and infant-maternal dyad microbial variations have been linked to childhood behavioral traits and mental health outcomes. However, how the gut microbiome influences mental health, including potential bidirectional relations between mother and child, remains poorly understood.<br><br>METHOD: Using metagenomic sequencing and behavioral questionnaires, we examined within-person and between-person (mother-infant dyad) associations between the gut microbiota and behavior across the first year of postnatal life (N&#x2009;=&#x2009;121 dyads; N&#x2009;=&#x2009;514 stool samples).<br><br>RESULTS: There were rapid changes in taxa diversity and gut microbiota composition for infants, whereas the maternal microbiome remains relatively constant. Gut microbes and functional terms (e.g., antibiotic resistance genes and virulence factors)&#xa0;were associated with infant temperament but not maternal depression symptoms. Whereas maternal depression was not associated with any maternal taxa or functional terms.<br><br>CONCLUSIONS: Our findings provide evidence for complex within- and between-person relations between maternal and infant gut microbiomes and behavioral traits.<br><br>IMPACT: How the gut microbiome influences maternal mental health and infant behavior remains poorly understood. We measured mothers' and infants' gut microbiota composition and behavior across the first year of the infant's life. Individual taxa from the infant, but not the maternal, gut were associated with infant behavioral temperament. Our findings provide evidence for complex bidirectional gut-behavior associations between mothers and infants.}, }
@article {pmid41387706, year = {2025}, author = {Bonnet, N and Capeding, MR and Siegwald, L and Garcia-Garcera, M and Desgeorges, T and Tytgat, HLP and Krattinger, LF and Lebumfacil, J and Phee, LC and Moll, JM and Gudjonsson, A and Rodriguez-Garcia, P and Baruchet, M and Feige, JN and Jankovic, I and Chen, Y and Egli, D and Horcajada, MN}, title = {A young child formula with Limosilactobacillus reuteri and GOS modulates gut microbiome and enhances bone and muscle development: a randomized trial.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {237}, pmid = {41387706}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Limosilactobacillus reuteri/physiology ; Female ; Male ; Child, Preschool ; Feces/microbiology/chemistry ; Double-Blind Method ; *Infant Formula/chemistry ; *Oligosaccharides/administration &amp; dosage/pharmacology ; *Bone Development/drug effects ; Muscle Strength/drug effects ; Vitamin D/blood ; Probiotics/administration &amp; dosage ; Synbiotics/administration &amp; dosage ; }, abstract = {In this randomized, double-blind controlled trial, 182 Filipino children aged 2-3 years received either an experimental young child formula (EYCF) containing a combination of Limosilactobacillus reuteri DSM 17938 and galacto-oligosaccharides (GOS; n = 91) or a minimally fortified milk (CM; n = 91) for 6 months. Primary outcome was tibia speed of sound and secondary outcomes were muscle strength, blood vitamin D levels, bone turnover markers, gut microbiota, fecal calcium fatty acid soaps and gastro-intestinal tolerance. Compared to CM, those in the EYCF group showed increased tibia speed of sound after 3 and 6 months. The intervention remodeled the stool microbiome composition, assessed by shotgun metagenomics, with enrichment of L. reuteri and higher bifidobacteria presence in the EYCF group. Increased L. reuteri abundance after 6 months of EYCF consumption associates with higher bone quality and muscle strength. Stool metabolomics show 45 metabolites modulated by EYCF consumption and associated to microbiome compositional changes, leading to enrichment of tryptophane and indole metabolism. In summary, consumption of EYCF containing a L. reuteri + GOS synbiotic improves musculoskeletal development in toddlers via modulation of microbiota composition and function. These results provide insights on gut-musculoskeletal crosstalk during early life. Clinicaltrial.gov NCT04799028.}, }
@article {pmid41387926, year = {2025}, author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H}, title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {30}, pmid = {41387926}, issn = {2049-2618}, support = {32192463//The Major Program of National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; Grassland ; *Gastrointestinal Microbiome ; Sheep/microbiology ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenomics/methods ; Poaceae ; *Nutrients/metabolism ; Fermentation ; Multiomics ; }, abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.<br><br>RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.<br><br>CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.}, }
@article {pmid41388019, year = {2025}, author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA}, title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {638}, pmid = {41388019}, issn = {2041-1723}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI099243/AI/NIAID NIH HHS/United States ; T32 HD007233/HD/NICHD NIH HHS/United States ; R01 AI136979/AI/NIAID NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI106878/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Cholera Vaccines/immunology/administration &amp; dosage ; *Immunity, Innate/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; *Sphingolipids/metabolism/immunology ; Vibrio cholerae/immunology ; *Cholera/prevention &amp; control/immunology/microbiology ; Administration, Oral ; Feces/microbiology ; Macrophages/immunology ; Bacteroides/metabolism/immunology ; Female ; Male ; Adult ; }, abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.}, }
@article {pmid41388485, year = {2026}, author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL}, title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.}, journal = {Alcohol, clinical &amp; experimental research}, volume = {50}, number = {1}, pages = {e70210}, doi = {10.1111/acer.70210}, pmid = {41388485}, issn = {2993-7175}, support = {R21 AA029925/AA/NIAAA NIH HHS/United States ; AA029925/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Ethanol/administration &amp; dosage ; *Up-Regulation/drug effects ; *Dysbiosis/metabolism/chemically induced ; *alpha7 Nicotinic Acetylcholine Receptor/metabolism/genetics/biosynthesis ; *Binge Drinking/metabolism ; *Limbic System/metabolism/drug effects ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.<br><br>METHODS: B6 mice were given ethanol (EtOH; 5&#x2009;g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24&#x2009;h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96&#x2009;h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12&#x2009;h, 24&#x2009;h, and 192&#x2009;h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-&#x3b1;, IL-1&#x3b2;, P2Y12, ITG&#x3b2;2, and &#x3b1;7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.<br><br>RESULTS: Data revealed increased TNF-&#x3b1; expression in the Amg, Hyp, and NAc and increased IL-1&#x3b2; expression in the Amg and NAc, 12&#x2009;h after the first EtOH injection. &#x3b1;7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24&#x2009;h after the third EtOH dose, compared to the control group. &#x3b1;7nAChR expression in the Hyp was observed at 2&#x2009;min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24&#x2009;h after the third EtOH dose. ITG&#x3b2;2 showed an increasing trend in the Amg at 12&#x2009;h after the first dose, followed by a significant reduction at 24&#x2009;h, and 192&#x2009;h after the third dose. 16S rRNA sequencing revealed a significant difference in &#x3b2;-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.<br><br>CONCLUSION: This study showed that brain inflammation, indicated by &#x3b1;7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.}, }
@article {pmid41388659, year = {2025}, author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G}, title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.}, journal = {Environmental microbiology}, volume = {27}, number = {12}, pages = {e70214}, pmid = {41388659}, issn = {1462-2920}, support = {C03X1802//Ministry of Business, Innovation and Employment/ ; }, mesh = {*Biofilms/drug effects/growth &amp; development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; }, abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.}, }
@article {pmid41389008, year = {2026}, author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S}, title = {Antibiotics alter duodenal immune populations upon gluten exposure in mice: implications for non-coeliac gluten sensitivity.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {330}, number = {2}, pages = {G137-G153}, doi = {10.1152/ajpgi.00159.2025}, pmid = {41389008}, issn = {1522-1547}, support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Animals ; *Glutens/immunology ; *Anti-Bacterial Agents/pharmacology ; *Duodenum/immunology/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred BALB C ; Intestinal Mucosa/immunology/drug effects/microbiology ; Eosinophils/immunology/drug effects ; Male ; Feces/microbiology ; }, abstract = {A growing proportion of the non-celiac population experiences adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesized that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5 mg/kg) or PBS-vehicle daily for 5 days. Mice were then treated with a 3-mg wheat-gluten suspension, or vehicle, on days 4 and 5 before euthanasia on day 7. Duodenal immune cells were analyzed by histology and flow cytometry, whereas the duodenal MAM and fecal microbiome were characterized via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in feces, and resulted in altered microbial carbohydrate and lipid metabolism, compared with vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared with vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.NEW &amp; NOTEWORTHY A mouse model examined how microbial modulation affects immune responses to gluten. Antibiotic treatment followed by gluten reintroduction reduced duodenal Staphylococcus and altered microbial carbohydrate and lipid metabolism pathways in the fecal microbiome. Antibiotics and gluten treatment resulted in increased abundance and activation of duodenal eosinophils and elevated γδ T-cells in the duodenal epithelium. These findings highlight the role the microbiome plays in gluten-induced immune responses, providing insights into mechanisms behind non-celiac gluten sensitivity.}, }
@article {pmid41389146, year = {2026}, author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E}, title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.}, journal = {International forum of allergy &amp; rhinology}, volume = {16}, number = {1}, pages = {114-118}, pmid = {41389146}, issn = {2042-6984}, support = {R21 AI171306/AI/NIAID NIH HHS/United States ; /NH/NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Nasal Polyps/surgery/microbiology ; *Sinusitis/surgery/microbiology ; *Rhinitis/surgery/microbiology ; Chronic Disease ; *Paranasal Sinuses/surgery/microbiology ; Female ; Male ; Middle Aged ; Endoscopy ; Adult ; Staphylococcus aureus/isolation &amp; purification ; *Microbiota ; Aged ; Staphylococcal Infections/microbiology ; Rhinosinusitis ; }, abstract = {Staphylococcus aureus showed a significant increase in relative abundance in CRSwNP patients following endoscopic sinus surgery compared to pre-surgery samples. Other Staphylococcus species were found to correlate positively with S. aureus in patients with nasal polyps; among those, S. caprae correlated strongly while being the most represented in samples. Patients with recurrent nasal polyp growth exhibited a substantially greater postoperative increase in the relative abundance of S. aureus.}, }
@article {pmid41389554, year = {2026}, author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L}, title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128418}, doi = {10.1016/j.micres.2025.128418}, pmid = {41389554}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Angelica sinensis/microbiology/growth &amp; development/metabolism ; *Plant Growth Regulators/metabolism ; *Microbiota ; *Microalgae/metabolism/physiology ; Nitrogen/metabolism ; Soil Microbiology ; Coumaric Acids/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Biomass ; Soil/chemistry ; Metagenomics ; Metabolomics ; Carbon/metabolism ; Chlorella vulgaris/metabolism ; Multiomics ; }, abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.}, }
@article {pmid41389850, year = {2026}, author = {Petrov, VA and Schade, S and Laczny, CC and Hällqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P}, title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.}, journal = {Brain, behavior, and immunity}, volume = {132}, number = {}, pages = {106217}, doi = {10.1016/j.bbi.2025.106217}, pmid = {41389850}, issn = {1090-2139}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Parkinson Disease/diet therapy/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Inflammation/metabolism/diet therapy ; *Resistant Starch/administration &amp; dosage ; *Starch ; Quality of Life ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; }, abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids alongside a reduction in opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.}, }
@article {pmid41389890, year = {2026}, author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW}, title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.}, journal = {Journal of ethnopharmacology}, volume = {358}, number = {}, pages = {121035}, doi = {10.1016/j.jep.2025.121035}, pmid = {41389890}, issn = {1872-7573}, mesh = {Animals ; *Fatigue/drug therapy/metabolism/etiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Signal Transduction/drug effects ; Male ; Mice ; Physical Conditioning, Animal ; Gastrointestinal Microbiome/drug effects ; Hippocampus/drug effects/metabolism/pathology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.<br><br>PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.<br><br>METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.<br><br>RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2 (COX-2), MAPK14, BCL2, TLR4, TNF-&#x3b1;, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.<br><br>CONCLUSION: SQFNXNP regulated the TNF/NLR signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.}, }
@article {pmid41390384, year = {2025}, author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S}, title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {118}, pmid = {41390384}, issn = {1472-6831}, support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; }, mesh = {Humans ; *Pulpitis/microbiology ; Adult ; *Metagenomics ; Adolescent ; Young Adult ; *High-Throughput Nucleotide Sequencing ; Male ; *Microbiota/genetics ; Chronic Disease ; Female ; *Dental Pulp/microbiology ; }, abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.<br><br>METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906&#xa0;million paired-end reads per specimen.<br><br>RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.<br><br>CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.}, }
@article {pmid41390654, year = {2025}, author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L}, title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {84}, pmid = {41390654}, issn = {1479-5876}, mesh = {*Breast Neoplasms/microbiology/genetics/metabolism ; Humans ; *Siderophores/metabolism ; Female ; *Escherichia coli/metabolism/genetics ; *Metagenomics/methods ; Multivariate Analysis ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Breast cancer remains a leading cause of cancer-related mortality in women. Recent evidence implicates the gut microbiome and metabolites in breast cancer pathogenesis. This study explores associations between gut microbial species, their predicted metabolites, and breast cancer to uncover potential mechanistic insights. METHODS: Comprehensive metagenomic analyses were conducted on the gut microbiome of pre- and postmenopausal breast cancer patients, where microbial species were profiled through AMPHORA2 and metabolites were predicted through antiSMASH. Multivariate association analysis was used to identify significant associations between specific microbial species, predicted metabolites, and breast cancer status. A custom ensemble machine learning classifier was developed to classify pre- and postmenopausal breast cancer cases and controls based on microbial and predicted metabolite features. Additionally, a synthetic microbiome dataset was generated through MIDASim to validate the reproducibility of the ML results. Using our results, we explored the underlying dynamics of identified taxa and metabolite in breast cancer through literature and statistical support. RESULTS: Our analysis identified 471 microbial species and predicted 40 key metabolites in the metagenomic data. Multivariate analysis identified significant positive associations (p-value < 0.05) of E. coli, siderophore, and thiopeptide with breast cancer. The custom ensemble model achieved accuracy and AUC as high as 78% and 90%, respectively, in classifying pre- and postmenopausal cases and controls. The high-ranking features i.e., E. coli, siderophore, and thiopeptide were consistent with the results of the multivariate association analysis, thereby substantiating their biological significance. Using these findings, we propose a mechanistic model in which E. coli secretes siderophores under iron-limited conditions in breast cancer patients, for iron sequestration from the host, which can potentially promote angiogenesis and tumor progression. CONCLUSION: Our findings suggest that microbial iron acquisition mechanisms may play a critical role in breast cancer pathophysiology. Functional validation of these mechanisms is needed to assess therapeutic potential. This study highlights gut microbiota and their metabolites as promising targets for breast cancer research and intervention.}, }
@article {pmid41390665, year = {2025}, author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , }, title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {15}, pmid = {41390665}, issn = {2041-1723}, support = {2127509//American Society for Engineering Education (ASEE)/ ; P30 ES007033/ES/NIEHS NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; R01 AI162867/AI/NIAID NIH HHS/United States ; R01AI162867//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; //University of Washington Interdisciplinary Center for Exposures, Diseases, Genomics &amp; Environment/ ; }, mesh = {Humans ; Female ; Ecuador ; *Gastrointestinal Microbiome/genetics/drug effects ; Pregnancy ; Child ; Adult ; Child, Preschool ; Infant ; *Environmental Exposure/adverse effects ; Klebsiella pneumoniae/genetics/isolation &amp; purification/drug effects ; Escherichia coli/genetics/isolation &amp; purification/drug effects ; *Drug Resistance, Bacterial/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Young Adult ; Male ; Hygiene ; Adolescent ; Sanitation ; Feces/microbiology ; Bacteria/genetics/classification/drug effects ; }, abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.}, }
@article {pmid41390780, year = {2025}, author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D}, title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {235}, pmid = {41390780}, issn = {2055-5008}, support = {R01 AI151075/AI/NIAID NIH HHS/United States ; }, mesh = {*Azithromycin/pharmacology/therapeutic use ; Female ; Humans ; *Chlamydia trachomatis/drug effects/genetics ; *Chlamydia Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects ; *Drug Resistance, Bacterial ; Vagina/microbiology ; Metagenomics ; Adult ; Gardnerella vaginalis/drug effects/genetics/isolation &amp; purification ; Cervix Uteri/microbiology ; Rectum/microbiology ; Biofilms/drug effects/growth &amp; development ; Lactobacillus/drug effects/genetics ; }, abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.}, }
@article {pmid41390863, year = {2025}, author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM}, title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1211}, pmid = {41390863}, issn = {2045-2322}, support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; }, mesh = {Animals ; Bees/microbiology/drug effects ; *Neonicotinoids/toxicity/adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; *Dysbiosis/chemically induced/microbiology ; *Insecticides/toxicity ; Guanidines/toxicity ; Thiamethoxam ; Metagenome ; Thiazoles/toxicity ; }, abstract = {The Western honey bee (Apis mellifera) plays an essential role in agriculture around the world. In Canada, honey bees contribute up to $7 billion in economic value annually by pollinating crops and producing honey. However, since 2006–2007 North American beekeepers have lost more than a quarter of their colonies each winter. In recent years, the losses have been up to 50% in some regions. The causes of losses are complex, including the interacting effects of nutrition, pathogens, and pesticides. Although the bee gut microbiome plays a crucial role in colony health and disease, studies on the effects of agricultural pesticides on the bee microbial community are sparse. We report the use of shotgun metagenomic sequencing to investigate bee gut microbiota changes, or dysbiosis, in response to two neonicotinoid insecticides, clothianidin and thiamethoxam. Common dysbiosis signatures included an increase in Bifidobacterium spp. after chronic sublethal exposure and an increase in Apibacter adventoris after short-term acute exposure. Other dysbiosis signatures were unique to each compound, such as an increase in Snodgrassella alvi for clothianidin and a decrease in Lactobacillus spp. for thiamethoxam. These findings enhance our understanding of how the honey bee gut microbiome responds to stressors and highlight identifiable microbial profile signatures which underscores the potential utility of gut microbiome profiling as a bee health diagnostic tool. Access to timely and accurate bee health diagnosis will inform regulatory actions to decrease and mitigate exposure to stressors and will facilitate managing and improving bee health.}, }
@article {pmid41391314, year = {2026}, author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J}, title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140802}, doi = {10.1016/j.jhazmat.2025.140802}, pmid = {41391314}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Nitrogen Cycle ; *Microplastics/toxicity ; Ecosystem ; *Water Pollutants, Chemical/toxicity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Polyethylene ; }, abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.}, }
@article {pmid41391639, year = {2026}, author = {Yuan, F and Wang, L and Nguyen, SM and Shu, XO and Shrubsole, MJ and Wen, W and Cai, Q and Yu, D and Zheng, W}, title = {Plant-based diets, gut microbiota, blood metabolome, and risk of colorectal, liver, and pancreatic cancers: results from a large prospective cohort study of predominantly low-income Americans.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {2}, pages = {101135}, pmid = {41391639}, issn = {1938-3207}, support = {R01 CA092447/CA/NCI NIH HHS/United States ; R01 HL149779/HL/NHLBI NIH HHS/United States ; U01 CA202979/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Pancreatic Neoplasms/epidemiology/blood ; *Diet, Vegetarian ; Prospective Studies ; *Colorectal Neoplasms/epidemiology/blood ; *Liver Neoplasms/epidemiology/blood ; *Metabolome ; Aged ; Adult ; Risk Factors ; Cohort Studies ; Diet, Plant-Based ; }, abstract = {BACKGROUND: Plant-based diets have been advertised for environmental and health benefits. Their effects on cancer risk, gut microbial, and blood metabolomic profiles remain unclear.<br><br>OBJECTIVES: We investigated plant-based diets in relation to cancer incidence as well as gut microbial composition and blood metabolites in the Southern Community Cohort Study.<br><br>METHODS: Included in the analysis were 71,533 participants. Habitual dietary intake assessed at baseline (2002-2009) was used to derive the overall plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Incident cancer cases were ascertained via linkage to state cancer registries and the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazards models after adjusting for potential confounders. We examined associations of the 3 indices with gut microbiota and blood metabolites using fecal metagenomic and blood metabolomic data from 2 subsets of 417 and 1581 participants, respectively.<br><br>RESULTS: During a median follow-up time of 11.6 y, 783, 316, and 295 incident colorectal, liver, and pancreatic cancer cases were identified. High hPDI was related to a lower liver cancer risk (HR: 0.67, 95% CI: 0.45, 0.99 comparing extreme quartiles, P-trend = 0.03). No apparent association was observed for colorectal cancer (CRC) in the whole cohort. However, among 49,132 CRC screening-na&#xef;ve participants at baseline, PDI was inversely associated (HR: 0.74, 95% CI: 0.58, 0.96, P-trend = 0.01), whereas uPDI was positively associated (HR: 1.39, 95% CI: 1.06, 1.82, P-trend = 0.02) with CRC risk. No index was associated with pancreatic cancer. These diet indices were associated with microbial taxa and blood metabolites that have been implicated in the tumorigenesis of the colorectum and liver.<br><br>CONCLUSIONS: A diet high in healthy plant foods and low in animal foods was inversely associated with liver cancer risk and with CRC risk among screening-na&#xef;ve participants. These associations may be partly mediated through gut microbiota and systemic metabolism.}, }
@article {pmid41391818, year = {2026}, author = {Zhou, H and Gao, Y and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K}, title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.}, journal = {Journal of advanced research}, volume = {87}, number = {}, pages = {39-54}, doi = {10.1016/j.jare.2025.12.017}, pmid = {41391818}, issn = {2090-1224}, mesh = {*Antimicrobial Peptides/genetics/biosynthesis ; *Microbiota/genetics ; *Grassland ; Metagenome ; *Plant Leaves/microbiology ; Phylogeny ; Metagenomics ; *Plants/microbiology ; *Bacteria/genetics ; Multigene Family ; }, abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.<br><br>OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.<br><br>METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).<br><br>RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61&#xa0;% of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97&#xa0;% of the BGCs and 99.76&#xa0;% of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean&#xa0;=&#xa0;14.76, P&#xa0;=&#xa0;0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean&#xa0;=&#xa0;7.13, P&#xa0;=&#xa0;6.1e-05), Lamiaceae (mean&#xa0;=&#xa0;7, P&#xa0;=&#xa0;0.015), Ranunculaceae (mean&#xa0;=&#xa0;8.22, P&#xa0;=&#xa0;0.0053), and Rosaceae (mean&#xa0;=&#xa0;7.75, P&#xa0;=&#xa0;0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.<br><br>CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.}, }
@article {pmid41392116, year = {2025}, author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H}, title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {1801}, pmid = {41392116}, issn = {2045-2322}, support = {81860142//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ketamine/adverse effects ; *Cystitis/chemically induced/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Rats ; Metabolomics/methods ; Male ; Rats, Sprague-Dawley ; Urinary Bladder/metabolism ; *Metabolome ; Disease Models, Animal ; Bacteria/genetics/classification ; }, abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.}, }
@article {pmid41392335, year = {2025}, author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J}, title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.}, journal = {Journal of diabetes}, volume = {17}, number = {12}, pages = {e70175}, pmid = {41392335}, issn = {1753-0407}, support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).<br><br>METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.<br><br>RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-&#x3b1;, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.<br><br>CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.}, }
@article {pmid41392764, year = {2026}, author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z}, title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.}, journal = {Food &amp; function}, volume = {17}, number = {1}, pages = {475-493}, doi = {10.1039/d5fo04374c}, pmid = {41392764}, issn = {2042-650X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Serotonin/metabolism ; Mice ; *gamma-Aminobutyric Acid/metabolism ; *Sleep Initiation and Maintenance Disorders/metabolism/microbiology/chemically induced ; Male ; *Probiotics ; *Bifidobacterium animalis/physiology ; Humans ; Signal Transduction ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.}, }
@article {pmid41394107, year = {2025}, author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ}, title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1628594}, pmid = {41394107}, issn = {2235-2988}, mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration &amp; dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; }, abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.<br><br>AIM: This study aimed to investigate the effects of the JWC on gastric mucosal&#xa0;inflammation and the expression of drug-resistance genes in H.&#xa0;pylori-infected mice.<br><br>METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.<br><br>RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1&#x3b2;, and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.<br><br>CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.}, }
@article {pmid41395693, year = {2026}, author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM}, title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.}, journal = {Diabetes, obesity &amp; metabolism}, volume = {28}, number = {3}, pages = {1826-1835}, pmid = {41395693}, issn = {1463-1326}, support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestl&#xe9; Health Science/ ; //Pierre Mercier Foundation/ ; }, mesh = {Humans ; *Diet, Ketogenic ; *Gastrointestinal Microbiome/physiology ; *Prediabetic State/microbiology/diet therapy/complications ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/diet therapy ; *Obesity, Morbid/microbiology/diet therapy/complications ; *Obesity/microbiology/diet therapy ; Caloric Restriction ; }, abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).<br><br>METHODS: In a randomised trial, patients with BMI >35&#x2009;kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.<br><br>RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.<br><br>CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.}, }
@article {pmid41395946, year = {2026}, author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J}, title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.}, journal = {mSystems}, volume = {11}, number = {1}, pages = {e0129025}, pmid = {41395946}, issn = {2379-5077}, support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; IDN/20/024//Internal funds KU Leuven/ ; }, mesh = {Humans ; *Virome/genetics ; *Skin/virology/microbiology ; Male ; Female ; Adult ; *Hidradenitis Suppurativa/virology/microbiology ; Middle Aged ; Microbiota ; Bacteriophages/genetics ; Metagenomics ; }, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.}, }
@article {pmid41395968, year = {2026}, author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S}, title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {1}, pages = {e0198525}, pmid = {41395968}, issn = {1098-5336}, support = {4421050//USDA-Evans-Allen/ ; 2021-38821-34583//USDA-CBG/ ; }, mesh = {Animals ; *Microbiota ; *Aquaculture/methods ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus/genetics/isolation &amp; purification ; *Vibrio vulnificus/genetics/isolation &amp; purification ; *Vibrio ; Population Dynamics ; Metagenomics ; }, abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.}, }
@article {pmid41396034, year = {2026}, author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y}, title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.}, journal = {Food &amp; function}, volume = {17}, number = {1}, pages = {513-530}, doi = {10.1039/d5fo04527d}, pmid = {41396034}, issn = {2042-650X}, mesh = {Humans ; *Milk, Human/microbiology/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; *Gastrointestinal Microbiome ; Pregnancy ; *Diabetes, Gestational/metabolism/microbiology ; Infant, Newborn ; Adult ; Feces/microbiology ; Infant ; Bacteria/classification/isolation &amp; purification/genetics ; Tandem Mass Spectrometry ; Male ; }, abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.}, }
@article {pmid41396065, year = {2026}, author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E}, title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0180625}, pmid = {41396065}, issn = {2165-0497}, mesh = {Humans ; *Saliva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Specimen Handling/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Mouthwashes ; Adult ; *Mouth/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Young Adult ; Glycerol ; Middle Aged ; }, abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.<br><br>IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.}, }
@article {pmid41396495, year = {2025}, author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A}, title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {6}, pages = {168}, pmid = {41396495}, issn = {1436-2236}, support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; }, abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.}, }
@article {pmid41398180, year = {2025}, author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W}, title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {14}, pmid = {41398180}, issn = {2055-5008}, support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Fetal Blood/virology ; Female ; *Virome ; *Infectious Disease Transmission, Vertical ; Pregnancy ; Phylogeny ; Infant, Newborn ; *Viruses/classification/genetics/isolation &amp; purification ; *Maternal Health ; Metagenomics ; Adult ; Genome, Viral ; Health Status ; }, abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.}, }
@article {pmid41398218, year = {2025}, author = {Huang, R and Zhang, Y and Arif, M and Song, C and Yang, L}, title = {16S rDNA sequencing of the intestinal metagenome of Wanxi White Goose (Anser cygnoides) with different egg production abilities.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {12}, pmid = {41398218}, issn = {2730-6844}, support = {202423l10050055//Anhui Province Science and Technology Innovation Project/ ; }, mesh = {Animals ; *Geese/microbiology/genetics/physiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Female ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; *Metagenome ; }, abstract = {OBJECTIVES: The Wanxi White Goose (Anser cygnoides) is a large waterfowl of the Anatidae family and one of the most prominent medium-sized goose breeds in China. This breed has been observed to exhibit several distinctive characteristics, including accelerated early growth, robust stress resistance, substantial egg-laying performance, and elevated down production. The egg-laying performance of Wanxi White Geese is influenced by genetic factors, as well as by environmental and feeding management factors. In this study, the intestinal contents from the high-laying and low-laying Wanxi white geese were collected, and the 16 S amplicon sequencing method was used to evaluate the relationship between the composition of intestinal bacterial communities and their egg-laying ability. DATA DESCRIPTION: The 16 S rDNA sequencing technology was utilized to sequence and identify the microorganisms present in the duodenum, jejunum, ileum, and cecum of Wanxi white geese with varying egg-laying abilities. Four biological replicates were collected from each sample across all sections, resulting in a total of 32 samples for subsequent sequencing studies. All raw DNA sequences were uploaded to the Genome Sequence Archive (GSA) database of the National Genomics Data Center (NGDC), which is under the China National Center for Bioinformation. The accession number assigned to the submission is CRA028174, and the BioProject number is PRJCA043467. The clean read sequencing lengths for most samples ranged from 200 to 450 bp. CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid41398277, year = {2025}, author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H}, title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.}, journal = {BMC biology}, volume = {24}, number = {1}, pages = {16}, pmid = {41398277}, issn = {1741-7007}, support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&amp;D Program of China/ ; 2022YFC2805505//the National Key R&amp;D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; }, mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics ; Metagenome ; *Water Microbiology ; }, abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.<br><br>RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553&#xa0;m) and sediments (3060-9232&#xa0;m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher &#x251;-diversity than the deep-sea waters and sediments (p&#x2009;<&#x2009;0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.<br><br>CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.}, }
@article {pmid41398701, year = {2025}, author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J}, title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {257}, pmid = {41398701}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology/virology/metabolism ; *Lactation ; Cattle ; Female ; *Bacteriophages/classification/genetics/isolation &amp; purification/physiology ; *Metabolome ; *Bacteria/classification/virology/genetics/metabolism/isolation &amp; purification ; Milk/metabolism ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.<br><br>RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.<br><br>CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.}, }
@article {pmid41398941, year = {2025}, author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M}, title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {40}, pmid = {41398941}, issn = {1471-2180}, support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology/metabolism ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fermentation ; Metabolome ; Metabolomics ; Metagenomics ; }, abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.}, }
@article {pmid41401693, year = {2026}, author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J}, title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.}, journal = {Poultry science}, volume = {105}, number = {2}, pages = {106246}, pmid = {41401693}, issn = {1525-3171}, mesh = {China/epidemiology ; Animals ; *Virome ; Metagenomics ; *Galliformes/virology ; *Metagenome ; }, abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.}, }
@article {pmid41401858, year = {2026}, author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L}, title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.}, journal = {Journal of invertebrate pathology}, volume = {215}, number = {}, pages = {108518}, doi = {10.1016/j.jip.2025.108518}, pmid = {41401858}, issn = {1096-0805}, mesh = {Animals ; *Bombyx/microbiology/virology/immunology ; *Gastrointestinal Microbiome ; *Nucleopolyhedroviruses/physiology ; *Disease Resistance ; Species Specificity ; }, abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (An3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.}, }
@article {pmid41403401, year = {2025}, author = {Lin, H and Zhu, X and Zhu, J and Chen, N and Bao, W and Peng, Z}, title = {High-Throughput Sequencings Revealed That Gut Microbiota Dysbiosis is Implicated in Gouty Arthritis of Red-Crowned Crane (Grus japonensis).}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {2422900}, pmid = {41403401}, issn = {1865-1682}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Arthritis, Gouty/veterinary/microbiology ; *Dysbiosis/veterinary/microbiology/complications ; High-Throughput Nucleotide Sequencing/veterinary ; *Bird Diseases/microbiology ; Feces/microbiology ; China/epidemiology ; RNA, Ribosomal, 16S ; }, abstract = {The red-crowned crane (Grus japonensis) is one of the rarest cranes with a global population of less than 4000 individuals. The population of red-crowned crane could be influenced by health threats, including metabolic and infectious diseases. In the Wildlife Rescue Center of Suining County of Jiangsu Province, gouty arthritis (GA) was observed in all four red-crowned cranes since March 2024. A pooled fecal supernatant was first submitted to metagenomics sequencing for screening disease-associated pathogens. Enterobacteria phage phiEcoM-GJ1 was detected as the predominant virus while Escherichia coli and Aeromonas hydrophila were the dominated bacteria in the mixed fecal sample from red-crowned cranes. The 16S rRNA gene sequencing was further performed on both the mixed fecal sample and four individual samples, which showed that Escherichia-Shigella, Lactobacillus, and Enterococcus were the most abundant gut flora in both mixed and individual fecal samples. Furthermore, bacteria isolation and identification with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) confirmed that Escherichia coli was predominant (19/29 colonies, 65.52%) in the feces. Therefore, anti-uricacid and antibacteria treatments using plantain herb, doxycycline, Vitamin AD3 and multivitamin B were adopted, leading to a full behavioral recovery within 1 month. Overall, this case-based observational study provides first clue on the gut-joint axis in red-crowned cranes, supporting that gut microbiota dysbiosis is closely associated with GA in red-crowned cranes.}, }
@article {pmid41404370, year = {2025}, author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y}, title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1663645}, pmid = {41404370}, issn = {2235-2988}, mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Absorptiometry, Photon ; }, abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.<br><br>METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.<br><br>RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.<br><br>CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.}, }
@article {pmid41404904, year = {2026}, author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM}, title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0203625}, pmid = {41404904}, issn = {2165-0497}, support = {101103059//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {Animals ; *Goats/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Tanzania ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification/metabolism ; *Vehicle Emissions/toxicity ; *Environmental Pollutants/toxicity/metabolism ; Metagenome ; Environmental Pollution/adverse effects ; Biodegradation, Environmental ; Metagenomics ; }, abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.}, }
@article {pmid41405224, year = {2026}, author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA}, title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0047425}, pmid = {41405224}, issn = {2165-0497}, support = {Y1-Al-5072//National Institute of Allergy and Infectious Diseases/ ; HU0001190002//U.S. Department of Defense/ ; 20-FS-029//Laboratory Directed Research and Development/ ; }, mesh = {Humans ; *Military Personnel ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; United States ; Metagenomics ; Fungi/classification/genetics/isolation &amp; purification ; Male ; Female ; Adult ; }, abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.}, }
@article {pmid41406442, year = {2026}, author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B}, title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-9}, doi = {10.1139/cjm-2025-0056}, pmid = {41406442}, issn = {1480-3275}, mesh = {Animals ; Temperature ; *Bacteria/genetics/classification/isolation &amp; purification ; *Shellfish/microbiology ; RNA, Ribosomal, 16S/genetics ; *Food Storage ; China ; Fresh Water/microbiology ; Food Microbiology ; Microbiota ; }, abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4 °C) and room-temperature (25 °C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25 °C while Bacillota increased compared to 4 °C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.}, }
@article {pmid41406735, year = {2026}, author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, M&#xc1; and Muñoz-González, C}, title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.}, journal = {Food chemistry}, volume = {501}, number = {}, pages = {147554}, doi = {10.1016/j.foodchem.2025.147554}, pmid = {41406735}, issn = {1873-7072}, mesh = {Humans ; *Mouth/microbiology/metabolism/chemistry/enzymology ; *Esters/metabolism/chemistry ; Male ; Adult ; Female ; *Saliva/microbiology/enzymology/chemistry/metabolism ; *Bacteria/enzymology/genetics/isolation &amp; purification/classification/metabolism ; Young Adult ; Microbiota ; *Bacterial Proteins/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; Middle Aged ; *Carboxylic Acids/metabolism/chemistry ; }, abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.}, }
@article {pmid41407286, year = {2025}, author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P}, title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.}, journal = {Journal of the American Chemical Society}, volume = {147}, number = {52}, pages = {48060-48071}, pmid = {41407286}, issn = {1520-5126}, mesh = {Humans ; *Mouth/microbiology ; Animals ; *Bacteriocins/genetics/chemistry/metabolism ; *Evolution, Molecular ; Phylogeny ; Microbiota ; Actinomyces/chemistry/metabolism ; *Antimicrobial Peptides/genetics/chemistry ; Biofilms ; }, abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.}, }
@article {pmid41408023, year = {2026}, author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q}, title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.}, journal = {Clinical rheumatology}, volume = {45}, number = {2}, pages = {857-873}, pmid = {41408023}, issn = {1434-9949}, support = {C2301008&#xff0c;C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; }, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Clostridium/genetics ; Female ; Adult ; Male ; Middle Aged ; Metagenomics ; Metabolomics ; Case-Control Studies ; Metabolome ; Dysbiosis/microbiology ; Eubacteriales ; }, abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.<br><br>METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.<br><br>RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.<br><br>CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points &#x2022;&#xa0;Gut microbial composition is significantly altered in SLE patients compared to healthy controls. &#x2022;&#xa0;Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. &#x2022;&#xa0;Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. &#x2022;&#xa0;The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.}, }
@article {pmid41408163, year = {2025}, author = {Yang, G and He, W and Ma, B and La, Y and Ma, X and Wu, X and Chu, M and Zhao, M and Liu, X and Zhao, Y and Guo, X and Wang, L and Liang, C}, title = {Effects of dietary supplementation with astragalus polysaccharides on growth performance, serum parameters, and rumen microbial function of yaks.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {64}, pmid = {41408163}, issn = {1471-2180}, support = {CARS-37//Modern Beef Yak Industry Technology System/ ; 25ZYJA008//Central Guidance Funds for Local science and technology Development projects/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/growth &amp; development/blood/microbiology/immunology ; *Polysaccharides/administration &amp; dosage/pharmacology ; *Astragalus Plant/chemistry ; *Dietary Supplements ; Male ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation &amp; purification ; Diet/veterinary ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; }, abstract = {BACKGROUND: Astragalus polysaccharide (APS) has become a natural feed additive that has attracted much attention in animal husbandry due to its significant immunomodulatory activity, low toxicity and promotion of animal growth performance. In this study, in order to explore the effects of dietary APS on the growth performance and rumen microorganisms of yaks, 20 male yaks aged 2–3 years were selected and randomly divided into two groups: experimental group (1.0 g/kg APS were added to the diet, AG) and control group (no APS were added to the diet, CG), with 10 yaks in each group. After 60 days of continuous feeding, 5 animals were randomly selected from each group to collect rumen fluid. Comparative analysis of rumen microbial composition, function, and metabolites was conducted using metagenomic and metabolomic approaches. RESULTS: The analysis of yak body weight index showed that the body weight of yak in the AG group was significantly higher than that in the CG group on the 60 th day (P < 0.05). In addition, APS significantly increased the immune indexes of IgA, IgM, IgG, IL-10, IGF1, GH, and NOS in yaks (P < 0.05). Metagenomic analysis showed that the beneficial bacteria (such as Euryarchaeota, Methanobrevibacter and Butyrivibrio) in the rumen of yaks were significantly increased after the addition of astragalus polysaccharides in the experimental group. Differential metabolites were significantly enriched in pathways such as Purine metabolism, Galactose metabolism and Tryptophan metabolism that may have a positive impact on the growth and development of yaks. This may promote the production of immune and growth-related metabolites by regulation, and ultimately enhance the immune function and growth performance of yak. CONCLUSIONS: The results showed that the addition of APS could significantly improve the growth performance and immune function of yak. It can also optimize the rumen microbial community. It shows that polysaccharides such as APS can be used as effective substitutes for antibiotics and other drugs for long-term improvement of yak growth performance and rumen health.}, }
@article {pmid41408188, year = {2025}, author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H}, title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {55}, pmid = {41408188}, issn = {1471-230X}, support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; }, mesh = {Humans ; Cholangitis, Sclerosing/microbiology/diagnosis ; *Microbiota ; Bile Duct Neoplasms/microbiology/diagnosis ; *Biliary Tract/microbiology ; *Pancreatic Neoplasms/microbiology/diagnosis ; Cholangiocarcinoma/microbiology/diagnosis ; Gallstones/microbiology/diagnosis ; *Pancreatic Diseases/microbiology/diagnosis ; *Biliary Tract Diseases/microbiology/diagnosis ; }, abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.<br><br>METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16&#xa0;S rRNA gene sequencing or metagenomics.<br><br>RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.<br><br>CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.}, }
@article {pmid41408356, year = {2026}, author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH}, title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.}, journal = {Rheumatology (Oxford, England)}, volume = {65}, number = {1}, pages = {}, doi = {10.1093/rheumatology/keaf668}, pmid = {41408356}, issn = {1462-0332}, support = {202330//National Clinical Key Speciality Capacity Building/ ; 2021818//Hainan Province Clinical Medical Center/ ; YSPTZX202313//The Innovation Platform for Academicians of Hainan Province/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; Qhyb2022-133//Hainan Provincial Postgraduate Innovation Research/ ; hnjg2024-67//Hainan Province Education Reform/ ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Metabolome/physiology ; Feces/microbiology ; Metabolomics ; Adult ; Aged ; Case-Control Studies ; Metagenomics ; Tandem Mass Spectrometry ; Multiomics ; }, abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.<br><br>METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted liquid chromatography-tandem mass spectrometry metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.<br><br>RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae and Parabacteroides distasonis were noticed. Conversely, Phocaeicola plebeius, Blautia hansenii and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.<br><br>CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.}, }
@article {pmid41409544, year = {2025}, author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT}, title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1719025}, pmid = {41409544}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology/parasitology ; }, abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.<br><br>METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.<br><br>RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).<br><br>DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.}, }
@article {pmid41409546, year = {2025}, author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H}, title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1694479}, pmid = {41409546}, issn = {2235-2988}, mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; }, abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.<br><br>METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.<br><br>RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p <&#xa0;0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p&#xa0;<&#xa0;0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p&#xa0;<&#xa0;0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.<br><br>CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.}, }
@article {pmid41410816, year = {2025}, author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z}, title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.}, journal = {Current atherosclerosis reports}, volume = {28}, number = {1}, pages = {1}, pmid = {41410816}, issn = {1534-6242}, support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; R01 HL170904/HL/NHLBI NIH HHS/United States ; R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; }, abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.<br><br>RECENT FINDINGS: Evidence on gut microbial &#x3b1;-diversity and &#x3b2;-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.}, }
@article {pmid41411799, year = {2026}, author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F}, title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119554}, doi = {10.1016/j.ecoenv.2025.119554}, pmid = {41411799}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Amino Acids/metabolism ; Mice ; *Lead/toxicity ; *Brain/drug effects/metabolism ; *Carbohydrate Metabolism/drug effects ; Male ; Feces/chemistry/microbiology ; *Brain-Gut Axis/drug effects ; }, abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.}, }
@article {pmid41412053, year = {2026}, author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D}, title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140847}, doi = {10.1016/j.jhazmat.2025.140847}, pmid = {41412053}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; Pacific Ocean ; *Temperature ; Halogenation ; Phylogeny ; *Bacteria/genetics/metabolism ; Microbiota ; }, abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.}, }
@article {pmid41412637, year = {2026}, author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L}, title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {224}, number = {}, pages = {117927}, doi = {10.1016/j.foodres.2025.117927}, pmid = {41412637}, issn = {1873-7145}, mesh = {*Bacteria ; *Cheese/microbiology ; Dairying ; *Fungi ; Italy ; Lactococcus lactis/genetics ; *Microbiota ; Raw Foods/microbiology ; *Seasons ; Food Microbiology ; }, abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.}, }
@article {pmid41412647, year = {2026}, author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J}, title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.}, journal = {Food research international (Ottawa, Ont.)}, volume = {224}, number = {}, pages = {117952}, doi = {10.1016/j.foodres.2025.117952}, pmid = {41412647}, issn = {1873-7145}, mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; }, abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.}, }
@article {pmid41412727, year = {2026}, author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S}, title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.}, journal = {Gut}, volume = {75}, number = {8}, pages = {1505-1519}, pmid = {41412727}, issn = {1468-3288}, mesh = {Animals ; *Diet, Western/adverse effects ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/etiology ; Mice ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Deoxycholic Acid/metabolism ; Swine ; Disease Models, Animal ; Female ; Feces/microbiology ; Cell Proliferation ; Colon/microbiology ; Mice, Inbred C57BL ; Germ-Free Life ; Eubacteriales ; }, abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.<br><br>OBJECTIVE: Investigate the causal role of BAs produced by 7&#x3b1;DH+ gut bacteria in CRC.<br><br>DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7&#x3b1;DH+ bacteria&#x2009;or a genetically modified strain to demonstrate causality.<br><br>RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7&#x3b1;DH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7&#x3b1;DH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.<br><br>CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7&#x3b1;DH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.}, }
@article {pmid41412926, year = {2026}, author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A}, title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.}, journal = {Trends in microbiology}, volume = {34}, number = {5}, pages = {472-484}, doi = {10.1016/j.tim.2025.11.016}, pmid = {41412926}, issn = {1878-4380}, mesh = {Humans ; *Noncommunicable Diseases/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Communicable Diseases/microbiology/therapy ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Dysbiosis/microbiology ; Computational Biology/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.}, }
@article {pmid41413233, year = {2026}, author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S}, title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.}, journal = {Hypertension research : official journal of the Japanese Society of Hypertension}, volume = {49}, number = {3}, pages = {958-968}, pmid = {41413233}, issn = {1348-4214}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Blood Pressure/physiology ; *Polyamines/metabolism ; Female ; *Hypertension/microbiology/metabolism/physiopathology ; Aged ; Adult ; Feces/microbiology ; }, abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.}, }
@article {pmid41413663, year = {2026}, author = {McAdams, Z and Gustafson, K and Ericsson, A}, title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.}, journal = {Lab animal}, volume = {55}, number = {1}, pages = {29-34}, pmid = {41413663}, issn = {1548-4475}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; }, mesh = {Animals ; Mice/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Sample Size ; Mice, Inbred C57BL ; Male ; }, abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.}, }
@article {pmid41413769, year = {2025}, author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F}, title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {70}, pmid = {41413769}, issn = {1471-2180}, support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; }, mesh = {*Feces/microbiology ; Humans ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Metagenome ; Butyrates/metabolism ; *Gastrointestinal Microbiome/genetics ; Methylamines/metabolism ; Methane/metabolism ; Phylogeny ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial condition in which the gut microbiome (GM) plays a central role. However, taxonomic associations derived from 16S ribosomal RNA (rRNA) gene studies have yielded inconsistent results, likely due to limited resolution and functional redundancy across taxa. We aimed to identify robust, functionally relevant microbial markers of MASLD using metagenomics and gene-centric profiling. METHODS: We analyzed 554 fecal metagenomes from three independent cohorts. Sequencing reads were quality-controlled and taxonomically profiled with multi-marker gene resolution. We quantified the abundance of over 50 target gene families involved in butyrate, methane, trimethylamine (TMA) and short-chain alcohol (SCAs, i.e., ethanol and propanol) metabolism. Their presence was also determined across complete GM genomes and plasmids. RESULTS: Genes involved in butyrate and methane production tended to show lower abundance in MASLD, particularly in cirrhosis, while TMA- and SCA-producing genes were frequently enriched. These functional shifts were accompanied by the depletion of Agathobacter rectalis. Many of the altered genes were highly accessory and encoded on plasmids, suggesting genome-specific functional divergence driven by horizontal gene transfer. CONCLUSION: MASLD is characterized by a shift toward alcohol- and TMA-producing metabolism, alongside reduced butyrate and methane production -changes driven by accessory and plasmid-borne genes. Gene-centric and mobile genetic element-aware profiling reveals mechanistic microbial contributions to MASLD that remain undetected by taxonomy-based approaches, offering new targets for diagnosis and intervention.}, }
@article {pmid41416110, year = {2025}, author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B}, title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1638464}, pmid = {41416110}, issn = {2235-2988}, mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation &amp; purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation &amp; purification/genetics ; }, abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.}, }
@article {pmid41416507, year = {2025}, author = {Wang, Y and Wan, Y and Wang, H and Yan, J and Sun, J and Yang, J and Zhang, F and Cao, H and Li, D}, title = {Oral Supplementation of Indole-3-acetic Acid Alleviates High-Fat-Induced Obesity by Activating the Gpha2-Mediated Thyroid-Stimulating Hormone Pathway.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {52}, pages = {33126-33140}, doi = {10.1021/acs.jafc.5c14556}, pmid = {41416507}, issn = {1520-5118}, mesh = {Animals ; *Indoleacetic Acids/administration &amp; dosage/metabolism ; Diet, High-Fat/adverse effects ; Mice ; *Obesity/metabolism/drug therapy/genetics ; Mice, Inbred C57BL ; Male ; Dietary Supplements/analysis ; Humans ; Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; PPAR gamma/metabolism/genetics ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Liver/metabolism/drug effects ; }, abstract = {Obesity is a major global public health challenge. Indole-3-acetic acid (IAA), a gut microbiota-derived tryptophan metabolite, exhibits antiobesogenic potential. In this study, we found that in high-fat-diet-induced obese mice, oral IAA supplementation dose dependently attenuated body weight gain, adiposity, hepatic steatosis, and dyslipidemia while improving insulin sensitivity. Notably, intraperitoneal administration of IAA (50 mg/kg/day) paradoxically exacerbated weight gain. Metagenomic sequencing showed that oral IAA selectively enriched beneficial genera (Ileibacterium, Anaerotignum, and Clostridium) and significantly increased short-chain fatty acid (SCFA) production, particularly acetate and butyrate. In vitro experiments in Saccharomyces cerevisiae further confirmed that IAA directly suppresses de novo fatty acid biosynthesis and triacylglycerol assembly. Mechanistically, IAA upregulated hepatic Gpha2 expression, thereby activating the TSH-THR-PGC-1α-PPARγ signaling cascade and concomitantly repressing key lipogenic genes (Fasn, Acaca, and Srebp-1c). Collectively, these findings position IAA as a promising microbiota-derived metabolite with substantial preventive and therapeutic potential for obesity and related metabolic disorders.}, }
@article {pmid41417461, year = {2026}, author = {Drew, G and Kraft, CS and Mehta, N}, title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.}, journal = {Clinical chemistry}, volume = {72}, number = {5}, pages = {554-563}, doi = {10.1093/clinchem/hvaf156}, pmid = {41417461}, issn = {1530-8561}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/therapy/prevention &amp; control ; *Feces/microbiology/chemistry ; *Metabolomics/methods ; *Donor Selection ; Clostridioides difficile ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.<br><br>CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.<br><br>SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.}, }
@article {pmid41418855, year = {2026}, author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC}, title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.}, journal = {Environmental research}, volume = {291}, number = {}, pages = {123588}, doi = {10.1016/j.envres.2025.123588}, pmid = {41418855}, issn = {1096-0953}, mesh = {Humans ; *Arsenic/urine/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Infant ; Rural Population ; *Environmental Exposure ; Cross-Sectional Studies ; Feces/microbiology/chemistry ; Cohort Studies ; Longitudinal Studies ; *Environmental Pollutants/urine ; }, abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.<br><br>METHODS: Participants provided urine and fecal samples at six weeks (6W; n&#xa0;=&#xa0;219) or twelve months (12M; n&#xa0;=&#xa0;219), a subset of whom provided samples at both (n&#xa0;=&#xa0;167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/gene pathway relative abundance.<br><br>RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [&#x3b2;&#xa0;=&#xa0;0.07 per doubling (95&#xa0;%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [&#x3b2;&#xa0;=&#xa0;-0.04 per doubling (95&#xa0;%CI: 0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.<br><br>CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.}, }
@article {pmid41418935, year = {2026}, author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y}, title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {35-47}, pmid = {41418935}, issn = {1995-820X}, mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; }, abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.}, }
@article {pmid41419527, year = {2025}, author = {Takeda, Y and Kato-Kogoe, N and Sakaguchi, S and Ieda, S and Tasaka, Y and Mizobata, N and Omori, M and Hamada, W and Nakamura, S and Nakano, T and Ueno, T and Matsumura, T}, title = {Characteristics of salivary IgA responses to oral microbiota in patients with oral lichen planus.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {44167}, pmid = {41419527}, issn = {2045-2322}, mesh = {Humans ; *Lichen Planus, Oral/microbiology/immunology ; *Saliva/immunology/microbiology ; Female ; Male ; Middle Aged ; *Microbiota/immunology ; RNA, Ribosomal, 16S/genetics ; Adult ; *Immunoglobulin A, Secretory/immunology ; Aged ; *Immunoglobulin A/immunology ; Bacteria/genetics/classification ; Metagenomics ; Case-Control Studies ; }, abstract = {Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa with a risk of malignant transformation. Oral bacteria are associated with OLP development and progression; however, the immune response, especially the salivary immunoglobulin A (IgA) response to these bacteria remains poorly understood. Therefore, this study aimed to characterize the salivary microbiota in patients with OLP and evaluate the corresponding salivary IgA response. Stimulated saliva samples were collected from 21 patients with OLP and 56 control participants, and 16S rRNA metagenomic analysis was performed to characterize the composition of the microbiota. In addition, IgA-enriched and non-enriched fractions from the saliva samples were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. To evaluate differences in IgA responses to each bacterium between the two groups, we calculated the IgA index. The diversity and bacterial composition of the salivary microbiota differed considerably between the OLP and control groups. Several bacterial genera, including Leptotrichia, Fusobacterium, and Streptococcus, showed markedly lower IgA index in the OLP group than the control group. In conclusion, patients with OLP exhibited a distinctive salivary IgA response to salivary microbiota, suggesting a potential association between OLP and this altered response.}, }
@article {pmid41419779, year = {2025}, author = {Liu, Y and Chen, S and Li, H and Mahtab, N and Sun, Y and Li, Y and Song, J and Sun, D and Liang, M and Chen, J and Sun, J and Gong, B and Jing, J and Bu, R}, title = {Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {125}, pmid = {41419779}, issn = {2052-4463}, support = {2024GXNSFBA010371//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069226//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069232//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; }, mesh = {China ; *Geologic Sediments/microbiology ; Wetlands ; Archaea/genetics ; *Genome, Bacterial ; *Genome, Microbial ; *Genome, Archaeal ; Bacteria/genetics/classification ; Metagenome ; Microbiota ; }, abstract = {Mangrove sediments, being organic-rich and anoxic, host diverse and functionally important microorganisms that play crucial roles in global biogeochemical cycling. In order to characterize this diversity at the genome-resolved level, we collected 38 sediment samples encompassing both surface (0-5 cm) and core (up to 90 cm) depths from six representative mangrove sites across Guangxi Province, China. Using a standardized pipeline for assembly, binning, and dereplication, we reconstructed 2,965 non-redundant metagenome-assembled genomes (MAGs), comprising 2,383 bacterial and 582 archaeal genomes spanning 78 microbial phyla. This dataset captures the high microbial diversity and functional potential within mangrove sediments under variable environmental conditions. It provides a valuable genomic resource for investigating the structure, metabolism, and ecological roles of sediment microbial communities in intertidal, nutrient-rich ecosystems, supporting future studies on microbial adaptation and biogeochemical cycling in global blue carbon environments.}, }
@article {pmid41420661, year = {2025}, author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB}, title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {1}, pages = {18}, pmid = {41420661}, issn = {1572-9699}, mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.}, }
@article {pmid41420859, year = {2026}, author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA}, title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.}, journal = {Cell reports}, volume = {45}, number = {1}, pages = {116724}, doi = {10.1016/j.celrep.2025.116724}, pmid = {41420859}, issn = {2211-1247}, mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Rural Population ; Male ; Female ; COVID-19/virology/microbiology ; Adult ; Metagenomics ; Middle Aged ; SARS-CoV-2 ; Metagenome ; }, abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.}, }
@article {pmid41421350, year = {2026}, author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L}, title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.}, journal = {Cell reports. Medicine}, volume = {7}, number = {1}, pages = {102516}, pmid = {41421350}, issn = {2666-3791}, mesh = {*Autism Spectrum Disorder/microbiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Host Microbial Interactions/genetics ; Metagenomics/methods ; Male ; Female ; Genomics/methods ; Polymorphism, Single Nucleotide/genetics ; Dysbiosis/microbiology ; Metabolomics/methods ; Genetic Variation ; Multiomics ; }, abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.}, }
@article {pmid41421358, year = {2026}, author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P}, title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.}, journal = {Cell genomics}, volume = {6}, number = {4}, pages = {101106}, pmid = {41421358}, issn = {2666-979X}, mesh = {*Bifidobacterium breve/genetics/physiology/metabolism ; Humans ; *Bacteriocins/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Adult ; Phylogeny ; *Adaptation, Physiological/genetics ; Infant ; Symbiosis ; Gene Transfer, Horizontal ; }, abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.}, }
@article {pmid41421776, year = {2026}, author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES}, title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.}, journal = {Environmental research}, volume = {291}, number = {}, pages = {123595}, doi = {10.1016/j.envres.2025.123595}, pmid = {41421776}, issn = {1096-0953}, mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; Denitrification ; Bioreactors/microbiology ; *Atmospheric Pressure ; *Microbiota ; *Waste Disposal, Fluid/methods ; Nitrification ; Altitude ; Bacteria/metabolism ; }, abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.}, }
@article {pmid41422269, year = {2025}, author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y}, title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {22}, pmid = {41422269}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity/drug effects ; Metagenomics ; Virulence Factors/genetics ; Animal Migration ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.}, }
@article {pmid41423629, year = {2025}, author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM}, title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {954}, pmid = {41423629}, issn = {2041-1723}, support = {CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; 109105z/15/a//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; Malawi ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics/drug effects ; Female ; Male ; Bayes Theorem ; Antimicrobial Stewardship ; Bacteria/drug effects/genetics/classification ; Sepsis/drug therapy/microbiology ; Metagenomics ; Young Adult ; }, abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.}, }
@article {pmid41423811, year = {2026}, author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and ,  and Lentine, J and Sockolow, RE and Sonnenberg, GF}, title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.}, journal = {Inflammatory bowel diseases}, volume = {32}, number = {2}, pages = {303-313}, pmid = {41423811}, issn = {1536-4844}, support = {//Weill Cornell Medicine Department of Pediatrics/ ; R01AI143842/NH/NIH HHS/United States ; R01AI123368/NH/NIH HHS/United States ; R01AI145989/NH/NIH HHS/United States ; U01AI095608/NH/NIH HHS/United States ; R01AI162936/NH/NIH HHS/United States ; R01CA274534/NH/NIH HHS/United States ; R37AI174468/NH/NIH HHS/United States ; //Pathogenesis of Infectious Disease/ ; //Burroughs Welcome Fund/ ; //Meyer Cancer Center Collaborative Research Initiative/ ; //Dalton Family Foundation/ ; //Rosanne H. Silbermann Foundation/ ; //Weill Cornell Medicine Division of Pediatric Gastroenterology and Nutrition/ ; }, mesh = {Humans ; *Crohn Disease/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Child ; *Anemia, Iron-Deficiency/microbiology/etiology ; Cross-Sectional Studies ; Adolescent ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.<br><br>METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.<br><br>RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.<br><br>CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.}, }
@article {pmid41427714, year = {2026}, author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR}, title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0183825}, pmid = {41427714}, issn = {2165-0497}, support = {[NE/R011524/1] (2401467)//Natural Environment Research Council/ ; }, mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Fishes/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Mucous Membrane/microbiology ; }, abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.<br><br>IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.}, }
@article {pmid41428281, year = {2025}, author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y}, title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {110}, pmid = {41428281}, issn = {1559-0267}, support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; }, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; }, abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.}, }
@article {pmid41428602, year = {2025}, author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J}, title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.}, journal = {Microbial biotechnology}, volume = {18}, number = {12}, pages = {e70242}, pmid = {41428602}, issn = {1751-7915}, support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; }, mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth &amp; development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.}, }
@article {pmid41429195, year = {2026}, author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C}, title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.}, journal = {The Journal of nutritional biochemistry}, volume = {150}, number = {}, pages = {110240}, doi = {10.1016/j.jnutbio.2025.110240}, pmid = {41429195}, issn = {1873-4847}, mesh = {Animals ; Male ; *Gastrointestinal Microbiome/physiology ; *Brain-Derived Neurotrophic Factor/metabolism ; *Neuronal Plasticity ; Mice ; *Electroconvulsive Therapy ; *Depression/therapy/metabolism ; *Wnt Signaling Pathway ; Mice, Inbred C57BL ; Fatty Acids, Volatile/metabolism ; Diet ; Probiotics ; Brain/metabolism ; }, abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/d for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multiomics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.}, }
@article {pmid41429225, year = {2026}, author = {Chen, J and Cao, H and Xu, Y and Chang, Y and Qin, X and Zhang, Z and Yang, W}, title = {Is light-to-moderate alcohol drinking associated with the onset of metabolic dysfunction-associated steatotic liver disease in a Chinese cohort?.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {2}, pages = {101144}, doi = {10.1016/j.ajcnut.2025.101144}, pmid = {41429225}, issn = {1938-3207}, mesh = {Humans ; Male ; *Alcohol Drinking/adverse effects ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; China/epidemiology ; *Fatty Liver/etiology/epidemiology ; Cohort Studies ; Risk Factors ; Aged ; *Metabolic Diseases/etiology ; East Asian People ; }, abstract = {BACKGROUND: The association between light-to-moderate alcohol drinking (≤14 g/d for females; ≤28 g/d for males) and the risk of steatotic liver disease (SLD), including its metabolic dysfunction-associated subtype (MASLD), remains unclear, as does the role of related gut microbiota.<br><br>OBJECTIVES: We investigated the association between light-to-moderate alcohol drinking and incident SLD/MASLD, identified gut microbial species associated with such drinking, and evaluated their associations with disease risk.<br><br>METHODS: Among 1297 adults from a Chinese community-based cohort, alcohol intake was assessed by a validated questionnaire, and SLD was diagnosed by vibration-controlled transient elastography. In a subset with fecal samples at follow-up (n = 665), gut microbiota was profiled using shotgun metagenomic sequencing. We used the mean alcohol intake from baseline and follow-up to represent long-term drinking habits. Species differentially associated with alcohol intake were identified using zero-inflated Gaussian models with false discovery rate (FDR) correction. Cox and logistic regression were used to estimate hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (CI), respectively.<br><br>RESULTS: During follow-up (2020-2025), 513 incident SLD cases were identified. Light-to-moderate drinkers showed higher risks of SLD (HR = 1.27, 95% CI: 1.03, 1.58) and MASLD (HR = 1.27, 95% CI: 1.01, 1.59) compared with abstainers. For the same comparison, liquor consumption was positively associated with SLD (HR = 1.29, 95% CI: 1.01, 1.65). We identified 89 microbial species associated with alcohol intake and constructed a microbial score, which was positively associated with SLD (ORT3 vs T1 = 1.54, 95% CI: 1.03, 2.31, Ptrend = 0.05) and MASLD (ORT3 vs T1 = 1.50, 95% CI: 1.00, 2.26, Ptrend = 0.05). Among these species, Stenotrophomonas maltophilia AQ, Olsenella E timonensis, and Firm 11 sp., which were less abundant in drinkers, showed inverse associations with both conditions after FDR correction.<br><br>CONCLUSIONS: Light-to-moderate alcohol consumption was associated with increased risks of SLD and MASLD. A gut microbial score based on alcohol-associated species also predicted higher disease risk.}, }
@article {pmid41429339, year = {2026}, author = {Li, M and Gao, S and Cheng, J and Chen, D and Li, H and Zhang, X and Wu, C and Chang, Y}, title = {Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic analyses: A case-control study.}, journal = {Journal of advanced research}, volume = {87}, number = {}, pages = {341-353}, doi = {10.1016/j.jare.2025.12.026}, pmid = {41429339}, issn = {2090-1224}, mesh = {Humans ; *Biomarkers/blood/metabolism ; *Metabolomics/methods ; Case-Control Studies ; Female ; *Aortic Aneurysm/microbiology/metabolism/diagnosis/blood ; Male ; *Metagenomics/methods ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Aged ; Feces/microbiology ; Multiomics ; }, abstract = {INTRODUCTION: Ascending aortic aneurysm (AsAA) is a high-risk cardiovascular condition; recent research indicates a possible association between gut microbiota, plasma metabolites, and the pathogenesis of AsAA.<br><br>OBJECTIVE: This study aims to investigate the compositional and metabolic alterations in the gut microbiota of AsAA patients to identify potential biomarkers for AsAA.<br><br>METHODS: This study enlisted 72 participants, comprising 44 individuals with AsAA and 28 healthy controls. All participants underwent examination for clinical features, and fecal and plasma samples were obtained for metagenomic and metabolomic studies.<br><br>RESULTS: Metagenomic analysis revealed a significant reduction of 23 bacterial species in AsAA patients, including Bifidobacterium adolescentis, Bifidobacterium longum, Lactiplantibacillus plantarum, Enterococcus faecalis, and Streptococcus thermophilus, while 52 bacterial species, such as Prevotella copri, Phascolarctobacterium faecium, and Eubacterium ventriosum, were found to be enriched. Furthermore, we identified seven microbial co-abundance groups (CAGs), of which three (predominantly comprising Roseburia, Agathobacter, and Prevotella) were significantly elevated in AsAA patients, whereas one (predominantly comprising Escherichia) was substantially diminished. KEGG pathway enrichment analysis indicated that the biosynthesis of unsaturated fatty acids pathway displayed the most pronounced differences between groups. Metabolomics data revealed that 22 metabolites, including ceramides, were significantly elevated, while 8 metabolites, such as threonine, were notably downregulated. Moreover, clinical indicators like C-reactive protein (CRP) and complement components C3 and C4 have shown strong correlations with specific gut microbiota (Streptococcus, Prevotella) and plasma metabolites (threonine, ceramides). These findings indicate that inflammatory responses, metabolic dysregulation, and gut microbiota imbalance are pivotal in the etiology of AsAA.<br><br>CONCLUSION: This study demonstrates substantial alterations in gut microbiota composition and plasma metabolites in patients with AsAA. Prevotella and ceramides exhibit potential as biomarkers for AsAA diagnosis. Furthermore, a synergy of Prevotella and ceramides may function as a potent disease prediction classifier, offering novel perspectives on the early diagnosis and targeted treatment of AsAA.}, }
@article {pmid41429819, year = {2025}, author = {Chen, Q and Xu, J and Yang, J and Qin, X and Fan, J and Ke, H and Yang, Z and Zheng, W and Li, X and Huang, L and Ning, W}, title = {Gut microbiota analysis in children with autism spectrum disorder and their family members.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {44282}, pmid = {41429819}, issn = {2045-2322}, support = {Grant No.3502Z20214001//Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China/ ; 2022YFC2704300//National Key Research and Development Program of China/ ; 32400532//National Natural Science Foundation of China/ ; 2024GGB18//Fujian Provincial Health Technology Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology ; Child ; Male ; Female ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; Siblings ; Bifidobacterium/isolation &amp; purification/genetics ; Clostridium/isolation &amp; purification/genetics ; Bacteroides/isolation &amp; purification/genetics ; Metagenomics/methods ; Family ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication and interaction, alongside restricted, and repetitive behaviors. Emerging evidence suggests that gut microbiota alterations may contribute to ASD pathogenesis via the gut-brain axis. However, many previous studies have not adequately controlled for confounding genetic and environmental variables. In this study, we examined the gut microbiota profiles of 19 children with ASD, 8 siblings with non-ASD, and 36 parents from 17 families, providing a unique design that minimized biases related to shared genetic and familial environments. Metagenomic sequencing revealed significant differences in gut microbiota diversity and composition between groups. Specifically, children with ASD had lower abundances of Bifidobacterium and higher abundances of both Bacteroides and Clostridium species compared to their siblings, with notable dysbiosis correlated to ASD-specific symptoms. These findings highlight the potential role of microbiota alterations in ASD pathogenesis and suggest familial microbiota traits influenced by both genetic and environmental factors. Further exploration of gut microbial therapies could offer promising avenues for ASD intervention.}, }
@article {pmid41430301, year = {2025}, author = {Wikki, I and Palmu, J and Kauko, A and Havulinna, A and Jousilahti, P and Lahti, L and Knight, R and Salomaa, V and Niiranen, T}, title = {Prospective association between the gut microbiota and incident pneumonia: a cohort study of 6419 individuals.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {354}, pmid = {41430301}, issn = {1465-993X}, support = {330887//Research Council of Finland/ ; 321351, 354447//Research Council of Finland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Prospective Studies ; Middle Aged ; Incidence ; *Pneumonia/epidemiology/microbiology/diagnosis ; Aged ; Cohort Studies ; Adult ; Follow-Up Studies ; Risk Factors ; Feces/microbiology ; }, abstract = {BACKGROUND: Previous animal studies have identified the protective capacity of the gut microbiota against respiratory infections. Nevertheless, the prospective association between human gut microbiota and pneumonia risk remains unknown.<br><br>OBJECTIVES: To evaluate the links between gut microbiota and incident pneumonia in a representative population sample.<br><br>METHODS: We performed shotgun metagenome sequencing on stool samples from 6419 FINRISK 2002 participants. Participants were followed up for incident pneumonia using nationwide health register data. We employed multivariable-adjusted Cox regression models and permutational multivariate analysis of variance (PERMANOVA) to assess the association of gut microbiome alpha diversity, compositional variation (beta diversity), and taxonomic composition with pneumonia risk.<br><br>RESULTS: Altogether, 685 patients (10.7%) developed pneumonia during a mean follow-up of 17.8 years. Alpha diversity was not associated with incident pneumonia (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.93&#x2009;-&#x2009;1.08), whereas community composition was (PERMANOVA R[2]&#x2009;=&#x2009;0.03%; P&#x2009;=&#x2009;0.02). We observed an inverse association between the relative abundance of butyrate-producing bacteria and incident pneumonia (HR per 1-SD increase 0.91; 95% CI 0.85-0.98). The relative abundance of Bacteroides_F pectinophilus, Eubacterium_G ventriosum, Agathobaculum butyriciproducens, Butyribacter intestini, Eubacterium_I ramulus, CAG-1427 sp000435675, and CAG-603 sp900066105 were inversely associated with pneumonia risk. The relative abundance of Clostridium_AQ innocuum was positively correlated with pneumonia risk.<br><br>CONCLUSIONS: The gut microbiota composition, and especially the relative abundance of butyrate-producing bacteria, was associated with lower pneumonia risk in the population. These findings warrant further studies to investigate whether microbiome modulation to increase short chain fatty acid production through diet, prebiotics, or probiotics could reduce pneumonia risk.}, }
@article {pmid41430427, year = {2025}, author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M}, title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {2586}, pmid = {41430427}, issn = {2045-2322}, mesh = {Italy ; *Metals, Heavy/analysis ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants/analysis ; *Soil/chemistry ; Environmental Monitoring/methods ; Metagenomics ; Models, Statistical ; }, abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.}, }
@article {pmid41431641, year = {2025}, author = {Nguyen, BN and Nguyen, LTN and Trinh, DTM and Nguyen, HT and Tran, TTT}, title = {Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20521}, pmid = {41431641}, issn = {2167-8359}, mesh = {Humans ; *Arthritis, Rheumatoid/microbiology ; Vietnam ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Pilot Projects ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; }, abstract = {In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam.}, }
@article {pmid41431647, year = {2025}, author = {Lu, X and Dai, H and Gu, X and Xie, J and Zhong, X and Dong, X and Su, B and Su, J and Wang, L and Sun, T and Geng, L}, title = {The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20526}, pmid = {41431647}, issn = {2167-8359}, mesh = {Aged ; Female ; Humans ; Male ; Biomarkers ; Case-Control Studies ; Clinical Relevance ; Disease Progression ; Enterococcus faecium ; Feces/microbiology ; *Gastrointestinal Diseases/complications/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Gastrointestinal Transit ; *Pulmonary Disease, Chronic Obstructive/complications/microbiology ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions-particularly intestinal transit and gas handling-rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.<br><br>METHODS: Fecal samples from 20 COPD &amp; FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.<br><br>RESULTS: COPD/COPD &amp; FABD patients showed significantly higher fecal microbiota &#x3b1;-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD &amp; FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. &#x3b2;-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD &amp; FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD &amp; FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04-26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).<br><br>CONCLUSION: Gut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation.}, }
@article {pmid41431864, year = {2026}, author = {Dowrick, JM and Roy, NC and Carco, C and James, SC and Heenan, PE and Frampton, CMA and Fraser, K and Young, W and Cooney, J and Trower, T and Keenan, JI and McNabb, WC and Mullaney, JA and Bayer, SB and Talley, NJ and Gearry, RB and Angeli-Gordon, TR}, title = {Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2604871}, pmid = {41431864}, issn = {1949-0984}, mesh = {Humans ; Cluster Analysis ; *Gastrointestinal Diseases/physiopathology/microbiology/classification ; Male ; Female ; *Brain/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Multiomics ; }, abstract = {Rome IV disorders of gut-brain interaction (DGBI) subtypes are known to be unstable and demonstrate high rates of non-treatment response, likely indicating patient heterogeneity. Cluster analysis, a type of unsupervised machine learning, can identify homogeneous sub-populations. Independent cluster analyses of symptom and biological data have highlighted its value in predicting patient outcomes. Integrated clustering of symptom and biological data may provide a unique multimodal perspective that better captures the complexity of DGBI. Here, integrated symptom and multi-omic cluster analysis was performed on a cohort of healthy controls and patients with lower-gastrointestinal tract DGBI. Cluster stability was assessed by considering how frequently pairs of participants appeared in the same cluster between different bootstrapped datasets. Functional enrichment analysis was performed on the biological signatures of stable DGBI-predominant clusters, implicating disrupted ammonia handling and metabolism as possible pathophysiologies present in a subset of patients with DGBI. Integrated clustering revealed subtypes that were not apparent using a singular modality, suggesting a symptom-only classification is prone to capturing heterogeneous sub-populations.}, }
@article {pmid41432144, year = {2026}, author = {Liu, J and Ni, H-B and Yu, M-Y and Qin, S-Y and Elsheikha, HM and Peng, P and Guo, L and Xie, L-H and Liang, H-R and Lei, C-C and Xu, Y and Tang, Y and Yu, H-L and Qin, Y and Liu, J and Sun, H-C and Zhang, X-X and Qiu, B}, title = {Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0144325}, pmid = {41432144}, issn = {2379-5077}, support = {2023YFF1305403//National Key Research and Development Program of China/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; No. 667/2425025//Horizontal Project of Qingdao Agricultural University/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Antelopes/microbiology ; Animals ; Tibet ; *Virulence Factors/genetics ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Bacteria/genetics/pathogenicity/drug effects ; Genes, Bacterial ; }, abstract = {UNLABELLED: Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.<br><br>IMPORTANCE: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.}, }
@article {pmid41432159, year = {2026}, author = {Lau, KJX and Ma, A and Chen, B and Thankaraj Salammal, MS and Ramachandran, S and Naqvi, NI}, title = {Controlled irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0297025}, pmid = {41432159}, issn = {2165-0497}, support = {Intramural//Temasek Life Sciences Laboratory/ ; //Philanthropy Asia Alliance/ ; //Bill and Melinda Gates Foundation (GF)/ ; }, mesh = {*Oryza/microbiology/growth &amp; development/metabolism ; *Methane/metabolism ; *Rhizosphere ; *Agricultural Irrigation/methods ; *Microbiota ; Soil Microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Archaea/metabolism/genetics/classification ; Plant Roots/microbiology ; Metagenomics ; Floods ; }, abstract = {The rhizosphere microbiomes of rice plants under conventional flood irrigation consist of highly complex consortia of microorganisms and, in particular, methanogens purportedly associated with methane emissions therein. Controlled irrigation has been proposed as a cultivation method of choice over continuous flooding to reduce water and fertilizer usage in an aerobic environment. However, a systematic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Using empirical analyses, we report a significant reduction in methane emissions in controlled irrigation compared to the flooded environment. Genotypic or varietal differences did not influence such methane emissions under conventional flooded cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affects the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse, was collected over 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favors microbes involved in the nitrifying-denitrifying processes, while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbiomes associated with methanogenesis were significantly reduced in drip irrigation. Several keystone taxa were evident in the co-occurrence network model related to methanogenic, methanotrophic, nitrifying, sulfur-oxidizing and sulfur-reducing activities. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota and the associated metabolic functional differences observed between the two irrigation regimes, leading up to the microbial mitigation of climate impact.IMPORTANCEUnlike previous studies in alternate wet-dry irrigation systems, this study characterized the rice microbiomes in a controlled drip irrigation setting where water levels were maintained at low levels and soil remained unflooded throughout the entire season in a greenhouse. A reduction of more than 90% in methane emissions was observed with drip irrigation compared to flood irrigation. A significant correlation was found between levels of methane emitted and mcrA gene copies detected, with a Pearson correlation coefficient R of 0.77 and P-value of 2.3e - 10. Methanogens are highly abundant in continuously flooded rice soil and are significantly reduced in drip-irrigated soil. Metagenomic profiling indicates that the shifts in microbial diversity under drip irrigation favor nitrifying microorganisms and are likely influenced by increased oxygen availability due to higher soil redox potential.}, }
@article {pmid41432253, year = {2026}, author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C}, title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41432253}, issn = {1751-7370}, support = {ECPF24-4273843556//Early Career Postdoctoral Fellowship/ ; //Faculty of Medicine, Nursing and Health Science at Monash University/ ; DE250101210//ARC DECRA Fellowships/ ; FT240100502//ARC Future Fellowship/ ; SR200100005//ARC SRIEAS/ ; //Securing Antarctica's Environmental Future/ ; }, mesh = {*Caves/microbiology ; *Bacteria/metabolism/genetics/classification ; *Geologic Sediments/microbiology ; *Archaea/metabolism/genetics/classification ; *Ecosystem ; Metagenome ; *Microbiota ; Photosynthesis ; Eukaryota/genetics/metabolism/classification ; Seawater/microbiology ; }, abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.}, }
@article {pmid41432437, year = {2026}, author = {Bowerman, KL and Lu, Y and McRae, H and Volmer, JG and Zaugg, J and Pope, PB and Hugenholtz, P and Greening, C and Morrison, M and Soo, RM and Evans, PN}, title = {Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0160825}, pmid = {41432437}, issn = {2379-5077}, support = {DP210103991//Department of Education and Training | Australian Research Council (ARC)/ ; DP150104202//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100812//Department of Education and Training | Australian Research Council (ARC)/ ; //Australian Government (Federal Government)/ ; B.STU.1909//Meat and Livestock Australia/ ; //University of Queensland/ ; }, mesh = {Animals ; *Hydrogen/metabolism ; *Marsupialia/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; *Metagenomics/methods ; *Metagenome ; Bacteria/genetics/metabolism/classification ; }, abstract = {Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.}, }
@article {pmid41432724, year = {2026}, author = {Zhang, Z and Ye, B and He, J and Xiang, L and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Li, Y and Ju, J and Liu, Y and Xia, M}, title = {Microbial metabolites associated with healthy lifestyles in relation to metabolic syndrome and vascular health: a cross-sectional study.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0143325}, pmid = {41432724}, issn = {2379-5077}, mesh = {Humans ; *Metabolic Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; Adult ; *Healthy Lifestyle/physiology ; Feces/microbiology ; Bacteria/metabolism/classification/genetics ; Metabolome ; Aged ; }, abstract = {UNLABELLED: Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.<br><br>IMPORTANCE: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.}, }
@article {pmid41435895, year = {2026}, author = {Zhang, PP and Cui, MY and Yang, SY and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF}, title = {Astragalus membranaceus improves blood glucose and renal function in diabetic kidney disease mice via gut microbial metabolite axis.}, journal = {Fitoterapia}, volume = {189}, number = {}, pages = {107048}, doi = {10.1016/j.fitote.2025.107048}, pmid = {41435895}, issn = {1873-6971}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Astragalus propinquus/chemistry ; Mice ; *Diabetic Nephropathies/drug therapy ; Male ; *Plant Extracts/pharmacology ; *Kidney/drug effects ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/drug therapy ; }, abstract = {Recent studies have demonstrated the therapeutic potential of Astragalus membranaceus in diabetic kidney disease (DKD); however, the underlying mechanisms remain incompletely elucidated. In this study, we established a streptozotocin-induced DKD mouse model to evaluate the effects of A. membranaceus extract (AME) on glycemic control, renal function, gut microbiota composition, and metabolic profiles. Biochemical analyzes revealed that A. membranaceus significantly attenuated hyperglycemia and improved renal function, as indicated by reduced serum creatinine and blood urea nitrogen levels. Metagenomic sequencing demonstrated that A. membranaceus reversed microbial dysbiosis by suppressing pathogenic bacteria (e.g., Aerococcus urinaeequi) and enriching beneficial probiotics (e.g., Thomasclavelia cocleata). Furthermore, LC/MS-based metabolomics identified key metabolic pathways, including glycerophospholipid metabolism and bile acid synthesis, as potential mediators of the therapeutic effects. These findings underscore the crucial role of the gut-renal axis in DKD pathogenesis and provide a mechanistic basis for the clinical application of A. membranaceus.}, }
@article {pmid41436448, year = {2025}, author = {Manghi, P and Antonello, G and Schiffer, L and Golzato, D and Wokaty, A and Beghini, F and Mirzayi, C and Long, K and Gravel-Pucillo, K and Piccinno, G and Gamboa-Tuz, SD and Bonetti, A and D'Amato, G and Azhar, R and Eckenrode, K and Zohra, F and Giunchiglia, V and Keller, M and Pedrotti, A and Likhotkin, I and Elsafoury, S and Geistlinger, L and Blanco-Miguez, A and Thomas, AM and Zolfo, M and Ramos, M and Valles-Colomer, M and Tamburini, S and Asnicar, F and Jones, HE and Huttenhower, C and Carey, V and Davis, S and Pasolli, E and Oh, S and Segata, N and Waldron, L}, title = {Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {196}, pmid = {41436448}, issn = {2041-1723}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; *Mouth/microbiology ; }, abstract = {Large public datasets of the human microbiome now exist but combining them for large-scale analysis is difficult due to a lack of standardization. We developed curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata from 94 studies and 42 countries. This large and diverse resource allows for meta-analysis of the links between microbes and human health. Through meta-analysis, we identified hundreds of microbial species and thousands of microbial functions significantly associated with a person's sex, age, body mass index, and disease status, and catalog these as references. We developed an "oral enrichment score" (OES) based on the relative abundance of bacteria typically found in the oral cavity and not in the gut. Higher OES in the gut is a consistent feature in individuals with disease, suggesting that the relative abundance of oral bacteria in the gut is a simple and quantifiable signal of altered microbiome health. These analyses identify modest but widely shared patterns in human microbiomes, serving as a reproducible and readily updatable reference.}, }
@article {pmid41437205, year = {2026}, author = {Dinesh, D and Morgan, XC and Kim, H and Scott, TM and Garelnabi, M and Lee, JS and Mangano, KM and Nguyen, LH and Huttenhower, C and Tucker, KL and Palacios, N}, title = {Gut Microbial Variations Associated With Proton Pump Inhibitor Use in the Boston Puerto Rican Health Study.}, journal = {Pharmacology research &amp; perspectives}, volume = {14}, number = {1}, pages = {e70205}, pmid = {41437205}, issn = {2052-1707}, support = {RF1AG075922/AG/NIA NIH HHS/United States ; P01 AG023394/NH/NIH HHS/United States ; R01 NS09772/NH/NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; P50 HL105185/NH/NIH HHS/United States ; R01 AG055948/NH/NIH HHS/United States ; //University of Massachusetts/ ; R01 AG055948/AG/NIA NIH HHS/United States ; P50 HL105185/HL/NHLBI NIH HHS/United States ; P01 AG023394/AG/NIA NIH HHS/United States ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Boston ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Hispanic or Latino ; Prospective Studies ; *Proton Pump Inhibitors/adverse effects/pharmacology ; Puerto Rico/ethnology ; }, abstract = {Proton pump inhibitors (PPI), used to treat gastrointestinal disorders, are associated with alterations in the gut microbiome. However, this is understudied in Puerto Ricans who have unique lifestyle characteristics. Puerto Ricans, including participants of the Boston-Puerto Rican Health Study (BPRHS), report high PPI use. Therefore, we examined gut microbial variations associated with PPI use in the BPRHS. BPRHS is a prospective cohort. 309 BPRHS participants self-reported PPI use and self-collected, metagenomically profiled, stool samples. PPI use was classified as any use in the past 30 days. Cross-sectional associations between gut microbial taxa, functional pathways, and PPI use were examined using omnibus analyses, multivariate linear modeling in MaAsLin2, and random forest classifier in feature-wise analyses. We further compared our results with the non-Hispanic Health Professionals Follow-Up Study (HPFS) to validate key findings and examine ethnicity-related differences. Among 309 participants (mean age 68.8 years; female 74.6%), 112 (36%) self-reported PPI use. After adjusting for relevant covariates, we observed an enrichment of Streptococcus parasanguinis (β = 3.16, FDR p = 0.01), S. anginosus (β = 2.89, FDR p < 0.01), S. salivarius (β = 2.56, FDR p = 0.01), S. gordonii (β = 1.98, FDR p = 0.15), and Rothia mucilaginosa (β = 1.54, FDR p = 0.06), among PPI users compared to non-users. Streptococci, Lactobacilli, and Enterococci predominantly contributed to the functional pathways associated with PPI use. The observed enrichment of oral-typical taxa, such as Streptococci, among PPI users in the BPRHS suggests the potential of PPIs to alter gut microbial composition. More studies are needed to understand the impact of PPI use on the gut microbiome in different ethnicities. Trial Registration: Parent study (BPRHS) NCT01231958.}, }
@article {pmid41437386, year = {2025}, author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R}, title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {45}, pmid = {41437386}, issn = {2049-2618}, mesh = {*Microbiota/genetics ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Sewage/microbiology ; Cities ; Metagenomics/methods ; Machine Learning ; Genome, Bacterial ; }, abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.<br><br>METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97&#x2009;&#xb1;&#x2009;0.01. Synthetic donor-recipient simulations (&#x3b1;&#x2009;=&#x2009;0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.<br><br>RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2]&#x2009;=&#x2009;0.12, p&#x2009;<&#x2009;0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC&#x2009;=&#x2009;0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC&#x2009;&#x2265;&#x2009;0.8). Entropy-based uncertainty analysis identified tipping zones (&#x3b1;&#x2009;=&#x2009;0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.<br><br>CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.}, }
@article {pmid41439481, year = {2026}, author = {Zou, Y and Li, N and Li, X and Kuang, M and Xu, X and Guan, L and Li, X and Zheng, P and Li, L and Wan, J and Lu, N and Liu, J and He, C and Zhu, Y}, title = {Gut microbiota dysbiosis exacerbates acute pancreatitis via Escherichia coli-driven neutrophil heterogeneity and NETosis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2606480}, pmid = {41439481}, issn = {1949-0984}, mesh = {Animals ; *Dysbiosis/microbiology/immunology/complications ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Neutrophils/immunology ; *Extracellular Traps/immunology/metabolism ; *Escherichia coli/physiology ; *Pancreatitis/microbiology/immunology/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Specific Pathogen-Free Organisms ; }, abstract = {Gut microbiota dysbiosis contributes to acute pancreatitis (AP) severity, but the specific microbes and mechanisms remain unclear. In this study, we employed both germ-free (GF) and specific-pathogen-free (SPF) murine models of AP to investigate the role of the intestinal microbiota. Our findings demonstrate that GF mice exhibited markedly attenuated pancreatic injury, inflammatory cell infiltration, and neutrophil extracellular traps (NETs) formation. Through fecal microbiota transplantation (FMT) from AP patients, differential antibiotic modulation, and single-bacterial colonization experiments, we identified Gram-negative bacteria, particularly Escherichia coli (E. coli), as critical microbial drivers of disease exacerbation. Single-cell RNA sequencing revealed that microbiota dysbiosis profoundly reprogrammed both local pancreatic and systemic immune landscapes. Specifically, dysbiosis promoted emergency granulopoiesis in the bone marrow, enhanced neutrophil mobilization and activation, and facilitated the expansion of pro-inflammatory neutrophil subpopulations (Neutrophils_2 and Neutrophils_3). These subsets exhibited upregulated signaling through NETosis-associated pathways, including TLR, NF-κB, and IL-17 axes. Conversely, in GF conditions, we observed a predominance of an anti-inflammatory neutrophil subset (Neutrophils_4), characterized by the expression of tissue repair-associated genes such as Reg1 and Reg2. Shotgun metagenomic profiling of fecal samples from patients with AP revealed an enrichment of E. coli during the acute phase, positively correlating with circulating cell-free DNA, a marker of NETosis. Together, these insights suggest that gut microbiota dysbiosis, notably increased E. coli abundance, may aggravate AP by reshaping immunity and promoting aberrant NETs formation, supporting microbiota or NETs targeted therapies.}, }
@article {pmid41443199, year = {2026}, author = {Lucas, TN and Biehain, U and Gautam, A and Gemeinhardt, K and Lass, T and Konzalla, S and Ley, RE and Angenent, LT and Huson, DH}, title = {MMonitor for real-time monitoring of microbial communities using long reads.}, journal = {Cell reports methods}, volume = {6}, number = {1}, pages = {101266}, pmid = {41443199}, issn = {2667-2375}, mesh = {Humans ; *Metagenomics/methods ; *Software ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; }, abstract = {Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations.}, }
@article {pmid41444596, year = {2025}, author = {Tang, R and Shi, M and Ji, X and Zhang, Y and Fan, L and Huang, F and Li, X}, title = {Integrative oral and gut microbiome profiling highlights microbial correlates of complications in type 1 diabetes: a cross-sectional analysis.}, journal = {Cardiovascular diabetology}, volume = {24}, number = {1}, pages = {461}, pmid = {41444596}, issn = {1475-2840}, support = {2024XQLH049//Graduate Innovation Project of Central South University/ ; grant 2023ZD0508200 and 2023ZD0508205//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; grant 82470871//National Natural Science Foundation of China/ ; grant R2023001//Hunan Provincial Health High-Level Talent Scientific Research Project/ ; LYF2022039//Sinocare Diabetes Foundation/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications ; Male ; Female ; Adult ; Dysbiosis ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Mouth/microbiology ; Case-Control Studies ; Middle Aged ; *Diabetic Angiopathies/microbiology/diagnosis ; Young Adult ; Risk Factors ; Feces/microbiology ; Biomarkers/blood ; Host-Pathogen Interactions ; Risk Assessment ; Metagenomics ; Blood Glucose/metabolism ; }, abstract = {BACKGROUND/OBJECTIVE: Chronic vascular complications are the primary threat in long-standing type 1 diabetes (T1D) patients. We examined the associations between oral-gut microbiome dysbiosis and these complications, offering novel insights into therapeutic strategies and underlying mechanisms.<br><br>METHODS: This cross-sectional study enrolled 75 T1D participants (disease duration&#x2009;&#x2265;&#x2009;10&#xa0;years) and 43 healthy controls who underwent comprehensive clinical assessment, including blood glucose, lipid profile, and complication-related examinations. Fecal and oral rinse samples were collected for shotgun metagenomic sequencing. T1D participants were stratified by the presence of microvascular (retinopathy, nephropathy, or neuropathy) or macrovascular complications separately. Microbial differences across groups were assessed.<br><br>RESULTS: Significant differences in oral and gut microbiota compositions were observed between T1D participants with and without complications (both microvascular and macrovascular). A core set of 26 gut and 8 oral microbial species was specifically associated with vascular complications. Butyrate-producing gut bacteria (Blautia wexlerae, Anaerobutyricum hallii, Roseburia inulinivorans, A. soehngenii) and specific oral Neisseria species were enriched in T1D without complications individuals, suggesting protective effects against complications. Mediation analysis indicated associations consistent with partial mediation between certain microbial species and the relationships of glycemic control or insulin resistance (HbA1c, glucose risk index, estimated glucose disposal rate) with complication risk. Moreover, potential oral-gut microbiome interconnections were implicated in complication development. Finally, classification models integrating both oral and gut microbial features significantly outperformed models based on either site alone in distinguishing T1D patients with complications.<br><br>CONCLUSIONS: Distinct oral and gut microbiome features are associated with chronic vascular complications in T1D. These findings highlight the potential of microbiome-targeted strategies for understanding and preventing T1D-related complications.}, }
@article {pmid41446276, year = {2025}, author = {Chen, S and Jiang, Y and Lv, D and Zheng, Y and Zhang, R and Dai, H and Wang, Z and Li, S and Qi, R and Xu, H and Yu, Y and Xu, C and Lu, X and Xu, Y and Jin, S and Wu, X}, title = {Identification of subtypes and construction of a predictive model for novel subtypes in severe community-acquired pneumonia based on clinical metagenomics: a multicenter, retrospective cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1676502}, pmid = {41446276}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Community-Acquired Infections/microbiology/mortality/classification/diagnosis ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; China/epidemiology ; *Pneumonia/microbiology/classification/mortality ; Adult ; Microbiota/genetics ; Prognosis ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Intensive Care Units ; High-Throughput Nucleotide Sequencing ; Nomograms ; Community-Acquired Pneumonia ; }, abstract = {OBJECTIVE: It is well recognized that high heterogeneity represents a key driver of the elevated mortality in severe community-acquired pneumonia (sCAP). Precise subtype classification is therefore critical for both treatment strategy formulation and prognostic evaluation in this patient population. This study aimed to develop a predictive model for novel clinical subtypes of sCAP, leveraging microbiome profiles identified via metagenomic next-generation sequencing (mNGS).<br><br>METHODS: This retrospective multicenter cohort study enrolled adult patients with sCAP who underwent clinical mNGS testing of bronchoalveolar lavage fluid in intensive care units (ICUs) across 17 medical centers in China. Based on mNGS-identified microbiome characteristics, unsupervised machine learning (UML) was employed for clustering analysis of sCAP patients. LASSO regression and random forest (RF) algorithms were applied to screen and identify predictors of novel sCAP subtypes. A predictive model for the new clinical subtypes was constructed according to the screening results, with a nomogram generated. The discriminative ability, calibration, and clinical utility of the model were evaluated using ROC curves, calibration curves, and decision curve analysis, respectively.<br><br>RESULTS: A total of 1,051 sCAP patients were included in the final analysis. The 28-day all-cause mortality rate was 45% (473/1,051). UML clustering identified two distinct sCAP subtypes: the 28-day mortality rate was 42.19% (343/813) in subtype 1 and 54.62% (130/238) in subtype 2. Incorporating clinical and microbial features, a predictive model for the novel sCAP subtypes was developed using the following predictors: immunosuppression (OR = 37,411.46, P < 0.001), connective tissue disease (CTD) (OR = 12,144.60, P = 0.004), hematological malignancy (HM) (OR = 107,768.13, P < 0.001), chronic kidney disease (CKD) (OR = 49.71, P < 0.001), cytomegalovirus (CMV) (OR = 0.00, P < 0.001), Epstein-Barr virus (EBV) (OR = 131.97, P < 0.001), Pneumocystis (OR = 47,949.56, P < 0.001), and Klebsiella (OR = 0.02, P = 0.003). The model demonstrated excellent discriminative ability with an area under the ROC curve (AUC) of 0.992. Calibration curves showed good agreement between predicted and observed outcomes. Decision curve analysis confirmed high clinical utility for predicting novel sCAP subtypes.<br><br>CONCLUSION: This study identified novel clinical subtypes of sCAP based on mNGS-derived microbiome characteristics. This approach exhibits superior performance in identifying high-risk sCAP patients, facilitating precise subtyping.}, }
@article {pmid41448087, year = {2026}, author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M}, title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140887}, doi = {10.1016/j.jhazmat.2025.140887}, pmid = {41448087}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Metformin/pharmacology ; *Microbiota/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics/drug effects ; }, abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.}, }
@article {pmid41448339, year = {2026}, author = {Ghosh, S and Ganguly, A and Dong, TS and Lagishetty, V and Jacobs, JP and Devaskar, SU}, title = {Intestinal microbiome in response to air pollutant exposure in pregestational and gestational murine females and their male and female offspring.}, journal = {Reproductive toxicology (Elmsford, N.Y.)}, volume = {140}, number = {}, pages = {109150}, doi = {10.1016/j.reprotox.2025.109150}, pmid = {41448339}, issn = {1873-1708}, support = {R01 HD041230/HD/NICHD NIH HHS/United States ; R01 HD081206/HD/NICHD NIH HHS/United States ; R01 HD81206//NIH/ ; R01 HD41230//NIH/ ; }, mesh = {Female ; Animals ; Male ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Prenatal Exposure Delayed Effects/microbiology ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Mice ; Maternal Exposure ; Bacteria/genetics/drug effects/classification ; }, abstract = {We investigated the impact of chronic air pollutant (AP) exposure upon intestinal microbial diversity, composition, and metagenomic inferred functional pathways in murine pregestational and late gestational adult females, and male and female postnatal offspring (P21), compared to age- and sex- matched controls (CON). Intestinal microbiome analysis was undertaken with certain phenotypic characteristics in adult non-pregnant and pregnant females and the male and female offspring. In response to AP, pooled male and female offspring displayed no difference in E19 fetal and P1 postnatal body weights. At P21, females exposed in-utero to AP were heavier with increased fat and muscle mass at one month versus CON. Males were no different at P21 and 1 month revealing decreased fat mass and hyperglycemia. In pregestational/gestational females, AP did not change microbial α- or β-diversity from the respective CON. Gestational females showed AP induced changes in taxonomic composition such as reduced Bacteroides and increased Firmicutes, Verrucomicrobia, and Akkermansia, among others. In response to intra-uterine AP exposure, the offspring intestinal microbiome revealed more compelling differences in α- and β- diversity than adult females. While certain microbial changes were common in both sexes, sex-specific differences also emerged with reduced α-diversity, decreased Bacteroides and increased Akkermansia in males only. The metagenomic inferred pathways revealed perturbations in multiple pathways. We conclude that the offspring exposed in-utero to AP revealed sex-specific changes in microbial diversity, composition and function, displaying certain similarities with distinct differences from mothers. These early life changes were associated with the subsequent emergence of pre-diabetes and adiposity.}, }
@article {pmid41448605, year = {2026}, author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Johnson, S and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT}, title = {Dietary Nitrate Intake and 16S rRNA-Inferred Nitrite-Generating Capacity of the Subgingival Microbiome May Influence Glucose Metabolism: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).}, journal = {Journal of clinical periodontology}, volume = {53}, number = {4}, pages = {508-519}, pmid = {41448605}, issn = {1600-051X}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R03 DE031296/DE/NIDCR NIH HHS/United States ; UL1TR001873/TR/NCATS NIH HHS/United States ; DK-63608//Vagelos College of Physicians and Surgeons, Columbia University/ ; R21 DE022422/DE/NIDCR NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32 HL007779/HL/NHLBI NIH HHS/United States ; R00 DE018739/DE/NIDCR NIH HHS/United States ; R03 DE027773/DE/NIDCR NIH HHS/United States ; R00 DE018739/NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *RNA, Ribosomal, 16S/genetics ; Male ; *Insulin Resistance ; *Nitrates/administration &amp; dosage/metabolism ; *Gingiva/microbiology ; *Microbiota/genetics ; *Nitrites/metabolism ; *Diet ; Blood Glucose/metabolism ; *Glucose/metabolism ; Biomarkers ; Cardiometabolic Risk Factors ; *Glucose Intolerance/metabolism/microbiology ; }, abstract = {AIMS: To investigate whether the association between the nitrite-generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake.<br><br>MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31&#x2009;&#xb1;&#x2009;9&#x2009;years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome-Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA-IR), blood pressure) on nitrate intake and MINES together with a MINES &#xd7; nitrate intake interaction term.<br><br>RESULTS: Mean nitrate intake was 190&#x2009;&#xb1;&#x2009;171&#x2009;mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p&#x2009;<&#x2009;0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA-IR (1.2 [1.1-1.4] vs. 1.5 [1.3-1.6]; p&#x2009;=&#x2009;0.002), but levels were similar in those with high MINES (p&#x2009;=&#x2009;0.84).<br><br>CONCLUSIONS: A biomarker of higher microbial NO-generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate-rich diets should incorporate measures of the entire oral microbiome.}, }
@article {pmid41450573, year = {2025}, author = {Zhang, G and Zeng, L and Chen, B and Dai, H and Tang, K and Huang, R and Xiang, X and Yang, J and Yang, J and Song, X and Ma, Y and Lin, R and Huang, Y}, title = {Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1674341}, pmid = {41450573}, issn = {2235-2988}, mesh = {Humans ; *Bile/microbiology ; *Biliary Tract/microbiology ; Drainage/adverse effects ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Metagenomics ; Adult ; }, abstract = {INTRODUCTION: Despite years of research, knowledge about the microbial populations of human physiological bile has remained limited. Bile sampling techniques, such as Endoscopic Retrograde Cholangiopancreatography (ERCP), percutaneous biliary drainage, and intra-operative sampling, are invasive procedures typically performed only in the presence or suspicion of biliary tract disease. Furthermore, the increased incidence of bacterial infections following biliary drainage poses a significant clinical concern; however, the relationship between biliary drainage and biliary flora remains poorly understood. In this study, we present a distinct taxonomic composition of bacterial communities identified in bile samples from disease-free individuals, as well as from obstructive and post-drainage biliary tracts.<br><br>METHODS: A metagenomic sequence analysis of bile samples from patients with MBO who underwent percutaneous biliary drainage (PTBD) at our center from 1st May 2021 to 1st March 2022, which were divided into 2 groups, as the MBO group (n = 29) and BD group (n = 27). Eight liver donors were included as a control group.<br><br>RESULTS: Abundant bacterial populations were detected in the bile of liver donors, revealing a highly similar microbial composition in both disease-free and malignant obstructive biliary trees. Notably, biliary drainage was found to alter the composition of bile microbiota, resulting in decreased microbial diversity and an association with an increase in antibiotic resistance genes.<br><br>DISCUSSION: These findings provide fundamental knowledge on the composition of the human bile microbiota and present new evidence to support that biliary drainage induces a shift in bile microbiota, rendering it more aggressive and resistant to antibiotics.}, }
@article {pmid41451983, year = {2026}, author = {Fan, Y and Ju, T and Bhardwaj, T and Korver, DR and Willing, BP}, title = {Chicken cecal microbial functional gene content and resistome differ by age and barn disinfection practice.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0373725}, pmid = {41451983}, issn = {2165-0497}, support = {RGPIN-2019-06336//Natural Sciences and Engineering Research Council of Canada/ ; //Agriculture Funding Consortium/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Disinfection/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; Disinfectants/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Age Factors ; Housing, Animal ; Metagenomics ; }, abstract = {Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Studies showed that disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functional gene content. The current study compared the effects of disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after two production cycles at seven barns. Shotgun metagenomic sequencing performed on cecal contents collected at days 7 and 30 also allowed the evaluation of age-associated characteristics of the microbiome. The age of the chickens had the largest effects on the resistome, with younger birds having higher relative abundance of total ARGs (P < 0.05) and differences in resistance mechanism; however, functional gene content and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically disinfected barns had decreased gene content related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically disinfected conditions (FDR-P < 0.05), suggesting the selection for stress resistance. Lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecal Helicobacter pullorum was observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P < 0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial gene function and resistome.IMPORTANCEThis is the first study to evaluate the effect of sanitation practices on microbial functional gene content and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.}, }
@article {pmid41452254, year = {2026}, author = {Pan, LH and Hu, WF and Fu, ZY and Yu, XC and Li, ZQ and Guo, MF and Wu, JW and Zhu, H}, title = {Yacon (Smallanthus sonchifolius) Root Increases Bowel Movement Frequency in Healthy Adults via Modulating Gut Microbiota and Intestinal Metabolites: A Pilot Study.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {1}, pages = {e70358}, doi = {10.1002/mnfr.70358}, pmid = {41452254}, issn = {1613-4133}, support = {TZKY2024RC01//Scientific Research Starting Foundation for High-level Talents of Taizhou School of Clinical Medicine, Nanjing Medical University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Adult ; *Plant Roots/chemistry ; Male ; Female ; Middle Aged ; Young Adult ; *Intestines/microbiology/drug effects ; *Plant Extracts/pharmacology ; *Defecation/drug effects ; }, abstract = {Yacon root (YR) is a functional food that can increase bowel movement frequency, but with an unclear mechanism. In this study, a UPLC-Orbitrap-MS/MS system was employed to characterize the chemical composition of YR. Subsequently, a 10-day pilot intervention trial involving 11 healthy adults was conducted to evaluate the effects of YR on bowel movement frequency. Concurrently, the involved mechanisms were explored through metagenomic and metabolomic approaches. A total of 82 chemical components were identified in YR. Clinical trials indicated that continuous intake of YR significantly increased bowel movement frequency without noticeable adverse effects. Metagenomic analysis revealed that YR substantially increased the abundance of beneficial bacteria such as Bifidobacterium and inhibited the generation of potential pathogens, including Escherichia-Shigella, thereby promoting a more balanced and healthier gut microbiota structure. Metabolomic analysis indicated that YR significantly upregulated metabolites, including cholic acid, taurine, and amino acids, which mainly focus on the biosynthesis of primary bile acid and the metabolism of taurine and hypotaurine. In summary, YR can safely and effectively increase bowel movement frequency in healthy individuals. The mechanism may involve synergistic regulation of gut microbiota and metabolites, which offered new insights to support YR as a natural functional food for laxative effects.}, }
@article {pmid41453848, year = {2026}, author = {Li, XL and Li, ZQ}, title = {Gut microbiota of economically important termites: functional convergence, harmfulness and precision control.}, journal = {Pest management science}, volume = {82}, number = {4}, pages = {2808-2824}, doi = {10.1002/ps.70490}, pmid = {41453848}, issn = {1526-4998}, support = {//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Isoptera/microbiology ; *Gastrointestinal Microbiome ; *Insect Control/methods ; }, abstract = {As typical social insects and key decomposers in ecosystems, termites, like other insects, harbor a complex array of microbial communities with diverse functions in their gut. These microorganisms are not only closely related to key survival aspects of termites, including nutritional acquisition, metabolic adaptation and colony resilience, but also play crucial roles in their ecological adaptability. This demonstrates that termite survival strategies are highly dependent on the synergistic interactions within their gut microbiota. Notably, some termites, such as Coptotermes formosanus, exhibit both decomposition ability and damaging capacity. Whether their gut microbiota is closely related to their destructive potential has become one of the core issues of concern to researchers. Moreover, with the rapid development of metagenomics and bioinformatics technologies in recent years, an increasing number of termite gut microbiota functions have been predicted and validated, making it possible to analyze their destructive capacity from a microbial perspective. Therefore, based on a systematic synthesis of the functional commonalities and mechanistic roles of gut microbiota in economically significant termite species, this review further highlights evidence linking microbial functions with termite damaging capacity and discusses microbiota-based strategies for precision control of pest termites. It aims to provide comprehensive references and a solid theoretical foundation for in-depth research and rational utilization of termite gut microbiota, as well as scientifically grounded and targeted management of destructive termite pests. © 2025 Society of Chemical Industry.}, }
@article {pmid41453903, year = {2025}, author = {Lin, Z and Li, S and Liu, M and Li, J and Liu, F and Cao, J and Chen, S and Huang, K and Wang, Y and Li, H and Wang, Y and Yang, B and Xing, D and Wang, Q and Ji, X and Bai, X and Hu, D and Zhang, M and Guo, D and Huang, J and Geng, B and Gu, D and Lu, X}, title = {Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {808}, pmid = {41453903}, issn = {2041-1723}, support = {91857118//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 12126602//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Female ; Humans ; Male ; Middle Aged ; Rats ; *Blood Pressure/drug effects/physiology ; *Carnitine/analogs &amp; derivatives/metabolism/blood ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology/drug effects ; *Hypertension/metabolism/microbiology ; Metabolome ; *Sodium Chloride, Dietary/adverse effects ; }, abstract = {This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt, and high-salt interventions. SSBP was assessed and used as the primary outcome, and fecal shotgun metagenome and plasma targeted metabolome were measured. We found that high salt significantly altered 85 gut-microbial species (p < 9.42 × 10[-5]) and 70 metabolites (p < 2.26 × 10[-4]). Among them, the changes in 22 species and 8 metabolites were associated with SSBP (p < 0.05), and a gut microbiota-acylcarnitine network implicated in SSBP was identified, with a gut microbiota-derived metabolite, isovalerylcarnitine, as the core metabolite. Isovalerylcarnitine was also inversely associated with SSBP in the GenSalt study (p = 0.0102). Importantly, increased isovalerylcarnitine attenuated SS hypertension and improved endothelial function in rats, and was associated with reduced risk (ranging from 13% to 19%) of BP progression and incident hypertension in a prospective cohort (n = 3907, median follow-up = 5.5 years). This study demonstrated that the gut-acylcarnitine axis may play roles in the development of SS hypertension. Trial number: ChiCTR1900025171.}, }
@article {pmid41454222, year = {2025}, author = {Li, J and Sun, Z and Chai, S and Li, H and Wang, Y and Tian, J}, title = {AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {23}, pmid = {41454222}, issn = {1471-2105}, support = {No.GZY-ZJ-SY-2303//Zhejiang Province Traditional Chinese Medicine Key Laboratory Project/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Deep Learning ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {Advances in metagenomic sequencing have increasingly implicated gut microbiome dysbiosis in numerous complex diseases, yet its application for precise differential diagnosis remains a major challenge. Existing computational approaches often show limited predictive performance and insufficient robustness when applied to large-scale, imbalanced microbiome datasets, and they typically lack mechanisms to effectively capture microbial community-level or functional guild interactions. To address these limitations, we developed AR-CDT Net, a novel deep learning framework that integrates a Multi-Scale Deformable Convolution (MS-DConv) module with a Channel-wise Dynamic Tanh (CD-Tanh) activation function to achieve more accurate and robust classification of host disease states. Evaluated on a large-scale cohort comprising over 8000 samples spanning eight disease phenotypes, AR-CDT Net demonstrated highly competitive within-cohort performance, outperforming nine representative models across the majority of classification tasks. Importantly, in a stringent cross-dataset generalization test, the model was trained on the highly imbalanced primary multi-disease cohort and validated on relatively balanced independent external cohorts. It achieved a statistically significant AUC of 0.7921 on the highly heterogeneous external T2D cohort, confirming that AR-CDT captures transferable biological signals rather than dataset-specific artifacts. Furthermore, by combining dimensionality reduction with SHAP-based interpretation of our One-vs-Rest (OvR) classifiers, AR-CDT disentangles disease-specific pathogenic signatures from the shared dysbiotic background among clinically distinct yet microbially similar diseases.}, }
@article {pmid41455002, year = {2025}, author = {Karim, F and Lin, Q and Xie, H and Nargis, S and Xiao, H and Yang, S and Xiong, Y and Xie, M and Ni, Q and Yao, Y and Xu, H}, title = {Seasonal dynamics of gut microbiota in rhesus macaques (Macaca mulatta) from western Sichuan Plateau and their adaptability to high altitude climate change.}, journal = {Current microbiology}, volume = {83}, number = {2}, pages = {99}, pmid = {41455002}, issn = {1432-0991}, support = {31870355//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; Seasons ; Altitude ; Feces/microbiology ; *Climate Change ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; }, abstract = {Seasonal fluctuations in diet and climate shape animal gut microbiota, especially those living in extreme climatic conditions. Yet their role in facilitating primate adaptation to high-altitude remains unclear. This study investigates the seasonal dynamics in gut microbiome of wild rhesus macaques (Macaca mulatta) from high altitude (over 3,000 m) in Yajiang couke. We collected 117 fecal samples across four seasons and analyzed using 16S rRNA high-throughput sequencing combined with predictive functional metagenomics. We observed clear seasonal shifts in gut microbial diversity and composition. High α-diversity in autumn and winter reflected increased dietary diversity during these periods. Firmicutes predominated in summer, while Bacteroidota increased during winter. LEfSe analysis revealed seasonal specific taxa: UCG-005, Christensenellaceae R-7, and Prevotella_9 were dominated in winter but declined in summer and spring, whereas Blautia peaked during summer and decreased toward winter. Redundancy analysis showed that temperature, humidity, and precipitation were positively associated with Blautia and Sarcina, but negatively with Monoglobus and Helicobacter, underscoring the strong influence of climatic variables on gut community structure. Functional predictions revealed seasonal differences in gut microbiota related to energy metabolism (spring), glycan biosynthesis (summer), membrane transport (autumn), and environmental adaptation (winter) indicating microbial contributions to host adaptation under fluctuating climatic conditions. These findings demonstrate that gut microbiome of high-altitude macaques is highly responsive to changes in seasonal diet and climate. By integrating microbiome dynamics with climatic drivers, our study provides new insights into host-microbe-environment interactions and advances our understanding of primate adaptation under extreme climatic conditions.}, }
@article {pmid41455311, year = {2026}, author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS}, title = {Harnessing methane proxies to understand and mitigate enteric emissions from ruminant production systems.}, journal = {The Science of the total environment}, volume = {1012}, number = {}, pages = {181258}, doi = {10.1016/j.scitotenv.2025.181258}, pmid = {41455311}, issn = {1879-1026}, mesh = {*Methane/analysis/metabolism ; Animals ; *Ruminants/metabolism ; *Environmental Monitoring/methods ; *Animal Husbandry ; Rumen/microbiology ; Gastrointestinal Microbiome ; *Air Pollutants/analysis ; }, abstract = {Methane emissions from livestock, particularly ruminants, significantly contribute to global warming, necessitating the development of accurate methane monitoring systems. Direct methane measurement is technically complex, time-consuming, labour-intensive, and costly. Recent advances in methane inhibitors, such as 3-nitrooxy propanol and halogenated analogues, plant secondary compounds, including polyphenols and essential oils, to reduce methane emissions have necessitated the discovery of processes underlying rumen methane synthesis and inhibition. The identification of methane proxies, such as behavioural and input proxies (dry matter intake, neutral detergent fibre), microbial community proxies (rumen metagenome profiles), metabolic pathway proxies (fatty acids), molecular and genetic proxies (microbial genes), and downstream and non-invasive proxies (milk fatty acids and faecal lipidomes), is leading to more viable solutions. New developments in 'omic' techniques, including lipidomics, metagenomics and metatranscriptomics, have enabled the detection of proxies at the molecular level utilising rumen liquor, milk, blood, urine, and faeces. In addition to traditional methane proxies, rumen microbiota profiles, and specific genes involved in rumen methanogenesis (such as mcr and mrt, which encode methyl coenzyme reductase 1 and 2), these markers can be used to identify methane-producing pathways. Protozoa-associated methanogens (PAMs), propionate-producing bacteria, and methane-oxidising methanotrophs (Methylocystis sp.) are emerging as new proxies. Methane proxies provide scalable, affordable, and mechanistically insightful alternatives to conventional direct measuring techniques, which improve the understanding of rumen function and the biological causes of methane releases, enabling large-scale methane monitoring and will enable designing effective methane mitigation strategies in livestock production systems.}, }
@article {pmid41455545, year = {2026}, author = {Zhang, JS and Zhang, Y and Huang, S and Chu, CH and Jakubovics, NS and Yu, OY}, title = {High-resolution microbial changes in root caries revealed by Type IIB Restriction-site associated DNA for microbiome.}, journal = {Journal of dentistry}, volume = {165}, number = {}, pages = {106319}, doi = {10.1016/j.jdent.2025.106319}, pmid = {41455545}, issn = {1879-176X}, mesh = {Humans ; *Root Caries/microbiology ; *Microbiota/genetics ; Male ; Female ; Aged ; Biofilms ; Dental Plaque/microbiology ; Middle Aged ; *DNA, Bacterial/genetics/analysis ; *Tooth Root/microbiology ; Case-Control Studies ; }, abstract = {OBJECTIVES: This study aimed to characterize the species-level microbial and functional alterations in the dental biofilms associated with root caries leveraging the high-resolution sequencing.<br><br>METHODS: Twenty-five older adults with active root caries (Patients) and 31 older adults without untreated caries (Healthy controls) were enrolled. Site-specific supragingival plaque was collected from spatially-matched carious (CC) and caries-free (CH) root surfaces from patients, and from caries-free root surfaces of healthy controls (HH). Plaque samples were analysed using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M). Microbial diversity, species-level relative abundance, and predicted functional pathways were compared across groups using nonparametric tests.<br><br>RESULTS: No significant differences in overall microbial diversity were observed between groups. The microbial divergence between paired carious (CC) and caries-free (CH) root microbiota from patients was significantly greater than that between paired caries-free (HH) root microbiota in healthy controls. Several species showed increased abundance in CC microbiota compared to CH microbiota, with Propionibacterium acidifaciens, Prevotella multisaccharivorax, Mitsuokella sp000469545, and Parascardovia denticolens exhibiting the highest level of abundance difference. Predicted metagenomic analysis indicated that nine KEGG pathways, primarily involved in alternative carbohydrate metabolism, were positively associated with root caries status.<br><br>CONCLUSION: Within-subject comparison revealed a significant difference in microbiota between carious and caries-free root surfaces. These differences were characterized by shifts in specific species and their associated metabolic potentials, rather than by broad changes in community diversity.<br><br>CLINICAL SIGNIFICANCE: This study underscores the importance of tooth-level resolution in investigating the microbial etiology of root caries and revealed the species-level changes in carious root microbiota.}, }
@article {pmid41455576, year = {2026}, author = {Kitagawa, H and Kajihara, T and Yahara, K and Kitamura, N and Shigemoto, N and Doi, H and Shimbara, K and Yoshimura, K and Nakashima, I and Uegami, S and Watadani, Y and Kawada-Matsuo, M and Komatsuzawa, H and Ohge, H and Sugai, M}, title = {Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study.}, journal = {Journal of global antimicrobial resistance}, volume = {46}, number = {}, pages = {227-234}, doi = {10.1016/j.jgar.2025.12.014}, pmid = {41455576}, issn = {2213-7173}, mesh = {Humans ; Prospective Studies ; Male ; Female ; *Colorectal Neoplasms/surgery/microbiology ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Feces/microbiology ; Aged ; *Antibiotic Prophylaxis ; *Anti-Bacterial Agents/therapeutic use ; *Mouth/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/drug effects ; Metagenomics ; Drug Resistance, Bacterial ; }, abstract = {BACKGROUND: The use of antibiotics may facilitate the colonisation of antimicrobial-resistant organisms and genes within the host microbiome. However, studies on the effects of antibiotics on microbiomes and resistomes in clinical settings are limited.<br><br>AIM: The aim of this study was to determine the effects of antibiotic prophylaxis during colorectal cancer surgery on the oral and gut microbiomes and resistomes of patients.<br><br>METHODS: We conducted a single-centre prospective observational cohort study on patients who underwent colorectal cancer surgery with antibiotic prophylaxis. DNA was extracted from oral and stool samples 1 day prior to the procedure and on postoperative days 1, 7, and 28. Subsequently, metagenomic sequencing was performed.<br><br>FINDINGS: Among the eight patients with colorectal cancer, &#x3b1;-diversity in the oral and stool samples significantly decreased from baseline to each of the three post-administration time points. The abundance of anaerobic genera significantly decreased from baseline to Day 7. In the stool samples, Enterococcus, Limosilactobacillus, and Lacticaseibacillus abundances were markedly increased. Total antibiotic resistance gene (ARG) abundance significantly increased from the baseline to Day 7 in both oral and stool samples. The impact of the increase observed on Day 7 decreased but still persisted until Day 28 for diversity and total abundance of ARGs.<br><br>CONCLUSIONS: Oral and gut microbiomes and resistomes exhibited marked alterations that gradually reversed over time. Changes in the microbiome were associated with the spectrum of antibiotics used.}, }
@article {pmid41455901, year = {2025}, author = {Li, X and Zhao, Y and Wu, K and Li, X and Lv, G and Chen, Y and He, L and Sun, W}, title = {Responses of cotton roots and soil microbiota adaptation to drought hardening.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {184}, pmid = {41455901}, issn = {1471-2229}, support = {2022ZD0115801//National Science and Technology Major Project/ ; }, mesh = {*Gossypium/physiology/microbiology/growth &amp; development ; *Plant Roots/physiology/microbiology ; *Soil Microbiology ; *Droughts ; *Microbiota/physiology ; Drought Resistance ; Adaptation, Physiological ; Rhizosphere ; }, abstract = {BACKGROUND: Global climate change has intensified the frequency and severity of drought events, posing significant threats to agriculture in arid regions. As an important economic crop, cotton is highly vulnerable to drought stress, which adversely affects its growth, yield, and associated soil microbial communities. AIMS: This study aimed to conduct an in-depth investigation the effects of drought hardening on cotton root physiology and rhizosphere microbial dynamics by integrating physiological and metagenomic analyses. By analyzing aboveground responses and yield performance of cotton, this study sought to elucidate the comprehensive impact of drought hardening on cotton growth and yield, with the goal of providing a scientific basis for water-saving irrigation strategies in cotton fields in arid regions. METHODS: The experiment was conducted in 2024 at Huaxing Farm in Changji, Xinjiang, using the Zhongmian 113 variety. The experiment used the field water requirement as the control (CK, including the water for seedling emergence, totaling 4950 m[3]/ha), and set three different drought hardening treatments: mild (D1, with 20% water saving during the seedling stage), moderate (D2, with 30% water saving during the seedling stage), and severe (D3, with 40% water saving during the seedling stage). Compared with the control, the total water savings for the entire growth period of treatments D1, D2, and D3 were 12.5%, 15%, and 17.5%, respectively. RESULTS: Based on the performance of cotton growth, development, and yield, the D1 treatment significantly enhanced the antioxidant capacity of cotton roots and effectively maintained cell membrane integrity. Additionally, the D1 treatment significantly altered the diversity of soil fungi, to some extent, this water management practice optimized the structure of the microbial community, and promoted the formation of the dominant bacterial group, Gemmatimonadales. CONCLUSIONS: The study preliminarily revealed the interaction between Gemmatimonadales and cotton roots during the budding stage. Meanwhile, through a comprehensive analysis of cotton growth characteristics, root physiological and biochemical processes, and yield performance, it was shown that the stress resistance of cotton was enhanced under the D1 treatment. This research provided a scientific basis for water-saving irrigation strategies in cotton fields in arid regions, demonstrating that under the D1 condition, it is possible to enhance the stress resistance of cotton while conserving water.}, }
@article {pmid41456557, year = {2026}, author = {Li, Y and Chen, Y and Du, Z and Guo, Y and Zhang, W and Xu, X and Liu, Z and Duan, H and Duan, X and Zhang, A and Zhou, A and Li, X and Makinia, J}, title = {Oriented butyrate production through a novel bacteria-yeast microbiome: batch verification, key electron donor identification, and long-term validation.}, journal = {Bioresource technology}, volume = {443}, number = {}, pages = {133892}, doi = {10.1016/j.biortech.2025.133892}, pmid = {41456557}, issn = {1873-2976}, mesh = {*Saccharomyces cerevisiae/metabolism ; *Butyrates/metabolism ; Ethanol/metabolism ; *Microbiota ; Fermentation ; *Electrons ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; Clostridium/metabolism ; }, abstract = {Recovering butyrate from organic waste enables its high-value conversion, aligning with the principles of a circular economy. Traditional butyrate fermentation emphasizes carbohydrates and protein degradation, with limited focus on chain elongation (CE). This study, for the first time, systematically evaluated the effects of different Saccharomyces cerevisiae (SC) concentrations (1, 2, 4, 6, and 8 g/L) on ethanol production (a key electron donor) and subsequent CE for butyrate synthesis, identifying 2 g/L as the optimal SC dosage. At this concentration, butyrate production reached 15.41 ± 2.84 g COD/L, which was 2.72 times higher than that of the blank. Metabolic pathway analysis revealed that yeast not only enhanced substrate degradation (＞90 %) but also facilitated the in situ generation and utilization of ethanol. 16S rRNA indicated 54.10 % relative abundance of butyrate-producing bacteria (Clostridium). Long-term tests found that adding SC reversed the halt in production from prolonged distiller yeast inoculum, stabilising output at 15 g COD/L. Metagenomic analysis revealed that SC inoculation primarily enriched Clostridium luticellarii and Clostridium tyrobutyricum. In addition to raising reverse β-oxidation gene abundance, this treatment also enhanced lactate utilization genes, thereby strengthening acetyl-CoA to butyrate conversion. Through further experiments involving different electron donor ratios and long-term operation, this study highlights the critical role of yeast-bacteria synergy in enhancing butyrate synthesis, providing a theoretical foundation and technical strategy for food waste valorization in line with circular economy principles.}, }
@article {pmid41456824, year = {2026}, author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W}, title = {Elucidating the therapeutic mechanism of Orthosiphon aristatus in hyperuricemic nephropathy: An integrated microbiome-metabolomics approach.}, journal = {Journal of ethnopharmacology}, volume = {359}, number = {}, pages = {121115}, doi = {10.1016/j.jep.2025.121115}, pmid = {41456824}, issn = {1872-7573}, mesh = {Animals ; *Hyperuricemia/drug therapy/complications ; Male ; Rats ; *Plant Extracts/pharmacology/therapeutic use/isolation &amp; purification ; *Kidney Diseases/drug therapy/pathology ; Metabolomics ; Rats, Sprague-Dawley ; Uric Acid/blood ; *Gastrointestinal Microbiome/drug effects ; *Orthosiphon/chemistry ; Kidney/drug effects/pathology/metabolism ; Disease Models, Animal ; }, abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.<br><br>AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.<br><br>METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750&#xa0;mg/kg) and uric acid (300&#xa0;mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25&#xa0;g/kg/day), using allopurinol (5&#xa0;mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&amp;E and Masson's trichrome staining), immunohistochemistry (&#x3b1;-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.<br><br>RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p&#xa0;<&#xa0;0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p&#xa0;<&#xa0;0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p&#xa0;<&#xa0;0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p&#xa0;<&#xa0;0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.<br><br>CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.}, }
@article {pmid41457077, year = {2025}, author = {Peng, L and Chen, JW and Chen, YZ and Di, XP and Lin, LD and Li, BY and Zhang, C and Wang, W and Gao, XS and Ma, YC and Shen, SH and Li, HR and Xu, XF and Zeng, X and Shen, H and Sun, Q and Jin, T and Luo, DY}, title = {Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1299}, pmid = {41457077}, issn = {2041-1723}, support = {82422015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82270720//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400904//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82500827//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M752250//China Postdoctoral Science Foundation/ ; 2025T180613//China Postdoctoral Science Foundation/ ; }, mesh = {*Cystitis, Interstitial/microbiology/metabolism/pathology ; Animals ; *Toll-Like Receptor 3/metabolism/genetics ; *Urinary Bladder/pathology/metabolism/microbiology/injuries ; Signal Transduction ; Humans ; Mice ; *Bile Acids and Salts/metabolism ; Female ; Urothelium/metabolism/pathology ; Metabolomics/methods ; *Microbiota ; Single-Cell Analysis ; Mice, Inbred C57BL ; Male ; Multiomics ; }, abstract = {Hunner-type interstitial cystitis/bladder pain syndrome (HIC) is a debilitating condition defined by bladder pain and urinary urgency, yet its upstream drivers remain poorly understood. To identify upstream mechanisms that exacerbate urothelial injury, here we apply an integrative multi-omics framework combining metagenomic sequencing, targeted metabolomics of urine and serum, and single-cell RNA sequencing. This approach reveals a microbial signature enriched in Enterococcus avium and a marked alteration in bile acid metabolism, including increased taurochenodeoxycholic acid (TCDCA). Single-cell analysis indicates that these changes converge on Toll-like receptor 3 (TLR3) activation in urothelial cells. Further validations show that a microbiota-bile acid-TLR3 axis disrupts epithelial barrier integrity and triggers inflammatory responses in experimental models. Transplantation and metabolite administration confirm the causal role of E. avium and TCDCA, while TLR3 inhibition ameliorates injury. These findings uncover an upstream pathway linking gut-derived metabolites to bladder pathology and suggest opportunities for biomarker development and targeted therapies for HIC.}, }
@article {pmid41457176, year = {2025}, author = {Paul, D and Talukdar, D and Kapuganti, RS and Gupta, V and Narendrakumar, L and Jana, P and Kumar, P and Singh, J and Kumari, S and Basak, C and Kamboj, K and Bakshi, S and Lal, S and Tanwar, S and Kumar, R and Babele, P and Bajpai, M and Kumar, Y and Mutreja, A and Mandal, S and Wadhwa, N and Banerjee, SK and Das, B}, title = {Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1274}, pmid = {41457176}, issn = {2041-1723}, support = {RAD/22017/19/2022-KGD-DBT//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; GCI-13012/2/2025-GCl//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; }, mesh = {*Sewage/microbiology ; India ; *Anti-Bacterial Agents/pharmacology/analysis ; *Microbiota/genetics/drug effects ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Humans ; Interspersed Repetitive Sequences/genetics ; Cities ; Microbial Sensitivity Tests ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.}, }
@article {pmid41457274, year = {2025}, author = {Catry, A and Abrouk, D and Fierling, N and Mendoza, AIS and Rey, M and Vesga, P and Heiman, CM and Garrido-Sanz, D and Bouffaud, ML and Buscot, F and Giongo, A and Smalla, K and Comte, G and Keel, C and Muller, D and Moënne-Loccoz, Y}, title = {Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {16}, pmid = {41457274}, issn = {1474-760X}, support = {BiodivERsA3 ERA-Net SuppressSOIL//Biodiversa+/ ; grant SuppressSOIL no. ANR19-EBI3-0007//Agence Nationale de la Recherche/ ; grant SuppressSOIL no. 31BD30_186540//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {*Nicotiana/microbiology ; *Soil Microbiology ; Rhizosphere ; *Plant Diseases/microbiology ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; }, abstract = {BACKGROUND: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant-microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.<br><br>RESULTS: Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.<br><br>CONCLUSIONS: Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.}, }
@article {pmid41457319, year = {2026}, author = {Smith, DDN and Subasinghe, RM and Kehoe, C and Grégoire, DS}, title = {Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {1}, pages = {e0198425}, pmid = {41457319}, issn = {1098-5336}, support = {GRDI-AMR2 One Health,STAGE//Environment and Climate Change Canada/ ; 2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Microbial Consortia ; Ammonia/metabolism ; *Nitrification ; Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Multiomics ; }, abstract = {UNLABELLED: Microbial consortia show promise for bioremediation of environmental pollution, but performance optimization and risk assessment remain challenging due to unculturable species and limitations of traditional biochemical and sequencing tools. This study demonstrates how a multi-omics approach can provide deeper insight into the performance and risks of using a model aerobic ammonia-oxidizing consortium under conditions representative of wastewater treatment. Long-read DNA sequencing recovered several high-quality genomes, revealing dominance by an unclassified Nitrosospira species with expected ammonia oxidation capabilities. Lower-abundance taxa with nitrogen cycling potential were also detected, though species-level identification was limited by poor taxonomic database representation. Multi-omics and nitrogen analyses showed shifts in community composition and nitrogen cycling activity when the consortium was grown along a redox gradient typical of wastewater. All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter. The dominant Nitrosospira population declined in abundance and activity in aerobic cultures while shifting toward nitrogen reduction under anoxic conditions. This metabolic shift would not have been detected using amplicon sequencing alone. Multi-omics also supported risk assessment through detection of waterborne pathogens from the Legionella genus and other lineages harboring virulence genes resembling those from known pathogens. This study highlights the value of multi-omics for optimizing microbial consortia and assessing biosafety risks but also underscores challenges related to effective data analyses and the feasibility of risk assessment under realistic conditions. Addressing these challenges will be essential to support the broader adoption of multi-omics strategies by stakeholders working with microbial consortia across diverse environmental applications.<br><br>IMPORTANCE: Microbial consortia are increasingly used to advance a sustainable bioeconomy. Optimizing consortia for environmental applications and ensuring regulatory compliance remains challenging, largely due to reliance on culturing microbes with unknown physiology. In this study, we apply cutting-edge sequencing to a consortium designed for ammonia removal from wastewater. Long-read DNA sequencing enabled complete genome recovery and revealed that populations integral to nitrogen cycling are poorly represented in taxonomic databases. By integrating multi-omics with biochemical assays, we uncovered how environmental conditions drive off-target nitrogen reactions and the potential risks of exposure to pathogens carrying virulence genes. Our findings underscore how whole-community approaches provide insights that are not obtainable with traditional amplicon sequencing and biochemical analysis methods. However, our study also provides recommendations on how hurdles related to data integration and environmental representation must be addressed to support stakeholders adopting such approaches in the context of commercializing microbial consortia.}, }
@article {pmid41459742, year = {2026}, author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, S and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM}, title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41459742}, issn = {1751-7370}, support = {RS-2022-RD010405//Cooperative Research Program for Agriculture Science and Technology Development/ ; //Rural Development Administration/ ; //National Research Foundation/ ; NRF-2021M3A9I5021439//Ministry of Science and ICT/ ; RS-2023-00219213//Ministry of Science and ICT/ ; KRIBB//Korea Research Institute of Bioscience and Biotechnology/ ; //Initiative Program, South Korea/ ; }, mesh = {*Oryza/genetics/microbiology/metabolism ; *Rhizosphere ; *Methane/metabolism ; *Nitrogen/metabolism ; *Microbiota ; Soil Microbiology ; Alleles ; *Crops, Agricultural/genetics ; Metagenomics ; Metagenome ; Plant Roots/microbiology ; Nitrogen Fixation ; Bacteria/genetics/metabolism/classification ; }, abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line Saeilmi particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation and promoting microbial nitrogen fixation. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. Our study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.}, }
@article {pmid41460655, year = {2026}, author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE}, title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {109}, number = {4}, pages = {1542-1557}, doi = {10.1177/13872877251407700}, pmid = {41460655}, issn = {1875-8908}, mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolomics/methods ; *Artificial Intelligence ; Biomarkers/metabolism ; *Metagenomics/methods ; *Brain/metabolism ; Dysbiosis/metabolism ; }, abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.}, }
@article {pmid41461466, year = {2026}, author = {Cui, M and Chen, S and Zhang, Z and Yu, Y and Xu, Y and Liu, L and Gao, H and Chen, X and Liu, Z and Zhang, X and Yuan, W and Chen, S and Li, D and Chen, L and Xing, X and Xiao, Y and Chen, W and Liu, Y and Wang, Q}, title = {Nanoplastics and triclosan co-exposure aggravates DSS-induced colitis in mice by interfering with Akkermansia muciniphila and tryptophan metabolism.}, journal = {Journal of environmental sciences (China)}, volume = {161}, number = {}, pages = {189-200}, doi = {10.1016/j.jes.2025.06.029}, pmid = {41461466}, issn = {1001-0742}, mesh = {Animals ; Mice ; *Colitis/chemically induced ; *Tryptophan/metabolism ; *Triclosan/toxicity ; Dextran Sulfate/toxicity ; *Microplastics/toxicity ; Akkermansia ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; }, abstract = {The global incidence of inflammatory bowel disease (IBD) has been escalating. Recent studies have identified co-exposure to polystyrene nanoplastics (PSNP) and triclosan (TCS), two prevalent environmental pollutants, as emerging risk factors for IBD. However, the molecular mechanisms contributing to its deteriorative effect remain elusive. To explore the mechanisms, we conducted an integrative analysis of metagenomic and metabolomic data in a mouse model of colitis induced by dextran sulfate sodium (DSS) following co-exposure to PSNP and TCS. Results demonstrated that co-exposure to PSNP and TCS significantly exacerbated DSS-induced colitis, as evidenced by elevated disease activity indices and pro-inflammatory cytokine levels. Mechanistically, this aggravation correlated with a marked reduction in Akkermansia muciniphila abundance, which was further associated with the disruption of tryptophan metabolism. Specifically, the disruption of this metabolic pathway led to decreased production of two key tryptophan-derived metabolites: indole acetic acid (IAA) and indole acetamide (IAM). In-vitro experiments confirmed that co-exposure to PSNP and TCS inhibited the growth of A. muciniphila rather than affecting the integrity of intestinal epithelial cells. Additionally, IAA and IAM reduced inflammatory cytokine secretion in THP-1 cells. These findings suggest that the reduction in A. muciniphila abundance might decrease the production of IAA and IAM by disrupting tryptophan metabolism. This disruption ultimately contributes to the inflammatory response induced by co-exposure to PSNP and TCS. Our study offers a novel insight into microbiota-host interactions and potential therapeutic targets for intestinal disease.}, }
@article {pmid41461486, year = {2026}, author = {Kang, S and Lee, JY and Cho, KS}, title = {Bacterial and fungal metagenomes associated with atmospheric particulates in Republic of Korea: Comparison of PM2.5 and TSP larger than PM2.5.}, journal = {Journal of environmental sciences (China)}, volume = {161}, number = {}, pages = {400-410}, doi = {10.1016/j.jes.2025.08.021}, pmid = {41461486}, issn = {1001-0742}, mesh = {*Particulate Matter/analysis ; Republic of Korea ; Bacteria/genetics ; *Air Pollutants/analysis ; *Environmental Monitoring ; Particle Size ; *Fungi/genetics ; *Metagenome ; *Air Microbiology ; Microbiota ; Air Pollution/statistics &amp; numerical data ; }, abstract = {Particulate matter (PM) significantly contributes to air pollution, potentially causing health issues, with PM-associated microorganisms implicated in some cases. While studies have explored microbial concentration and structure in PM based on particle size, comprehensive analysis of microbial functional traits and environmental influences is limited. This study evaluated microbial concentrations and diversity in PM with a diameter of 2.5 µm or lower (PM2.5) and total suspended particles (TSP) greater than PM2.5 (PM>2.5) samples relative to air temperature and other factors. DNA extracted from PM2.5 and PM>2.5 filters was sequenced to characterize bacterial and fungal community structures and functional genes. Results showed that microbial concentrations and diversity were greater in PM>2.5, with similar dominant species across PM sizes. Higher air temperatures correlated with increased microbial concentrations and diversity in PM>2.5, attributed to enhanced microbial growth. An Asian dust event from the Mongolian desert disrupted the PM microbiome. Despite consistent species dominance, gene function analysis revealed abundant drug resistance pathways in bacterial communities of both particle types, while pathotroph prevalence was higher in PM2.5 fungal communities. These findings indicate that PM2.5 microbial community analysis suffices for understanding PM ecosystems, offering valuable insights for air quality management and microbial pollution control, especially concerning potential pathogens.}, }
@article {pmid41461922, year = {2026}, author = {Jin, S and Cenier, A and Wetzel, D and Arefaine, B and Moreno-Gonzalez, M and Stamouli, M and Mohamad, M and Lupatsii, M and Ríos, E and Lee, S and Zamalloa, A and Chokshi, S and Mardinoglu, A and Shoaie, S and Beraza, N and Patel, VC and Schirmer, M}, title = {Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.}, journal = {Nature microbiology}, volume = {11}, number = {1}, pages = {211-227}, pmid = {41461922}, issn = {2058-5276}, support = {426120468//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BBS/E/F/000PR13632//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/CCG1860/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 268211/1134579//Foundation for Liver Research/ ; }, mesh = {Humans ; Feces/microbiology ; *Collagenases/metabolism/genetics ; *Gastrointestinal Microbiome ; Mice ; Animals ; Saliva/microbiology ; Male ; Female ; Veillonella/genetics/enzymology/isolation &amp; purification ; Middle Aged ; Streptococcus/genetics/enzymology/isolation &amp; purification ; Metagenome ; *Bacterial Translocation ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; Adult ; Disease Models, Animal ; *Mouth/microbiology ; Aged ; Liver Cirrhosis/microbiology ; *Liver Diseases/microbiology ; }, abstract = {Microbiome perturbations are associated with advanced chronic liver disease (ACLD), but how microorganisms contribute to disease mechanisms is unclear. Here we analysed metagenomes of paired saliva and faecal samples from an ACLD cohort of 86 individuals, plus 2 control groups of 52 healthy individuals and 14 patients with sepsis. We identified highly similar oral and gut bacterial strains, including Veillonella and Streptococcus spp., which increased in absolute abundance in the gut of patients with ACLD compared with controls. These microbial translocators uniquely share a prtC gene encoding a collagenase-like proteinase, and its faecal abundance was a robust ACLD biomarker (area under precision-recall curve = 0.91). A mouse model of hepatic fibrosis inoculated with Veillonella and Streptococcus prtC-encoding patient isolates showed exacerbation of gut barrier impairment and hepatic fibrosis. Furthermore, faecal collagenase activity was increased in patients with ACLD and experimentally confirmed for the prtC gene of translocating Veillonella parvula. These findings establish mechanistic links between oral-gut translocation and ACLD pathobiology.}, }
@article {pmid41465246, year = {2025}, author = {Sokolova, EA and Smirnova, NV and Fedorets, VA and Khlistun, IV and Mishukova, OV and Tromenschleger, IN and Savenkov, OA and Saprikin, OI and Rogaev, EI and Buyanova, MD and Filippova, IM and Mayorova, TM and Glukhova, MA and Ivanovna, MM and Manakhov, AD and Voronina, EN}, title = {Microbial Consortium Application Under Temperature Stress: Effects on the Rhizosphere Microbiome and Plant Growth.}, journal = {International journal of molecular sciences}, volume = {26}, number = {24}, pages = {}, pmid = {41465246}, issn = {1422-0067}, support = {075-15-2025-473//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019-2030)/ ; }, mesh = {*Rhizosphere ; Soil Microbiology ; *Microbiota ; *Microbial Consortia ; *Stress, Physiological ; *Plant Development ; Crops, Agricultural/growth &amp; development/microbiology ; Temperature ; Bacteria/genetics ; Triticum/growth &amp; development/microbiology ; Fagopyrum/growth &amp; development/microbiology ; }, abstract = {The aim of the present study was to investigate the effect of a synthetic microbial consortium (SMC) containing five functionally different bacterial strains (Rahnella aquatilis, Rothia endophytica, Stenotrophomonas indicatrix, Burkholderia contaminans, Lelliotia amnigena) on the growth and development of three agricultural crops (wheat, buckwheat, and rapeseed) on two soil types (chernozem and gray forest soil) under field conditions. The experiment was conducted from June to September 2024 under extreme field conditions, with temperatures reaching 43.8 °C. This study evaluates SMC efficacy under severe abiotic stress, reflecting increasingly common climate extremes. Metagenomic data analysis showed that the introduced strains did not establish stable populations in the soil, possibly due to heat-induced bacterial mortality, though other factors including competition with indigenous microflora and lack of protective formulations may have also contributed. No statistically significant effects on plant morphometric parameters were observed. The extreme temperature and water stress conditions appear to have been the dominant limiting factors, overriding any potential benefits from microbial inoculation, as evidenced by the lack of response to mineral fertilizer application as well. Crop-specific effects were revealed: when cultivating rapeseed on chernozem, a significant increase in available phosphorus content was noted (from 278 ± 45 to 638 ± 92 mg/kg with SMC application, p < 0.001).}, }
@article {pmid41465567, year = {2025}, author = {Zhao, H and Wang, H and Zhao, X and Song, Y and Liang, D and Ma, Y and Xu, Z}, title = {Bifidobacterium adolescentis Strengthens Gut Barrier in Post-Voyage Functional Constipation.}, journal = {International journal of molecular sciences}, volume = {26}, number = {24}, pages = {}, pmid = {41465567}, issn = {1422-0067}, support = {2024QN019//University-level research project of the Naval Medical University/ ; }, mesh = {*Constipation/microbiology/therapy/etiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Bifidobacterium adolescentis/physiology ; *Probiotics ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Humans ; Gastrointestinal Motility ; }, abstract = {Prolonged periods of sailing may contribute to the development of functional constipation, which can significantly impair an individual's work efficiency. Currently, the efficacy of Bifidobacteria in treating functional constipation is gaining recognition. However, since the therapeutic effects of Bifidobacteria are strain-specific, further research is required on strains isolated from pre-voyage fecal samples. This study examines the role of gut microbiota in post-stroke constipation, aiming to identify specific microbial biomarkers for the development of targeted therapeutic strategies. B. adolescentis was identified through metagenomic analysis and subsequently isolated for validation. In the experimental group (EG), C57BL/6J mice received fecal suspension treatment following a 12-day navigation period, which was subsequently followed by a 12-day oral administration of B. adolescentis. After treatment, EG significantly improved fecal volume, intestinal motility, and goblet cells; reversed microbial ecological imbalance; reduced pathogens (E. coli and Klebsiella) by restoring arginine/bile acid metabolism, decreasing Tauro-ursodeoxycholic acid (TUDCA) content, 5-Hydroxytryptamine 4 Receptor (5-HT4R)/Slc8a1 signaling, and Ca[2+] signaling pathway; and restoring beneficial species (B. adolescentis, Pseudomonas aeruginosa). This study provides new insights into probiotics in improving human intestinal health.}, }
@article {pmid41466105, year = {2025}, author = {Zhang, H and Shen, C and Lei, W and Wang, J and Liu, J and Qiu, Z}, title = {Pilot Clinical Trial of Fecal Microbiota Transplantation for Constipation in Parkinson's Disease.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2509029}, pmid = {41466105}, issn = {1738-8872}, mesh = {Humans ; *Constipation/therapy/etiology/microbiology ; *Fecal Microbiota Transplantation/methods ; *Parkinson Disease/complications/therapy/microbiology ; Aged ; Pilot Projects ; Middle Aged ; Male ; Gastrointestinal Microbiome ; Female ; Prospective Studies ; Feces/microbiology ; Treatment Outcome ; Dysbiosis/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The purpose of this study was to evaluate the safety and efficacy of fecal microbiota transplantation in patients with constipation due to parkinson's disease. Gut dysbiosis has long been associated with parkinson's and recent studies have shown that FMT can restore the normal flora of the gut. Therefore, this clinical trial aimed to test the therapeutic efficacy of FMT in 5 patients aged 55 to 71 diagnosed with PD who presented with constipation. The study was conducted as an open label, prospective trial and consisted of FMT performed every 3 days via nasojejunal tube placement followed by 8 weeks of patient follow-up to evaluate response to drug therapy and to assess neurological function using UPDRS-III OFF scores, and improvement in constipation assessed with Wexner scores. Samples taken before and after FMT were collected for shotgun metagenomic sequencing to analyze the composition of the microbial communities present in patients. Untargeted non-targeted metabolomic studies were performed to investigate the impact of FMT on metabolome changes due to FMT. The results indicate an improvement in constipation and neurological functioning following FMT, and significant alteration of the gut microbiota. Significant increases in Bifidobacteria bifidus, Alistipes shahi, Anaerotruncus coli, and uncharacterized Flavonifractor were found post-treatment compared to the baseline. Many of the other strains present prior to treatment, including Acinetobacter sp. and Proteobacteria sp., had significantly decreased after the FMT. The metabolomic studies found shifts in metabolic pathways involved with unsaturated fatty acid synthesis and amino acid metabolism due to FMT. FMT may be an effective treatment option for constipation and neurological symptoms associated with PD.}, }
@article {pmid41466331, year = {2025}, author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X}, title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {259}, pmid = {41466331}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; *Bacteria/classification/genetics/isolation &amp; purification ; Farms ; }, abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.<br><br>RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.<br><br>CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.}, }
@article {pmid41467315, year = {2025}, author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y}, title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.}, journal = {Journal of leukocyte biology}, volume = {118}, number = {1}, pages = {}, doi = {10.1093/jleuko/qiaf169}, pmid = {41467315}, issn = {1938-3673}, support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; }, mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; }, abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.}, }
@article {pmid41467786, year = {2026}, author = {McParland, EL and Wittmers, F and Bolaños, LM and Carlson, CA and Curry, R and Giovannoni, SJ and Michelsen, M and Parsons, RJ and Kido Soule, MC and Swarr, GJ and Temperton, B and Vergin, K and Worden, AZ and Longnecker, K and Kujawinski, EB}, title = {Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0154025}, pmid = {41467786}, issn = {2379-5077}, support = {//Woods Hole Oceanographic Institution/ ; //Simons Foundation/ ; }, mesh = {*Seasons ; *Seawater/microbiology/chemistry ; *Microbiota ; Oceans and Seas ; *Organic Chemicals/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; }, abstract = {Hundreds of thousands of individual microbe-molecule interactions regulate the flux, transformation, and fate of carbon stored in the climatically important reservoir of marine dissolved organic matter (DOM). While marine microbial communities have been characterized at high resolution for over a decade, observations of the molecules cycled by the microbial-chemical network at similar resolution are limited. In addition, bulk characterizations of DOM can mask the complex network of interactions comprised of rich chemical diversities. Here, we present a three-year, depth-resolved, molecular time-series of DOM and prokaryoplankton at the Bermuda Atlantic Time-series Study (BATS) site. Both time-series exhibited seasonality that was compositionally distinct and primarily endemic to one sampling depth. We also putatively identified four exometabolites (gonyol, glucose-6-sulfate, succinate, and trehalose) that exhibit seasonal accumulation. We hypothesize these patterns result from environmental conditions that alter community composition on a seasonal timescale and thus shift the relative proportions of microbial functions that produce and consume the substrates. Critically, we observed the interannual composition of seasonal DOM molecules to be more stable than the taxonomy of the microbial community. This points to an important role of functional redundancy in regulating DOM composition. We tested this observation by querying metagenomes for pathways that utilize metabolic by-products putatively identified in the DOM time-series. We find that core microbial metabolisms, either those required by all or by a subset of marine microbes, are important predictors of DOM composition. The molecular-level characterization of DOM herein highlights the potential imprint of microbial activity on seasonal DOM composition.IMPORTANCEMarine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth's climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.}, }
@article {pmid41467811, year = {2026}, author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N}, title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0303325}, pmid = {41467811}, issn = {2165-0497}, support = {NRFI09-0015//National Research Foundation Singapore/ ; CIRG22jul-0023//National Medical Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bifidobacterium/isolation &amp; purification/genetics/classification ; Feces/microbiology ; *Single-Cell Analysis/methods ; Whole Genome Sequencing ; Genome, Bacterial ; Phylogeny ; }, abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.<br><br>IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.}, }
@article {pmid41468660, year = {2026}, author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M}, title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.}, journal = {International journal of food microbiology}, volume = {449}, number = {}, pages = {111600}, doi = {10.1016/j.ijfoodmicro.2025.111600}, pmid = {41468660}, issn = {1879-3460}, mesh = {Fermentation ; *Thiamethoxam/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Neonicotinoids/metabolism ; *Insecticides/metabolism ; *Vigna/microbiology/chemistry/metabolism ; Guanidines/metabolism ; Taste ; Metagenomics ; Multiomics ; Thiazoles ; }, abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.}, }
@article {pmid41468674, year = {2026}, author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S}, title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.}, journal = {Microbiological research}, volume = {305}, number = {}, pages = {128435}, doi = {10.1016/j.micres.2025.128435}, pmid = {41468674}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Angelica/microbiology/growth &amp; development/metabolism ; *Metagenomics/methods ; Soil Microbiology ; Plant Roots/microbiology/chemistry ; *Metabolome ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Microbiota ; Soil/chemistry ; Coumarins/analysis/metabolism ; Quorum Sensing ; Metabolomics ; Acyl-Butyrolactones/metabolism ; }, abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.}, }
@article {pmid41468749, year = {2026}, author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H}, title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.}, journal = {Poultry science}, volume = {105}, number = {2}, pages = {106308}, pmid = {41468749}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/physiology ; *Particulate Matter/analysis ; *Housing, Animal ; Metagenomics ; *Microbiota ; Risk Assessment ; *Air Microbiology ; Aerosols/analysis ; *Air Pollutants/analysis ; Bacteria/isolation &amp; purification/classification ; Age Factors ; Animal Husbandry ; }, abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.}, }
@article {pmid41469026, year = {2026}, author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW}, title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.}, journal = {ACS infectious diseases}, volume = {12}, number = {1}, pages = {224-236}, doi = {10.1021/acsinfecdis.5c00771}, pmid = {41469026}, issn = {2373-8227}, mesh = {Animals ; *Faecalibacterium prausnitzii/metabolism ; Mice ; *Anti-Inflammatory Agents/pharmacology/metabolism ; *Colitis/chemically induced/prevention &amp; control/drug therapy/microbiology ; Mice, Inbred C57BL ; Disease Models, Animal ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases ; Administration, Oral ; Female ; }, abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.}, }
@article {pmid41469598, year = {2025}, author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A}, title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {219}, pmid = {41469598}, issn = {1471-2334}, mesh = {Humans ; *Lung/microbiology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Tuberculosis/drug therapy/microbiology ; *Antitubercular Agents/therapeutic use ; *Microbiota/drug effects ; Metagenome ; }, abstract = {BACKGROUND: Tuberculosis (TB) remains the leading cause of bacterial disease-related mortality worldwide. While Koch’s single-agent model has long guided TB diagnostics and treatment, metagenomic studies reveal a resident lung microbiome disrupted by TB and its orally administered therapy, with downstream effects on the gut microbiome. Understanding these disruptions may uncover diagnostic and prognostic indicators. We systematically reviewed 38 studies involving 3394 individuals with TB and healthy controls across four continents to assess the impact of TB and its treatment on lung and gut microbiome diversity, structure, and composition. A meta-analysis of 29 studies and a patient-level amplicon metagenomic meta-analysis (AMMA) of 1617 individuals (1.3 billion reads) were conducted following PRISMA guidelines [PROSPERO: CRD42022329763]. RESULTS: No global consensus exists on TB's impact on lung microbial diversity. Pooled estimates suggest a reduction of ~0.14 in lung diversity and 0.41 in gut diversity. Patient-level analyses showed no overall significant difference in lung diversity (Shannon index), though reductions were evident in China but not South Africa. Conversely, gut diversity tended to be higher in TB cases. Disease status explained only 0.8–9% of variation in lung microbiota and 1.8–9% in gut communities. Composition-wise, TB was associated with depletion of anaerobic core lung genera (e.g. Prevotella, Neisseria, Veillonella, Haemophilus, Fusobacterium, Pseudomonas, Streptococcus, Porphyromonas, Treponema) and gut genera (e.g. Prevotella, Ruminococcus, Faecalibacterium, Clostridium, Roseburia, Rothia, Eubacterium, Escherichia). Treatment further reduced diversity at both sites, with additional loss of core taxa. CONCLUSION: TB is generally linked to reduced lung microbial diversity but increased gut diversity, with effects varying by country, suggesting context-specific rather than universal microbial signatures. Treatment consistently decreases diversity in both lung and gut. Although findings here primarily reflect the upper respiratory tract, they highlight potentially exploitable microbial dynamics. Future studies should integrate additional diversity metrics and broader metadata to refine these insights for advancing their clinical utility. CLINICAL TRIAL: Not applicable.}, }
@article {pmid41472294, year = {2025}, author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ}, title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.}, journal = {Viruses}, volume = {17}, number = {12}, pages = {}, pmid = {41472294}, issn = {1999-4915}, support = {0//Gyeongkuk National University/ ; }, mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; }, abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.}, }
@article {pmid41472301, year = {2025}, author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW}, title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.}, journal = {Viruses}, volume = {17}, number = {12}, pages = {}, pmid = {41472301}, issn = {1999-4915}, mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; }, abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.}, }
@article {pmid41473771, year = {2025}, author = {Mao, X and Hu, X and Fang, J}, title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1737234}, pmid = {41473771}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; }, abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.}, }
@article {pmid41474524, year = {2025}, author = {Luo, S and Li, Z and Peng, Y and Xie, X and Zeng, Y and Dai, L and Zhang, X}, title = {Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {1}, pages = {21}, pmid = {41474524}, issn = {1573-0972}, support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; 2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; }, mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/genetics ; *Crohn Disease/microbiology/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; }, abstract = {Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.}, }
@article {pmid41474788, year = {2025}, author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH}, title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0338801}, pmid = {41474788}, issn = {1932-6203}, mesh = {Child ; Child, Preschool ; Female ; Humans ; Male ; *Autism Spectrum Disorder/microbiology ; Case-Control Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Malaysia ; *Nutritional Status ; Saliva/microbiology ; Observational Studies as Topic ; }, abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.<br><br>METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.<br><br>CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.}, }
@article {pmid41476057, year = {2025}, author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC}, title = {Distinct diet-microbiome associations in autism spectrum disorder.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41476057}, issn = {2041-1723}, mesh = {*Autism Spectrum Disorder/microbiology ; Humans ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics/physiology ; *Diet/adverse effects ; Feces/microbiology ; Child, Preschool ; Adolescent ; Food Additives/adverse effects ; Metagenomics ; }, abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.}, }
@article {pmid41476181, year = {2025}, author = {Fedi, S and Ghezzi, D and Firrincieli, A and Lopo, E and Romeo, A and Sauro, F and Cappelletti, M}, title = {Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {126}, pmid = {41476181}, issn = {2045-2322}, mesh = {*Caves/microbiology ; *Bacteria/classification/genetics/metabolism ; Metagenomics ; *Microbiota ; Geologic Sediments/microbiology ; Metagenome ; Phylogeny ; Nitrogen Cycle ; *Ice Cover/microbiology ; Nitrogen/metabolism ; Carbon Cycle ; }, abstract = {Investigating the geomicrobiology of the cryosphere offers insights into past climate dynamics and the potential impacts of ongoing climate change. Here, we present the characterization of the microbial communities inhabiting ice sediments collected at various depths within the Cenote Abyss cave, located in the Italian Alps. First explored in 1994 following the drainage of an overlying lake, this site harbours one of the largest cave glaciers in the Dolomites. Metabarcoding and metagenomic analyses revealed a dominance of cold-adapted bacterial taxa, primarily Actinomycetota, Bacteroidota, and Pseudomonadota, with functional genes linked to distinct steps of the nitrogen cycle varying by cave depth. From the shallowest to the deepest ice cave zones, microbial communities shifted from nitrogen-fixing bacterial genera, including Parafrigobacterium, Polaromonas, and Pedobacter, to a higher prevalence of nitrifying bacteria such as Nitrospira. Functional metagenomic analyses revealed that genes involved in nitrogen and carbon cycling are broadly distributed across the cave depth zones, with the inner samples displaying the highest potential for nitrogen transformations, including complete denitrification pathways. CO2 fixation pathways, including the Calvin–Benson–Bassham and Wood–Ljungdahl cycles, were partially represented and taxonomically diverse across the cave depths. Culturable bacterial strains from all depths demonstrated enzymatic activities relevant to organic matter degradation, while phenotype microarray analysis highlighted the metabolic versatility of the inner microbial community in utilizing organic nitrogen substrates, supporting the higher diversity of the inner cave zone compared to the outer cave zone. These findings underscore the ecological complexity and functional potential of microbial life in subterranean ice, offering insights into biogeochemical processes in cold and nutrient-poor environments with implications for climate change studies.}, }
@article {pmid41478064, year = {2026}, author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H}, title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1270}, number = {}, pages = {124905}, doi = {10.1016/j.jchromb.2025.124905}, pmid = {41478064}, issn = {1873-376X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Depression/metabolism/drug therapy/microbiology ; Male ; *Polysaccharides/pharmacology/chemistry ; Metabolomics/methods ; Metagenomics/methods ; Rats, Sprague-Dawley ; *Bupleurum/chemistry ; *Antidepressive Agents/pharmacology/chemistry ; Brain/drug effects/metabolism ; *Stress, Psychological/metabolism ; Metabolome/drug effects ; Disease Models, Animal ; Behavior, Animal/drug effects ; }, abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.}, }
@article {pmid41478124, year = {2026}, author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G}, title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.}, journal = {Journal of hazardous materials}, volume = {501}, number = {}, pages = {140972}, doi = {10.1016/j.jhazmat.2025.140972}, pmid = {41478124}, issn = {1873-3336}, mesh = {*Rhizosphere ; Mining ; *Antimony/toxicity ; *Microbiota ; *Soil Pollutants/toxicity ; Adaptation, Physiological ; Soil Microbiology ; Plant Roots/microbiology/growth &amp; development ; }, abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.}, }
@article {pmid41478678, year = {2026}, author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L}, title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.}, journal = {Food microbiology}, volume = {136}, number = {}, pages = {105001}, doi = {10.1016/j.fm.2025.105001}, pmid = {41478678}, issn = {1095-9998}, mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation &amp; purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation &amp; purification/drug effects ; Shellfish/microbiology ; Phylogeny ; }, abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.}, }
@article {pmid41480317, year = {2025}, author = {Zakharzhevskaya, NB and Erdes, SI and Belousova, EA and Samolygo, IS and Manina, MA and Kondrashova, PV and Lomakina, EY and Kardonsky, DA and Vorobyeva, EA and Shagaleeva, OY and Silantyev, AA and Kazakova, VD and Kashatnikova, DA and Kalachnuk, TN and Kolesnikova, IV and Chaplin, AV and Markelova, MI and Grigoryeva, TV and Olekhnovich, EI and Veselovsky, VA and Morozov, MD and Zoruk, PY and Boldyreva, DI and Vanyushkina, AA and Efimov, BA}, title = {Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients.}, journal = {World journal of gastroenterology}, volume = {31}, number = {48}, pages = {112653}, pmid = {41480317}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolomics/methods ; *Colitis, Ulcerative/microbiology/diagnosis/metabolism ; *Crohn Disease/microbiology/diagnosis/metabolism ; Feces/microbiology ; Child ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Aged ; Biomarkers/metabolism/analysis ; Age Factors ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: The gut microbiota displays pronounced compositional differences between pediatric and adult populations, both under normal conditions and during the development of inflammatory bowel disease (IBD). These structural variations are accompanied by substantial changes in microbial metabolic activity.<br><br>AIM: To identify novel early diagnostic biomarkers of IBD, we performed an integrated multi-omics analysis that included assessing microbial community structure and profiling microbial metabolic activity in pediatric and adult cohorts with ulcerative colitis (UC) and Crohn's disease (CD).<br><br>METHODS: The study cohort consisted of two distinct age groups with confirmed IBD diagnoses: Adult patients (aged 45 to 70) and pediatric patients (aged 5 to 15), each diagnosed with either CD or UC. 16S rRNA gene sequencing was performed using the MinION&#x2122; Mk1B platform, with data acquisition carried out via MinKNOW software version 22.12.7 (Oxford Nanopore Technologies). Stool samples were analyzed using a Shimadzu QP2010 Ultra GC/MS system equipped with a Shimadzu HS-20 headspace extractor.<br><br>RESULTS: Comparative analysis revealed significant age-related differences in the abundance of Bacteroidota, with pediatric IBD patients showing a lower prevalence compared to adults. Microbial profiling identified Streptococcus salivarius and Escherichia coli as potential biomarkers for assessing IBD risk in children. Furthermore, metagenomic analysis uncovered five microbial signatures with diagnostic potential for CD: Ralstonia insidiosa, Stenotrophomonas maltophilia, Erysipelatoclostridium ramosum, Blautia spp., and Coprococcus comes. Using comprehensive metabolomic profiling, we developed and validated novel risk prediction algorithms for pediatric IBD. The CD risk stratification model identifies high-risk patients based on two key biomarkers: An elevated IBD risk coefficient score and reduced levels of 1H-indole-3-methyl. The UC risk prediction model incorporates three metabolic biomarkers indicative of increased disease risk: An elevated risk coefficient score, increased acetate levels, decreased pentanoic acid, and altered excretion of p-cresol (4-methylphenol).<br><br>CONCLUSION: Functional metabolomics holds transformative potential for IBD diagnostics across all age groups, with especially significant implications for pediatric patients. The distinct metabolic and metagenetic profiles observed in the pediatric cohort may represent primary alterations in IBD, providing valuable insights for exploring novel mechanisms underlying disease pathogenesis.}, }
@article {pmid41481285, year = {2026}, author = {Zhu, J and Huang, Z and Lin, Y and Zhu, J and Min, R and Wan, Z and Chen, Y and Zhu, J and Xing, L and Li, S and Olovo, CV and Wang, X and Li, G and Zhang, P}, title = {The potential immunological mechanisms of gut microbiota dysbiosis caused by antibiotics exacerbate the lethality of influenza viruses.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2609451}, pmid = {41481285}, issn = {1949-0984}, mesh = {Animals ; *Dysbiosis/immunology/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; *Influenza A virus/drug effects/pathogenicity/immunology ; Lung/immunology/virology/pathology/drug effects ; Humans ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Antibiotics are not recommended to treat influenza A virus (IAV). However, antibiotic misuse for IAV persists worldwide. How to scientifically use antibiotics for IAV-infected patients remains a considerable challenge.<br><br>RESULTS: Here, we investigated the impact of antibiotics on viral pathogenicity, pulmonary-intestinal antiviral immunity, and antiviral drug efficacy. Our findings indicated that antibiotic intervention exacerbated IAV-caused mortality and lung injury in mice, manifested as increased mortality rates, shortened survival time, aggravated pulmonary injury, and excessive inflammatory responses. Furthermore, antibiotic pretreatment significantly diminished the efficacy of antivirals. Metagenomic sequencing revealed that antibiotics reduced the diversity and abundance of beneficial gut microbiota, including Lactobacillus and Bifidobacterium, while promoting the proliferation of pathogenic bacteria such as Klebsiella pneumoniae and Escherichia coli. Mechanistically, antibiotic intervention exacerbated IAV-caused excessive inflammatory responses by the blockage of pulmonary-intestinal antiviral immune pathways, which were caused by the upregulation of PKR, RIG-I, ISG15, and TRIM25 levels while downregulating IPS-1 mRNA levels. However, it is noteworthy that the combination of antibiotics and antiviral drugs effectively offset the adverse effects of antibiotic pretreatment on influenza mortality by upregulating IPS-1 levels and partially restoring pulmonary-intestinal immune homeostasis.<br><br>CONCLUSIONS: Pulmonary-intestinal immune homeostasis imbalance caused by antibiotic misuse can not only markedly exacerbate the lethality of IAV, but also significantly attenuate the efficacy of antiviral drugs. A mechanistic study confirmed that gut microbes dysbiosis caused by antibiotic pretreatment exacerbates the homeostasis imbalance of host antiviral immunity by blocking the RIG/MDA5/IPS-1 antiviral signaling pathway. However, combination therapy with antibiotics and antivirals effectively reversed the fatal outcome exacerbated by antibiotic pretreatment. Collectively, our findings not only provide a scientific explanation from the perspective of antiviral immunity as to why antibiotics should not be arbitrarily used to treat viral infections but also lay the scientific foundation for the rational clinical use of antivirals and antibiotics for treating influenza.}, }
@article {pmid41481471, year = {2026}, author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV}, title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {1}, pages = {e2518978123}, pmid = {41481471}, issn = {1091-6490}, support = {21HLSRM06//Canadian Space Agency (CSA)/ ; IOS-1558044//NSF (NSF)/ ; P41 GM066326/GM/NIGMS NIH HHS/United States ; R24 GM141526/GM/NIGMS NIH HHS/United States ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; P41GM136463//HHS | NIH (NIH)/ ; P41 GM103399/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; }, abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.}, }
@article {pmid41482085, year = {2026}, author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J}, title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.}, journal = {Journal of ethnopharmacology}, volume = {360}, number = {}, pages = {121142}, doi = {10.1016/j.jep.2025.121142}, pmid = {41482085}, issn = {1872-7573}, mesh = {Animals ; *Respiratory Syncytial Virus Infections/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Phosphatidylinositol 3-Kinases/metabolism ; Mice, Inbred BALB C ; Apoptosis/drug effects ; Signal Transduction/drug effects ; Humans ; *Antiviral Agents/pharmacology ; Lung/drug effects/pathology/virology ; Molecular Docking Simulation ; Female ; Male ; }, abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.<br><br>AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.<br><br>MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of the key metabolite 4-hydroxyphenylacetic acid (4-HPA) was investigated in vivo and in vitro through qPCR, immunohistochemistry, ELISA, Western blot, cell viability assays and immunofluorescence.<br><br>RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota, while therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.<br><br>CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.}, }
@article {pmid41484024, year = {2026}, author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L}, title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {36}, number = {4}, pages = {104487}, doi = {10.1016/j.numecd.2025.104487}, pmid = {41484024}, issn = {1590-3729}, mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/blood/diet therapy/microbiology ; Male ; Cross-Sectional Studies ; Female ; Adult ; *Glycemic Control ; *Blood Glucose/metabolism/drug effects ; Glycated Hemoglobin/metabolism ; *Bacteria/genetics/growth &amp; development/classification ; Middle Aged ; Biomarkers/blood ; *Diet, Healthy ; Feces/microbiology ; Young Adult ; *Patient Compliance ; Treatment Outcome ; }, abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.<br><br>METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n&#xa0;=&#xa0;103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1&#xa0;% vs 7.7&#xa0;%; p&#xa0;<&#xa0;0.001), greater time in range (67.0&#xa0;% vs 59.4&#xa0;%; p-trend&#xa0;=&#xa0;0.03), and higher HDL cholesterol (1.62 vs 1.39&#xa0;mmol/L; p&#xa0;=&#xa0;0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.<br><br>CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.}, }
@article {pmid41484966, year = {2026}, author = {Fu, R and Liang, XJ and Yang, WM and Li, R and Shi, YR and Guo, L and Yu, H and Chen, YH and Wang, HN}, title = {Gut microbial signatures in schizophrenia: exploring archaea, fungi, and bacteria.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {113}, pmid = {41484966}, issn = {1471-244X}, support = {LHJJ24YF06//Interdisciplinary Integration Project of Xijing hospital/ ; 82201679//National Natural Science Foundation of China/ ; 82330043//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Schizophrenia/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; *Fungi/genetics/isolation &amp; purification ; *Dysbiosis/microbiology ; Feces/microbiology ; Middle Aged ; Case-Control Studies ; }, abstract = {BACKGROUND: Gut microbial, mainly bacterial dysbiosis, has been demonstrated in patients with schizophrenia (SCH). However, the signatures and differences of minority gut microbiota in SCH, such as archaea and fungi, have been poorly addressed.<br><br>METHODS: We obtained stool samples from 61 SCH patients and 69 healthy controls (HC), and analyzed the compositional and functional alterations of gut archaea, fungi, and bacteria using metagenomic shotgun sequencing (MSS). Additionally, we developed potential biomarkers to distinguish SCH from HC.<br><br>RESULTS: SCH patients showed significantly lower archaeal &#x3b1;-diversity compared with that of HC. Whereas there were significant differences between SCH and HC in &#x3b2;-diversity at the species level of archaea, fungi and bacteria. Meanwhile, the functional differences between the two groups were concentrated in glucose, lipid and amino acid metabolic pathways. Furthermore, we established potential diagnostic archaeal (9 species, AUC&#x2009;=&#x2009;0.73), fungal (8 species, AUC&#x2009;=&#x2009;0.69), and bacterial (22 species, AUC&#x2009;=&#x2009;0.74) microbiomes for differentiating SCH patients from HC.<br><br>CONCLUSIONS: This study describes a more comprehensive understanding of abnormal gut microbiome in SCH and might provide candidate targets for the development of a microbe-based diagnosis for SCH.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2000032118, registration date: 2020/04/20.}, }
@article {pmid41485252, year = {2026}, author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M}, title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.}, journal = {International immunopharmacology}, volume = {171}, number = {}, pages = {116155}, doi = {10.1016/j.intimp.2025.116155}, pmid = {41485252}, issn = {1878-1705}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Cellular Senescence/drug effects ; Mice, Inbred C57BL ; *Tumor Suppressor Protein p53/metabolism ; Signal Transduction/drug effects ; Mice ; Dextran Sulfate ; Male ; Disease Models, Animal ; Cell Cycle/drug effects ; Humans ; Colon/drug effects/pathology ; }, abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.}, }
@article {pmid41485293, year = {2026}, author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H}, title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {150}, number = {}, pages = {157744}, doi = {10.1016/j.phymed.2025.157744}, pmid = {41485293}, issn = {1618-095X}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Pyridoxamine/metabolism/pharmacology ; *Diabetic Nephropathies/drug therapy/metabolism ; Mice ; Male ; Transforming Growth Factor beta/metabolism ; Glycation End Products, Advanced/metabolism ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; Fecal Microbiota Transplantation ; Receptor for Advanced Glycation End Products/metabolism ; Kidney/drug effects/metabolism ; Signal Transduction/drug effects ; Vitamin B 6/metabolism ; }, abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.<br><br>PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).<br><br>METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.<br><br>RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-&#x3ba;B-AP-1 axis and TGF-&#x3b2; receptor signaling, thereby suppressing NF-&#x3ba;B-driven inflammation and Smad2-mediated fibrosis.<br><br>CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.}, }
@article {pmid41485494, year = {2026}, author = {Miyachi, H and Shibata, R and Javornik Cregeen, SJ and Surathu, A and Sijaric, M and Espinola, JA and Sullivan, AF and Mansbach, JM and Camargo, CA and Zhu, Z}, title = {Interactions between host genetics and gut microbiome influence susceptibility to childhood asthma and lung function.}, journal = {The Journal of allergy and clinical immunology}, volume = {157}, number = {4}, pages = {868-878}, pmid = {41485494}, issn = {1097-6825}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 ES036966/ES/NIEHS NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Humans ; *Asthma/genetics/microbiology/physiopathology/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Child ; Cross-Sectional Studies ; *Lung/physiopathology ; Genetic Predisposition to Disease ; Respiratory Function Tests ; }, abstract = {BACKGROUND: The gut microbiome is thought to influence risk of childhood allergic diseases; however, the data on species-level links to childhood asthma and lung function are limited, and the role of host genetics in the gut-lung axis remains unclear.<br><br>METHODS: In a multicenter cross-sectional study of children with a history of bronchiolitis from the 35th Multicenter Airway Research Collaboration, we performed shotgun metagenomic profiling of stool samples obtained at age 6 years and examined associations of the gut microbiome with asthma prevalence and lung function. We also calculated polygenic risk scores (PRSs) of asthma and lung function to investigate the interaction between host genetics and the gut microbiome in relation to these traits.<br><br>RESULTS: In the 300 children included for this study, 3 bacterial species (ie, Bacteroides vulgatus, Eisenbergiella massiliensis, and Butyricimonas virosa) were differentially associated with FEV1 value and 4 bacterial species were differentially associated with ratio of FEV1 value to forced vital capacity (FVC) (eg, Bifidobacterium longum) (false discovery rate [FDR] according to the R package MaAsLin < 0.25). Furthermore, host genetics-gut microbiome interaction analysis showed association of B vulgatus (FDR = 0.037) and Bacteroides uniformis (FDR = 0.037) with FEV1/FVC ratio among children with a high FEV1/FVC ratio PRS. Additionally, Ruminococcus bromii (FDR = 0.067) and Alistipes indistinctus (FDR = 0.13) were suggested to have protective associations with asthma, specifically in children with a high asthma PRS, indicating that host genetics can modulate the effect of the gut microbiome on these respiratory outcomes.<br><br>CONCLUSION: By applying the metagenomic approach to a multicenter cohort of children with a history of bronchiolitis during infancy, this study suggests potential interplay of host genetics with the gut microbiome, as well as their integrated relationship with childhood asthma and lung function.}, }
@article {pmid41485666, year = {2026}, author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X}, title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.}, journal = {International journal of biological macromolecules}, volume = {339}, number = {Pt 2}, pages = {150042}, doi = {10.1016/j.ijbiomac.2025.150042}, pmid = {41485666}, issn = {1879-0003}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Horses/microbiology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Glycosyltransferases/genetics/metabolism ; Substrate Specificity ; }, abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.}, }
@article {pmid41489025, year = {2026}, author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M}, title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.}, journal = {Physiologia plantarum}, volume = {178}, number = {1}, pages = {e70719}, pmid = {41489025}, issn = {1399-3054}, mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; }, abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.}, }
@article {pmid41490675, year = {2026}, author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C}, title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133923}, doi = {10.1016/j.biortech.2026.133923}, pmid = {41490675}, issn = {1873-2976}, mesh = {*Odorants/prevention &amp; control/analysis ; *Composting/methods ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Microbial Consortia ; *Bacteria/metabolism ; Hydrogen Sulfide ; Ammonia ; }, abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.}, }
@article {pmid41491581, year = {2026}, author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J}, title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {54}, pmid = {41491581}, issn = {2049-2618}, support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Propionates/metabolism ; Weaning ; Fermentation ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Stress, Physiological ; Animal Feed ; Liver/metabolism ; Metagenomics ; Gluconeogenesis ; }, abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.<br><br>RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n&#x2009;=&#x2009;24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.<br><br>CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.}, }
@article {pmid41491699, year = {2026}, author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L}, title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {13}, pmid = {41491699}, issn = {1474-760X}, support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; }, mesh = {*Vitis/microbiology/genetics ; *Disease Resistance/genetics ; *Microbiota ; *Plant Diseases/microbiology/genetics ; *Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; Fusarium/pathogenicity ; Metagenomics ; Bacteria/genetics ; }, abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.<br><br>RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.<br><br>CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.}, }
@article {pmid41491791, year = {2026}, author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO}, title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {2}, pmid = {41491791}, issn = {1471-2180}, support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; }, mesh = {*Vagina/microbiology ; Female ; *Specimen Handling/methods/standards ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; DNA Contamination ; }, abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy. RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes. CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.}, }
@article {pmid41493379, year = {2026}, author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA}, title = {A mathematical framework to correct for compositionality in microbiome data sets.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {1}, pages = {e0112625}, pmid = {41493379}, issn = {1098-5336}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; }, abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.}, }
@article {pmid41494246, year = {2026}, author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F}, title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.}, journal = {Waste management (New York, N.Y.)}, volume = {212}, number = {}, pages = {115332}, doi = {10.1016/j.wasman.2026.115332}, pmid = {41494246}, issn = {1879-2456}, mesh = {*Oligochaeta/physiology ; *Quorum Sensing ; Animals ; *Composting/methods ; *Sewage/microbiology ; Biodegradation, Environmental ; Humic Substances ; Microbiota ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; }, abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.}, }
@article {pmid41494287, year = {2026}, author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y}, title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.}, journal = {Redox biology}, volume = {89}, number = {}, pages = {104005}, pmid = {41494287}, issn = {2213-2317}, mesh = {Animals ; *Citrobacter rodentium/drug effects/pathogenicity ; Oxidation-Reduction/drug effects ; Rats ; *Antioxidants/pharmacology/administration &amp; dosage/chemistry ; *Colon/microbiology/drug effects/metabolism ; Delayed-Action Preparations/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy/metabolism ; Male ; Coumaric Acids/pharmacology/administration &amp; dosage ; }, abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.}, }
@article {pmid41494802, year = {2026}, author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C}, title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.}, journal = {Gut}, volume = {75}, number = {6}, pages = {1136-1146}, pmid = {41494802}, issn = {1468-3288}, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; Longitudinal Studies ; Middle Aged ; *Diet/adverse effects ; Inflammation/microbiology ; Diet, Mediterranean ; Case-Control Studies ; Feces/microbiology ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.<br><br>OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.<br><br>DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, &#xcd;ndice de Alimentaci&#xf3;n Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6&#x2009;months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.<br><br>RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.<br><br>CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.}, }
@article {pmid41495321, year = {2026}, author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K}, title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4066}, pmid = {41495321}, issn = {2045-2322}, support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Poecilia/genetics/physiology ; Male ; *Predatory Behavior ; Rivers ; *DNA, Environmental/analysis/genetics ; *Introduced Species ; Japan ; *Pigmentation ; Ecosystem ; DNA Barcoding, Taxonomic ; Color ; }, abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.}, }
@article {pmid41496069, year = {2026}, author = {Zhao, Y and Wang, H and Lu, Y and Lou, D}, title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.}, journal = {Medicine}, volume = {105}, number = {1}, pages = {e46594}, pmid = {41496069}, issn = {1536-5964}, support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTD&#xe3;&#x20ac;"2025&#xe3;&#x20ac;&#x2022;046//The Program for High level Innovative Talents in the Guizhou Province/ ; }, mesh = {Humans ; *Asthma/microbiology ; *Bibliometrics ; Child ; *Gastrointestinal Microbiome ; Dysbiosis ; }, abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.<br><br>METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.<br><br>RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.<br><br>CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.}, }
@article {pmid41496335, year = {2026}, author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K}, title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {194}, number = {}, pages = {118923}, doi = {10.1016/j.biopha.2025.118923}, pmid = {41496335}, issn = {1950-6007}, mesh = {Animals ; *Deoxyadenosines/pharmacology/therapeutic use ; *Cellular Senescence/drug effects ; *Hypertension, Pulmonary/drug therapy/microbiology/pathology/metabolism ; Humans ; *Gastrointestinal Microbiome/drug effects ; Myocytes, Smooth Muscle/drug effects/metabolism/pathology ; Tumor Suppressor Protein p53/metabolism ; Mice ; Male ; Rats ; Vascular Remodeling/drug effects ; Cyclin-Dependent Kinase Inhibitor p16/genetics/metabolism ; Pulmonary Artery/drug effects/pathology/metabolism ; Macrophages/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; Lung/drug effects ; }, abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.<br><br>OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.<br><br>METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).<br><br>RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.<br><br>CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.}, }
@article {pmid41496502, year = {2026}, author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO}, title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611543}, pmid = {41496502}, issn = {1949-0984}, mesh = {Humans ; Animals ; Immunoglobulin A/metabolism ; *Campylobacter jejuni/physiology ; *Serine Endopeptidases/metabolism/genetics ; Phylogeny ; *Campylobacter Infections/microbiology/immunology ; Epithelial Cells/microbiology ; Mice ; Neutrophils/immunology/microbiology ; Phagocytosis ; *Gammaproteobacteria/enzymology/genetics/classification ; Bacterial Proteins/genetics/metabolism ; *Gastrointestinal Microbiome ; Fiji ; }, abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.}, }
@article {pmid41498995, year = {2026}, author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A}, title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {1}, pages = {32}, pmid = {41498995}, issn = {1573-0972}, support = {42430404//National Natural Science Foundation of China/ ; }, mesh = {*Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Ice Cover/microbiology ; Altitude ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Metagenomics ; Phylogeny ; Ecosystem ; Nitrogen/metabolism ; Shotgun Sequencing ; }, abstract = {High-altitude rivers constitute ideal model systems for studying microbial roles in elemental cycling within complex ecosystems. Previous studies primarily addressed microbial community assembly, specific taxonomic groups, or antibiotic resistance gene risks, resulting in limited understanding of biogeochemical cycling profiles. Here, shotgun metagenomic sequencing was employed to profile the metabolic potential of planktonic and benthic microbiomes in the glacial-fed Rongbu River. We sequenced nine water and nine sediment samples along an altitudinal gradient, reconstructing 279 medium-to-high-quality metagenome-assembled genomes (MAGs), with 246 representing unclassified MAGs. Functional analyses revealed divergent niche specialization between habitats: (i) water MAGs encoded multifunctional carbohydrate-active enzymes (CAZymes), targeting labile polysaccharides while coupling nitrogen-sulfur metabolism to enhance nitrogen assimilation; and (ii) sediment MAGs specialized in complex polysaccharide degradation, exhibiting enriched denitrification and sulfide oxidation genes. Notably, a total of 13 plastic degradation genes (PDGs) were identified, which indicated altitudinal partitioning: high-elevation communities showed PBAT-degrading potential, while low-elevation MAGs harbored PVA-degrading genes. These findings indicated that altitude governed the spatial distribution of distinct biogeochemical potentials in high-altitude rivers. This study advances our understanding of elemental cycling processes in alpine river ecosystems.}, }
@article {pmid41499358, year = {2026}, author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H}, title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.}, journal = {Clinical and translational medicine}, volume = {16}, number = {1}, pages = {e70579}, pmid = {41499358}, issn = {2001-1326}, support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science &amp; Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.<br><br>METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.<br><br>RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs&#xa0;>&#xa0;.85.<br><br>CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.<br><br>TRIAL REGISTRATION: NCT05244837.<br><br>KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.}, }
@article {pmid41499519, year = {2026}, author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E}, title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0323038}, pmid = {41499519}, issn = {1932-6203}, mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Food Microbiology ; Candida/genetics/isolation &amp; purification ; }, abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.}, }
@article {pmid41499817, year = {2026}, author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z}, title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119669}, doi = {10.1016/j.ecoenv.2025.119669}, pmid = {41499817}, issn = {1090-2414}, mesh = {Animals ; *Phthalic Acids/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; Male ; Dysbiosis/chemically induced ; *Intestines/drug effects/microbiology ; *Plasticizers/toxicity ; Cytokines/metabolism ; }, abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.<br><br>METHODS: C57BL/6 mice (n&#x202f;=&#x202f;10 per group) were orally gavaged with DnPP (1-100&#x202f;mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).<br><br>RESULTS: DnPP exposure induced dose-dependent villus degeneration (100&#x202f;mg/kg/d, P&#x202f;<&#x202f;0.05) and colon shortening (P&#x202f;<&#x202f;0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-&#x3b1;) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P&#x202f;<&#x202f;0.001) and elevated antibiotic resistance genes (CARD, P&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.}, }
@article {pmid41499920, year = {2026}, author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S}, title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {57}, number = {}, pages = {106558}, doi = {10.1016/j.clnu.2025.106558}, pmid = {41499920}, issn = {1532-1983}, mesh = {Child ; Child, Preschool ; Female ; Humans ; Male ; Body Mass Index ; Body Weight ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Longitudinal Studies ; Overweight/microbiology ; *Pediatric Obesity/microbiology/epidemiology ; Risk Assessment ; Thinness/microbiology ; }, abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.<br><br>METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.<br><br>RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.<br><br>CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.<br><br>CLINICALTRIALS: gov ID NCT06317883.}, }
@article {pmid41499937, year = {2026}, author = {Wu, X and Zhang, T and Feng, J and Park, S}, title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {150}, number = {}, pages = {157758}, doi = {10.1016/j.phymed.2025.157758}, pmid = {41499937}, issn = {1618-095X}, mesh = {Humans ; *Parkinson Disease/microbiology/drug therapy/metabolism ; *Probiotics/pharmacology ; Animals ; *5-Hydroxytryptophan/metabolism ; *Methylamines/metabolism ; Rats ; *Plant Extracts/pharmacology ; Gastrointestinal Microbiome/drug effects ; PC12 Cells ; Faecalibacterium prausnitzii ; Lactiplantibacillus plantarum ; Oxidative Stress/drug effects ; Caco-2 Cells ; }, abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.<br><br>PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.<br><br>METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPK&#x3b1; signaling pathways.<br><br>RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPK&#x3b1; signaling.<br><br>CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPK&#x3b1; signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.}, }
@article {pmid41500299, year = {2026}, author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J}, title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.}, journal = {Environmental research}, volume = {292}, number = {}, pages = {123688}, doi = {10.1016/j.envres.2026.123688}, pmid = {41500299}, issn = {1096-0953}, mesh = {*Sulfamethoxazole/toxicity ; *Soil Microbiology ; *Herbicides/toxicity ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Agroecology ; Bacteria/drug effects/metabolism/genetics ; *Anti-Bacterial Agents ; }, abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.}, }
@article {pmid41501250, year = {2026}, author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X}, title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3801}, pmid = {41501250}, issn = {2045-2322}, support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Aged ; East Asian People ; }, abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.}, }
@article {pmid41501865, year = {2026}, author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H}, title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {56}, pmid = {41501865}, issn = {2049-2618}, support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; }, mesh = {Animals ; *Heteroptera/microbiology/physiology/classification ; *Gastrointestinal Microbiome ; *Predatory Behavior ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Phylogeny ; Proteobacteria/isolation &amp; purification/classification/genetics ; Adaptation, Physiological ; Biological Evolution ; Enterococcus/isolation &amp; purification/genetics/classification ; Serratia/isolation &amp; purification/genetics ; Bacillota/isolation &amp; purification/genetics/classification ; }, abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.<br><br>RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial&#xa0;symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.<br><br>CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.}, }
@article {pmid41502126, year = {2026}, author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM}, title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70226}, doi = {10.1111/1462-2920.70226}, pmid = {41502126}, issn = {1462-2920}, support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; }, mesh = {*Oxygen/analysis/metabolism ; *Seawater/microbiology/chemistry ; Metagenomics ; Pacific Ocean ; *Metagenome ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Photosynthesis ; Chlorophyll/analysis ; }, abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.}, }
@article {pmid41502197, year = {2025}, author = {Hasan, I}, title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.}, journal = {Acta medica Indonesiana}, volume = {57}, number = {4}, pages = {433-435}, pmid = {41502197}, issn = {2338-2732}, mesh = {Humans ; *Hepatic Encephalopathy/epidemiology/metabolism/etiology ; *Fatty Acids, Volatile/metabolism/analysis ; *Gastrointestinal Microbiome ; Indonesia/epidemiology ; *Liver Cirrhosis/complications ; *Brain/metabolism ; *Liver/metabolism ; }, abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.}, }
@article {pmid41503791, year = {2026}, author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q}, title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611645}, pmid = {41503791}, issn = {1949-0984}, mesh = {Female ; *Dysbiosis/virology/complications/microbiology ; Animals ; *Primary Ovarian Insufficiency/microbiology/virology/therapy/etiology ; Humans ; *Gastrointestinal Microbiome ; Rats ; *Virome ; Adult ; Fecal Microbiota Transplantation ; Feces/virology/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Ovary/physiopathology ; Young Adult ; }, abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.<br><br>RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.<br><br>CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.}, }
@article {pmid41504158, year = {2025}, author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F}, title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.}, journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition}, volume = {95}, number = {6}, pages = {42590}, doi = {10.31083/IJVNR42590}, pmid = {41504158}, issn = {0300-9831}, support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Hyperuricemia/microbiology ; *Overweight/microbiology ; Female ; Male ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Adult ; Middle Aged ; *Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).<br><br>METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.<br><br>RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced &#x3b1;-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.<br><br>CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.}, }
@article {pmid41504449, year = {2026}, author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H}, title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.}, journal = {Microbiology spectrum}, volume = {14}, number = {2}, pages = {e0305125}, pmid = {41504449}, issn = {2165-0497}, support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; Cattle/metabolism ; *Rumen/microbiology/metabolism ; Female ; *Dietary Fiber/metabolism ; *Animal Feed/analysis ; Fermentation ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Poaceae/metabolism ; Mongolia ; Metabolomics ; Digestion ; Fungi/classification/genetics/isolation &amp; purification/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.}, }
@article {pmid41505541, year = {2026}, author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C}, title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6781}, pages = {eadu2182}, doi = {10.1126/science.adu2182}, pmid = {41505541}, issn = {1095-9203}, mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; }, abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.}, }
@article {pmid41506424, year = {2026}, author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z}, title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.}, journal = {Environmental research}, volume = {292}, number = {}, pages = {123718}, doi = {10.1016/j.envres.2026.123718}, pmid = {41506424}, issn = {1096-0953}, mesh = {China ; *Geologic Sediments/microbiology ; *Wetlands ; Aquaculture ; *Microbiota ; Bacteria/classification/genetics ; *Environmental Restoration and Remediation ; Ponds/microbiology ; }, abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.}, }
@article {pmid41507585, year = {2026}, author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B}, title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {415-428}, pmid = {41507585}, issn = {2058-5276}, support = {K99 AA031328/AA/NIAAA NIH HHS/United States ; R21 AA030654/AA/NIAAA NIH HHS/United States ; R01 AA020098/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; I01 BX004594/BX/BLRD VA/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R00 AA031328/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Ethanol/metabolism ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metabolic Networks and Pathways/genetics ; Male ; Fermentation ; Female ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Middle Aged ; Metabolomics ; Adult ; }, abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.}, }
@article {pmid41507780, year = {2026}, author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L}, title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {126}, pmid = {41507780}, issn = {1471-2180}, support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; Animal Husbandry/methods ; *Drug Resistance, Bacterial ; Farms ; *Anti-Infective Agents/pharmacology ; Soil Microbiology ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.<br><br>STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.<br><br>RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.<br><br>CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.}, }
@article {pmid41507798, year = {2026}, author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J}, title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {130}, pmid = {41507798}, issn = {1471-2180}, support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; }, mesh = {Retrospective Studies ; Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; *Lung/microbiology ; Aged ; Nontuberculous Mycobacteria/genetics/isolation &amp; purification ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Middle Aged ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Bacilloscopy ; *Tuberculosis, Pulmonary/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.<br><br>OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.<br><br>METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.<br><br>RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.<br><br>CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.}, }
@article {pmid41508656, year = {2026}, author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL}, title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.}, journal = {Cancer research communications}, volume = {6}, number = {1}, pages = {70-76}, pmid = {41508656}, issn = {2767-9764}, support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; }, mesh = {Humans ; Pilot Projects ; *Feces/microbiology ; Female ; Prospective Studies ; *Gastrointestinal Microbiome/genetics ; Male ; Australia ; *Specimen Handling/methods ; Middle Aged ; Aged ; Occult Blood ; Surveys and Questionnaires ; Adult ; Metagenomics/methods ; *Neoplasms/microbiology ; Whole Genome Sequencing ; }, abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.<br><br>SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.}, }
@article {pmid41510663, year = {2026}, author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y}, title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {2}, pages = {1998-2011}, doi = {10.1021/acs.jafc.5c09250}, pmid = {41510663}, issn = {1520-5118}, mesh = {*Iron/metabolism/analysis ; *Plant Roots/microbiology/metabolism/growth &amp; development/genetics ; *Microbiota ; *Azetidinecarboxylic Acid/analogs &amp; derivatives/metabolism/pharmacology ; *Citrus/microbiology/metabolism/growth &amp; development/genetics ; Bacteria/genetics/isolation &amp; purification/classification/metabolism ; Rhizosphere ; Fertilizers/analysis ; *Proline/analogs &amp; derivatives/metabolism ; Soil Microbiology ; }, abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.}, }
@article {pmid41511078, year = {2026}, author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P}, title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41511078}, issn = {2057-5858}, support = {INV-044643/GATES/Gates Foundation/United States ; }, mesh = {Animals ; *Feces/microbiology ; *Marsupialia/microbiology ; Phylogeny ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; }, abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.}, }
@article {pmid41511111, year = {2026}, author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M}, title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0140525}, pmid = {41511111}, issn = {2379-5077}, support = {82571963//National Natural Science Foundation of China/ ; 2025A1515012162, 2024A1515010590//Natural Science Foundation of Guangdong Province/ ; JCYJ20250604145739052 and JCYJ20240813144117023//Shenzhen Science and Technology Program/ ; Y2024001//Resear Initaion Fund of Longgang District Maternity &amp; Child Healthcare Hospital of Shenzhen City/ ; Postdoctoral fellow stationed in Shenzhen second batch in 2022//Shenzhen Municipal Human Resources and Social Security Bureau/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/metabolism/etiology/virology/genetics ; Male ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; *Jaundice, Neonatal/metabolism/complications/genetics/virology ; *Machine Learning ; *Metagenome ; Bile Acids and Salts/metabolism ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Feces/microbiology ; Infant ; Multiomics ; Child, Preschool ; }, abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.<br><br>IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.}, }
@article {pmid41512665, year = {2026}, author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY}, title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106384}, pmid = {41512665}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; Cecum/microbiology ; *Poultry Diseases/microbiology/prevention &amp; control ; *Salmonella Infections, Animal/microbiology/prevention &amp; control ; *Ligilactobacillus salivarius/physiology/chemistry ; Amoxicillin/pharmacology ; *Probiotics/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Random Allocation ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.}, }
@article {pmid41512763, year = {2026}, author = {Liu, X and Li, J and Ma, C}, title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141076}, doi = {10.1016/j.jhazmat.2026.141076}, pmid = {41512763}, issn = {1873-3336}, mesh = {Animals ; Bees/drug effects/microbiology/genetics ; *Aflatoxin B1/toxicity ; Transcriptome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Gene Expression Profiling ; Microbiota/drug effects ; Apoptosis/drug effects ; Pollen ; }, abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.}, }
@article {pmid41513932, year = {2026}, author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A}, title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {4921}, pmid = {41513932}, issn = {2045-2322}, support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d&#xb4;Educaci&#xf3;, Cultura, Universitats i Ocupaci&#xf3;, cofinan&#xe7;at per la Uni&#xf3; Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d&#xb4;Educaci&#xf3;, Cultura, Universitats i Ocupaci&#xf3;/ ; }, mesh = {Humans ; *Symbiosis ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; Spain ; *Bacteria/genetics/classification ; Adult ; Child ; Feces/microbiology ; Infant ; Female ; Child, Preschool ; Male ; Phylogeny ; }, abstract = {While a proportion of the microbiota plays a beneficial role, there is no conclusive evidence that the entire microbiome is mutualistic. Here, we have studied the intestinal microbiota of three healthy age groups from the Valencian Region (Spain). We have periodically obtained stool samples to determine the 16S rRNA gene amplicons, metagenomes, and metatranscriptomes, and we have observed that the microbiota’s stability differs with age, being less stable in infants. Regarding analyses of the conserved microbiota across the three age groups throughout the study period, shared genera account for about 60%. In addition, we identified a core of microbial taxa present in all individuals, which could represent mutualistic symbionts. Finally, in a previous study, we detected that tryptophan and indole production by intestinal bacteria decreases substantially with host age. Metagenomics and metatranscriptomics analyses show that tryptophanase mRNA synthesis in the genus Akkermansia is approximately 10 times lower in adults and the elderly than in children, consistent with this enzyme’s low levels or absence in these groups. Consequently, this supports the hypothesis that an uncoupling might occur between some microbiota taxa and the human host at older ages.}, }
@article {pmid41514032, year = {2026}, author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S}, title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {39}, pmid = {41514032}, issn = {1432-184X}, support = {PAIDI-DOCTOR 21_00571//Junta de Andaluc&#xed;a/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology/classification ; Metagenome ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.}, }
@article {pmid41514203, year = {2026}, author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S}, title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41514203}, issn = {1471-2180}, mesh = {Animals ; Cattle/microbiology/growth &amp; development ; Male ; *Animal Feed/analysis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/classification/genetics/isolation &amp; purification ; *Diet/veterinary ; Metagenomics ; Feces/microbiology ; Weight Gain ; }, abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.}, }
@article {pmid41514270, year = {2026}, author = {González-Rovira, M and Sainz-Bueno, JA and García-Díaz, L and Martínez-Pancorbo, C and Sánchez, J and Gutiérrez, G and Magoutas, K and Mesías-Pérez, A and Mellado, E and Payne, M and Sousa, C and Moreno, ML}, title = {Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {273}, pmid = {41514270}, issn = {1479-5876}, support = {PID2024-157768OB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SUBN/2019/005//Federaci&#xf3;n de Asociaciones de Cel&#xed;acos de Espa&#xf1;a (FACE)/ ; US-15332/I+D+I//FEDER ANDALUCIA/ ; }, mesh = {Humans ; *Amniotic Fluid/microbiology ; Female ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/growth &amp; development/isolation &amp; purification ; *Sequence Analysis, DNA/methods ; Antimicrobial Peptides/metabolism ; Microbiota ; }, abstract = {BACKGROUND: The evidence of a low-biomass microbial community in the amniotic fluid (AF) is challenging the traditional concept of a sterile womb. To clarify microbial presence and host responses, a comprehensive, multi-methodological approach is required. METHODS: We designed an optimized culturing strategy that maximized microorganism recovery by implementing differential centrifugation and concentration of AF samples, followed by plating onto four distinct selective media types and incubation under both stringent aerobic (up to two weeks) and prolonged anaerobic (up to four weeks) conditions, including an initial pre-enrichment step in Brain Heart Infusion (BHI) broth for low-abundance organisms. These results were combined with PacBio 16S rRNA gene sequencing, Illumina shotgun metagenomics, and antimicrobial peptides (AMP) detection. Using this approach, we characterized microbial presence in 154 AF samples across gestational stages. Data normality was assessed with the Shapiro-Wilk test, guiding the selection of both parametric and non-parametric tests, and a p-value of < 0.05 was considered statistically significant. RESULTS: We detected culturable microorganisms in 33.1% of samples, with a higher proportion in elective caesarean Sect. (55.0%) compared to amniocentesis (29.5%), suggesting increased microbial load toward term. We applied stringent contamination controls, and repeatedly recovered viable microorganisms Bacillus, Cutibacterium, Micrococcus, and Staphylococcus, with Cutibacterium acnes and Staphylococcus epidermidis common. Both sequencing methods revealed a low-biomass, low-diversity microbial community with high inter-individual variability. Notably, striking microbial discordance in diamniotic twin pregnancies, challenged intrauterine homogeneity. Higher Human Beta Defensin (HBD) -1 levels correlated with absence of culturable bacteria or microbial DNA, while levels of HBD-1, HBD-3, and LL-37 were reduced in Staphylococcus-positive samples, suggesting a dynamic interplay between specific bacteria and host defences. CONCLUSIONS: Our findings indicate that viable bacteria and/or DNA can transiently access the prenatal environment microbial balance. We propose a novel perspective of a potential regulatory axis between microorganisms and AMP.}, }
@article {pmid41514433, year = {2026}, author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y}, title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {60}, pmid = {41514433}, issn = {2049-2618}, support = {2023YFD1801100//National Key R&amp;D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; Female ; *Rectum/microbiology ; Milk/metabolism/chemistry ; Lactation ; *Gastrointestinal Microbiome ; Metagenomics ; Purines/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification ; Metabolomics ; Dairying ; Longevity ; }, abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.<br><br>RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen &#x3b1;-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.<br><br>CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through &#x3b1;-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.}, }
@article {pmid41514445, year = {2026}, author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C}, title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {61}, pmid = {41514445}, issn = {2049-2618}, support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; Cattle ; Female ; *Stress, Physiological ; Oxidative Stress ; *Gastrointestinal Microbiome/physiology ; Metagenomics/methods ; Milk/metabolism ; Metabolomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Lipolysis ; Archaea/classification/genetics/isolation &amp; purification ; Methanobrevibacter/isolation &amp; purification/genetics ; *Microbiota ; Methane/metabolism ; }, abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.<br><br>RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.<br><br>CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.}, }
@article {pmid41514452, year = {2026}, author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K}, title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {24}, pmid = {41514452}, issn = {2049-2618}, support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium f&#xfc;r Forschung, Technologie &amp; Raumfahrt/ ; }, mesh = {*Wastewater/microbiology/virology ; *Bacteria/genetics/classification ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; *Eukaryota/genetics/classification ; Metagenomics ; *Viruses/genetics/classification ; Seasons ; Genetic Variation ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.<br><br>RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.<br><br>CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.}, }
@article {pmid41515159, year = {2025}, author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR}, title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.}, journal = {Nutrients}, volume = {18}, number = {1}, pages = {}, pmid = {41515159}, issn = {2072-6643}, support = {1R01CA291965/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1P30CA016672/NH/NIH HHS/United States ; na/MRA/Melanoma Research Alliance/United States ; R01 CA291965/CA/NCI NIH HHS/United States ; na//MD Anderson Melanoma Moon Shot/ ; na//Andrew Sabin Family Fellowship/ ; }, mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; *Patient Reported Outcome Measures ; Middle Aged ; Aged ; *Gastrointestinal Microbiome ; *Diet ; *Immunotherapy/adverse effects ; Quality of Life ; *Cancer Survivors ; Adult ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Anxiety ; Prospective Studies ; Depression ; Exercise ; }, abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.}, }
@article {pmid41515236, year = {2025}, author = {Zhang, Z and Wang, S and Sun, G and Pan, D}, title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {1}, pages = {}, pmid = {41515236}, issn = {2072-6643}, support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Humans ; Blood Glucose/metabolism ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Dysbiosis ; *Fasting ; *Gastrointestinal Microbiome/physiology ; Intermittent Fasting ; *Probiotics/therapeutic use/administration &amp; dosage ; }, abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.}, }
@article {pmid41516078, year = {2025}, author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD}, title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {1}, pages = {}, pmid = {41516078}, issn = {1422-0067}, support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy ; Multiomics ; Female ; Male ; Adult ; *Gastrointestinal Microbiome ; Biomarkers ; Feces/microbiology ; Middle Aged ; Treatment Outcome ; Micronutrients ; Inflammation/microbiology ; }, abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.}, }
@article {pmid41518158, year = {2026}, author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S}, title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.}, journal = {Aging cell}, volume = {25}, number = {2}, pages = {e70365}, pmid = {41518158}, issn = {1474-9726}, support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R&#x2009;+&#x2009;D&#x2009;+&#x2009;I/ ; //ERDF/ESF/ ; }, mesh = {Humans ; *Aging ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; Comorbidity ; Aged, 80 and over ; Syndrome ; }, abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.}, }
@article {pmid41518802, year = {2026}, author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG}, title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141026}, doi = {10.1016/j.jhazmat.2026.141026}, pmid = {41518802}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; Multiomics ; Bacteria/metabolism ; *Aniline Compounds/metabolism ; Triazines ; }, abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.}, }
@article {pmid41519162, year = {2026}, author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P}, title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.}, journal = {Journal of economic entomology}, volume = {119}, number = {2}, pages = {778-789}, pmid = {41519162}, issn = {1938-291X}, support = {NP104- 3020-32000-20-00D//USDA/ ; //The Boehringer Ingelheim Veterinary Scholars Program/ ; //Kansas State University College of Veterinary Medicine Office of Research/ ; //Kansas State University/ ; //USDA/ ; //Veterinary Research Scholars Programs/ ; }, mesh = {Animals ; *Microbiota ; *Animal Feed/microbiology ; *Bacteria/isolation &amp; purification/classification ; *Calliphoridae/microbiology ; Farms ; }, abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.}, }
@article {pmid41519314, year = {2026}, author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K}, title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111198}, doi = {10.1016/j.ygeno.2026.111198}, pmid = {41519314}, issn = {1089-8646}, mesh = {Animals ; *Liver/metabolism ; *Circadian Rhythm ; *Hyperlipidemias/metabolism/genetics ; Mice ; Male ; Gastrointestinal Microbiome ; Multiomics ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Transcriptome ; Lipid Metabolism ; Intestinal Mucosa/metabolism ; Circadian Clocks ; }, abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.<br><br>RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.<br><br>DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.<br><br>CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.}, }
@article {pmid41521588, year = {2026}, author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I}, title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.}, journal = {Journal of fish diseases}, volume = {49}, number = {6}, pages = {e70117}, doi = {10.1111/jfd.70117}, pmid = {41521588}, issn = {1365-2761}, support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; }, mesh = {Animals ; *Penaeidae/microbiology ; *Photobacterium/physiology ; RNA, Ribosomal, 16S/analysis ; Muscles/microbiology ; *Metagenome ; Microbiota ; Metagenomics ; }, abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.}, }
@article {pmid41522496, year = {2026}, author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S}, title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20566}, pmid = {41522496}, issn = {2167-8359}, mesh = {*Rhizosphere ; *Onions/microbiology/growth &amp; development/physiology ; *Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Azotobacter ; Bacteria/classification/genetics ; Fertilizers ; Azospirillum ; Plant Roots/microbiology/growth &amp; development ; Basidiomycota ; }, abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.}, }
@article {pmid41524715, year = {2026}, author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S}, title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {41524715}, issn = {2050-084X}, support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; }, mesh = {Humans ; *Microbial Interactions ; *Dysbiosis/microbiology ; *Microbiota ; Metagenomics ; Models, Biological ; }, abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.}, }
@article {pmid41524778, year = {2026}, author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK}, title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.}, journal = {Archives of microbiology}, volume = {208}, number = {2}, pages = {105}, pmid = {41524778}, issn = {1432-072X}, support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; }, mesh = {Animals ; *Fishes/microbiology ; Fresh Water/microbiology ; *Metagenomics/methods ; Seawater/microbiology ; *Microbiota ; Ecosystem ; Skin Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; Aquaculture ; }, abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.}, }
@article {pmid41524878, year = {2026}, author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M}, title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.}, journal = {Annals of surgical oncology}, volume = {33}, number = {4}, pages = {3203-3213}, pmid = {41524878}, issn = {1534-4681}, mesh = {Humans ; *Esophageal Neoplasms/microbiology/therapy/pathology/mortality ; *Microbiota ; Male ; *Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality ; Female ; Prognosis ; Survival Rate ; *Neoadjuvant Therapy/mortality ; *Esophagectomy/mortality ; Middle Aged ; *Mouth/microbiology ; Aged ; RNA, Ribosomal, 16S/genetics ; Follow-Up Studies ; }, abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.<br><br>PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.<br><br>RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.<br><br>CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.}, }
@article {pmid41524921, year = {2026}, author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M}, title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.}, journal = {Current microbiology}, volume = {83}, number = {2}, pages = {133}, pmid = {41524921}, issn = {1432-0991}, mesh = {Animals ; *Wolbachia/genetics/isolation &amp; purification/classification/physiology ; *Aedes/microbiology/classification ; Phylogeny ; Female ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Pakistan ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Symbiosis ; Electron Transport Complex IV/genetics ; *Metagenome ; Microbiota ; Mosquito Vectors/microbiology ; }, abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).}, }
@article {pmid41525137, year = {2026}, author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW}, title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41525137}, issn = {2057-5858}, mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; *Secondary Metabolism/genetics ; Phylogeny ; Multigene Family ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Seawater/microbiology ; Genome, Bacterial ; }, abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.}, }
@article {pmid41525322, year = {2026}, author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI}, title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013883}, pmid = {41525322}, issn = {1553-7358}, support = {S10 OD032203/OD/NIH HHS/United States ; UH3 AG064704/AG/NIA NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Shotgun Sequencing ; *Aging/genetics/physiology ; Longevity/genetics/physiology ; Feces/microbiology ; *Metagenome/genetics ; Classification/methods ; Male ; Female ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.}, }
@article {pmid41526362, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R}, title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {40}, pmid = {41526362}, issn = {2055-5008}, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Virulence Factors/genetics ; Cohort Studies ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Metagenome ; Drug Resistance, Bacterial ; }, abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.}, }
@article {pmid41527012, year = {2026}, author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P}, title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.}, journal = {Alzheimer's research &amp; therapy}, volume = {18}, number = {1}, pages = {23}, pmid = {41527012}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/microbiology ; Female ; Male ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged ; Aged, 80 and over ; Saliva/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.<br><br>METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.<br><br>RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.<br><br>CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.<br><br>TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.}, }
@article {pmid41527291, year = {2026}, author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J}, title = {Alterations of the gut virome in patients with Parkinson's disease.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {81}, number = {3}, pages = {}, doi = {10.1093/gerona/glag001}, pmid = {41527291}, issn = {1758-535X}, support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; }, mesh = {Humans ; *Parkinson Disease/virology/diagnosis ; *Gastrointestinal Microbiome ; *Virome ; Female ; Male ; Aged ; Metagenomics ; Case-Control Studies ; }, abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.}, }
@article {pmid41528122, year = {2026}, author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW}, title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41528122}, issn = {2057-5858}, mesh = {*Intensive Care Units ; Humans ; *Bacteria/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Queensland ; Drug Resistance, Bacterial/genetics ; *Environmental Monitoring/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.}, }
@article {pmid41529347, year = {2026}, author = {Singh, S and Bajaj, A and Manickam, N}, title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.}, journal = {The Science of the total environment}, volume = {1014}, number = {}, pages = {181331}, doi = {10.1016/j.scitotenv.2025.181331}, pmid = {41529347}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; *Plastics/metabolism/analysis ; India ; *Microbiota ; *Bacteria/classification/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Waste Disposal Facilities ; *Soil Pollutants/metabolism/analysis ; Metagenome ; }, abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).}, }
@article {pmid41529381, year = {2026}, author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R}, title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.}, journal = {Virology}, volume = {616}, number = {}, pages = {110789}, doi = {10.1016/j.virol.2026.110789}, pmid = {41529381}, issn = {1096-0341}, mesh = {Humans ; *Nanopore Sequencing/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; *Metagenomics/methods ; *Virus Diseases/virology ; High-Throughput Nucleotide Sequencing/methods ; Virome ; }, abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.}, }
@article {pmid41530018, year = {2026}, author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW}, title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {25}, number = {2}, pages = {232-239}, doi = {10.1016/j.jcf.2025.12.011}, pmid = {41530018}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Metagenomics/methods ; Child, Preschool ; Female ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; Microbiota ; Oropharynx/microbiology ; }, abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.<br><br>METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).<br><br>RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.<br><br>CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.}, }
@article {pmid41530166, year = {2026}, author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG}, title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1533}, pmid = {41530166}, issn = {2041-1723}, support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Food Chain ; *Cobamides/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification ; Animals ; Phylogeny ; Soil/chemistry ; Microbiota ; }, abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.}, }
@article {pmid41530170, year = {2026}, author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S}, title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {29}, pmid = {41530170}, issn = {2052-4463}, support = {Laboratoire international associ&#xe9; program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; }, abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.}, }
@article {pmid41530663, year = {2026}, author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX}, title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {40}, pmid = {41530663}, issn = {1471-2164}, support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Antelopes/microbiology/parasitology/metabolism ; *Blastocystis/physiology ; Metagenome ; *Vitamin B Complex/biosynthesis ; Humans ; }, abstract = {The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.}, }
@article {pmid41530917, year = {2026}, author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF}, title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611544}, pmid = {41530917}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; *Software ; *Big Data ; Humans ; *Metagenome ; Reproducibility of Results ; Microbiota/genetics ; Computational Biology/methods ; Colorectal Neoplasms/microbiology ; }, abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.}, }
@article {pmid41534755, year = {2026}, author = {Liu, K and Peng, W and Yang, X and Zeng, Y and Liu, Y and Yu, K and Zhu, Y and Gou, H and Li, L and Zhang, C}, title = {Efficacy and multi-omics regulatory effects of Guilou Tongluo formula in patients with chronic obstructive pulmonary disease combined with pulmonary hypertension: A prospective, multicenter, randomized controlled trial.}, journal = {Journal of ethnopharmacology}, volume = {361}, number = {}, pages = {121204}, doi = {10.1016/j.jep.2026.121204}, pmid = {41534755}, issn = {1872-7573}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/drug therapy/complications/physiopathology ; *Drugs, Chinese Herbal/therapeutic use/adverse effects ; Male ; Female ; *Hypertension, Pulmonary/drug therapy/physiopathology ; Prospective Studies ; Aged ; Middle Aged ; Treatment Outcome ; Gastrointestinal Microbiome/drug effects ; Medicine, Chinese Traditional ; }, abstract = {Pulmonary hypertension (PH) is a serious and common complication in patients with chronic obstructive pulmonary disease (COPD), and this clinical gap has been newly emphasized in the GOLD 2025 guidelines. Guilou Tongluo Formula (GLTLF) is a traditional Chinese herbal prescription widely used in clinical practice for the treatment of COPD combined with PH (COPD-PH). However, there is a lack of high-quality clinical trials to support its efficacy, and the underlying mechanisms of action remain unclear.<br><br>AIM OF THE STUDY: This study aims to evaluate the efficacy and safety of GLTLF in the treatment of COPD-PH, and to explore the potential mechanisms underlying its therapeutic effects.<br><br>MATERIALS AND METHOD: A total of 104 patients with COPD-PH were randomized to receive either conventional therapy alone (Control group) or in combination with GLTLF (GLTLF group). Clinical efficacy was assessed by changes in traditional Chinese medicine (TCM) syndrome scores, pulmonary artery systolic pressure (PASP), pulmonary function, arterial blood gases, COPD Assessment Test (CAT), modified Medical Research Council (mMRC) grade, WHO functional class (WHO-FC), 6-min walk distance (6MWD), and laboratory parameters. Potential mechanisms were explored via gut metagenomic and metabolomic analyses.<br><br>RESULTS: Clinical efficacy evaluation indicated that the TCM syndrome scores were significantly reduced in both groups post-treatment (P&#xa0;<&#xa0;0.001). PASP, FEV1, and FEV1/FVC improved significantly in the GLTLF group (P&#xa0;<&#xa0;0.05), and were superior to the control group post-treatment (P&#xa0;<&#xa0;0.05). PaO2, PaCO2, BNP, and D-dimer improved after GLTLF intervention (P&#xa0;<&#xa0;0.05). Both groups had increased 6MWD (P&#xa0;<&#xa0;0.001), with the GLTLF group performing better (P&#xa0;=&#xa0;0.006). CAT score, mMRC grade, and WHO-FC improved in both groups (P&#xa0;<&#xa0;0.05), with superior outcomes in the GLTLF group (P&#xa0;<&#xa0;0.05). Metagenomic sequencing revealed that GLTLF altered the structure and function of the gut microbiota in patients with COPD-PH. Metabolomic analysis identified a total of 87 differential metabolites following GLTLF intervention, which were significantly enriched in 18 metabolic pathways.<br><br>CONCLUSION: GLTLF can effectively treat patients with COPD-PH, enhance clinical efficacy, and modulate both metabolic status and gut microbiota composition.}, }
@article {pmid41535300, year = {2026}, author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC}, title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {36}, pmid = {41535300}, issn = {2055-5008}, support = {NCI202346//New Cornerstone Science Foundation/ ; }, mesh = {Humans ; Pilot Projects ; *Autism Spectrum Disorder/microbiology/complications/psychology ; Male ; Child ; *Synbiotics/administration &amp; dosage ; *Anxiety/therapy ; Female ; Feces/microbiology ; Metagenomics ; Gastrointestinal Microbiome ; Child, Preschool ; Pentanoic Acids ; Treatment Outcome ; }, abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.}, }
@article {pmid41535683, year = {2026}, author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q}, title = {Identification of antimicrobial peptides from ancient gut microbiomes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1788}, pmid = {41535683}, issn = {2041-1723}, support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science &amp; Technology)/ ; }, mesh = {Humans ; *Antimicrobial Peptides/pharmacology/isolation &amp; purification/chemistry ; Animals ; Feces/microbiology ; Metagenome ; *Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.}, }
@article {pmid41535719, year = {2026}, author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L}, title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.}, journal = {Cell research}, volume = {36}, number = {2}, pages = {103-120}, pmid = {41535719}, issn = {1748-7838}, support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Neoplasms/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Risk Factors ; Animals ; }, abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.}, }
@article {pmid41536169, year = {2026}, author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM}, title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.}, journal = {Molecular oral microbiology}, volume = {41}, number = {3}, pages = {117-130}, doi = {10.1111/omi.70018}, pmid = {41536169}, issn = {2041-1014}, mesh = {Humans ; Animals ; *Periodontal Diseases/microbiology ; Microbiota ; *Periodontitis/microbiology ; Eubacteriales ; }, abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.}, }
@article {pmid41536238, year = {2026}, author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C}, title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2607043}, pmid = {41536238}, issn = {1949-0984}, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; Infant, Newborn ; Feces/microbiology ; Adult ; *Gastrointestinal Microbiome ; Pregnancy ; Longitudinal Studies ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *Obesity/metabolism/microbiology ; Infant ; Mexico ; Body Mass Index ; Metagenomics ; Young Adult ; *Pregnancy in Obesity/metabolism/microbiology ; Mothers ; }, abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.}, }
@article {pmid41537582, year = {2026}, author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D}, title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.}, journal = {mSphere}, volume = {11}, number = {2}, pages = {e0084225}, pmid = {41537582}, issn = {2379-5042}, support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Solanum lycopersicum/microbiology/growth &amp; development ; *Microbiota ; Soil Microbiology ; *Acinetobacter/genetics/classification/physiology ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.}, }
@article {pmid41538522, year = {2026}, author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S}, title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {120}, number = {}, pages = {e250131}, pmid = {41538522}, issn = {1678-8060}, mesh = {Animals ; *Arboviruses/genetics/isolation &amp; purification/classification ; Colombia ; *Mosquito Vectors/virology/classification ; Metagenomics ; *Culicidae/virology/classification ; Seasons ; Caribbean Region ; *Virome/genetics ; *RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; }, abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.<br><br>OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.<br><br>METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across C&#xf3;rdoba, Sucre, Bol&#xed;var, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50&#x2122; platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.<br><br>FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.<br><br>MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.}, }
@article {pmid41539094, year = {2026}, author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z}, title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {151}, number = {}, pages = {157804}, doi = {10.1016/j.phymed.2026.157804}, pmid = {41539094}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Antihypertensive Agents/pharmacology ; Male ; Rats ; *Lipid Metabolism/drug effects ; Rats, Inbred SHR ; Blood Pressure/drug effects ; *Prehypertension/drug therapy/microbiology ; Fecal Microbiota Transplantation ; Dysbiosis ; Hypertension/drug therapy ; Disease Models, Animal ; }, abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.<br><br>PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.<br><br>METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.<br><br>RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.<br><br>CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.}, }
@article {pmid41539238, year = {2026}, author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K}, title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106371}, pmid = {41539238}, issn = {1525-3171}, mesh = {Animals ; *Bacillus subtilis/chemistry ; *Probiotics/pharmacology/administration &amp; dosage ; *Clostridium butyricum/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Thailand ; Diet/veterinary ; Metabolic Networks and Pathways/drug effects ; Animal Feed/analysis ; Male ; Cecum/microbiology ; *Metagenome ; Metagenomics ; }, abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.}, }
@article {pmid41539415, year = {2026}, author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL}, title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111204}, doi = {10.1016/j.ygeno.2026.111204}, pmid = {41539415}, issn = {1089-8646}, mesh = {*Fermentation ; *Vegetables/metabolism/microbiology ; *Fruit/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Germination ; Lactuca/growth &amp; development/microbiology ; }, abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.}, }
@article {pmid41539810, year = {2026}, author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C}, title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {226}, number = {}, pages = {118184}, doi = {10.1016/j.foodres.2025.118184}, pmid = {41539810}, issn = {1873-7145}, mesh = {*Moringa oleifera/microbiology/chemistry ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; *Plant Leaves/microbiology/chemistry ; *Taste ; Odorants/analysis ; Multiomics ; Amino Acids/analysis ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Microbiota ; *Bacteria/metabolism/classification ; *Fermented Foods/microbiology ; Food, Processed ; }, abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.}, }
@article {pmid41539854, year = {2026}, author = {Choi, S and Kwon, H and Kim, WK and Ko, G}, title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510017}, pmid = {41539854}, issn = {1738-8872}, mesh = {Animals ; *Clostridium Infections/microbiology/therapy/prevention &amp; control ; *Clostridioides difficile ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Feces/microbiology ; Bile Acids and Salts/metabolism ; }, abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.}, }
@article {pmid41540332, year = {2026}, author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L}, title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41540332}, issn = {1471-2180}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; *Drug Resistance, Microbial/genetics ; Female ; Metagenome ; China ; Sequence Analysis, DNA ; }, abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.}, }
@article {pmid41543328, year = {2026}, author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L}, title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {1}, pages = {e70375}, doi = {10.1002/mnfr.70375}, pmid = {41543328}, issn = {1613-4133}, support = {2023BCF01028//Key R &amp; D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R &amp; D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Probiotics/pharmacology ; *Lactiplantibacillus plantarum/physiology ; Liver/metabolism/drug effects ; *Liver Diseases, Alcoholic/therapy/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects/physiology ; Oxidative Stress ; Dysbiosis ; Intestinal Barrier Function ; }, abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.}, }
@article {pmid41544440, year = {2026}, author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X}, title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106373}, pmid = {41544440}, issn = {1525-3171}, mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Bacteriophages/drug effects/physiology ; Animal Feed/analysis ; *Chlortetracycline/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Virome/drug effects ; Dietary Supplements/analysis ; *Plant Extracts/administration &amp; dosage/pharmacology ; Gastrointestinal Tract/virology ; Diet/veterinary ; }, abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.}, }
@article {pmid41544986, year = {2026}, author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z}, title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111205}, doi = {10.1016/j.ygeno.2026.111205}, pmid = {41544986}, issn = {1089-8646}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology/metabolism ; Fermentation ; Female ; *Metabolome ; Metagenome ; Pregnancy ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.}, }
@article {pmid41547150, year = {2026}, author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W}, title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111622}, doi = {10.1016/j.ijfoodmicro.2026.111622}, pmid = {41547150}, issn = {1879-3460}, mesh = {Animals ; *Milk/microbiology ; Horses ; *Lactobacillales/genetics/physiology ; Metagenomics ; Fermentation ; Female ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation &amp; purification/classification ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.}, }
@article {pmid41547860, year = {2026}, author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA}, title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {25}, pmid = {41547860}, issn = {2049-2618}, mesh = {Animals ; Dogs/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA/methods ; Metagenome ; Phylogeny ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.<br><br>RESULTS: Here, we describe the recovery of 240 core species that account for&#x2009;>&#x2009;80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered&#x2009;>&#x2009;900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of&#x2009;~&#x2009;25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.<br><br>CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.}, }
@article {pmid41547908, year = {2026}, author = {Kim, YC and Won, SY and Jeong, BH}, title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {31}, pmid = {41547908}, issn = {1297-9716}, support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; }, mesh = {Animals ; *Prion Diseases/microbiology/drug therapy/prevention &amp; control ; *Catechin/analogs &amp; derivatives/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; }, abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.}, }
@article {pmid41548304, year = {2026}, author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T}, title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141134}, doi = {10.1016/j.jhazmat.2026.141134}, pmid = {41548304}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Water Microbiology ; Microbiota/genetics ; Bacteria/genetics ; }, abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.}, }
@article {pmid41548675, year = {2026}, author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A}, title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134038}, doi = {10.1016/j.biortech.2026.134038}, pmid = {41548675}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; Bacteria/metabolism ; *Microbial Consortia/physiology ; Bioreactors/microbiology ; Caproates/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.}, }
@article {pmid41549250, year = {2026}, author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J}, title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {}, pmid = {41549250}, issn = {1471-230X}, support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; }, mesh = {Animals ; Female ; *Benzimidazoles/adverse effects ; *Diarrhea/chemically induced/microbiology/blood/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Metabolome ; *Aminopyridines/adverse effects ; Rats ; *Metagenome ; Rats, Sprague-Dawley ; Intestinal Mucosa/pathology ; }, abstract = {Abemaciclib-induced diarrhea is a common side effect of HR+/ HER2 − breast cancer treatment. The aim of this study was to explore changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea. Female rats were randomly divided into abemaciclib (orally administered abemaciclib, n = 12) and control (orally administered 0.9% saline, n = 6) groups. When the rats reached grade 3 diarrhea, the jejunum, ileum, and colon tissues were collected for histological analysis to assess intestinal mucosal damage. Rat feces were obtained for metagenomic analysis to analyze changes in the gut microbial composition. Rat plasma was used for untargeted metabolomic analysis to analyze plasma metabolic alterations. Pearson’s correlation analysis was conducted to examine the association between differential gut microbiota and differential plasma metabolites, and a microbiota-metabolite-pathway network was constructed. Rats in the abemaciclib group developed noticeable diarrhea and exhibited histopathological changes in the ileal epithelium and jejunum. In the abemaciclib group, α-diversity indices (Shannon, Simpson, and Invsimpsom) were significantly lower than in the control group, with reductions of 0.5, 0.01, and 52.77, respectively. Firmicutes, Bacteroidetes, and Proteobacteria were the most abundant phyla in all groups. Compared with the control group, the abundance of Firmicutes remarkably decreased in the abemaciclib group, whereas that of Proteobacteria and Verrucomicrobia dramatically increased. Differentially abundant species in the abemaciclib group included Escherichia coli, Butyricimonas virosa, Desulfovibrionaceae bacterium, and Helicobacter ganmani. Functional analysis showed that pathways related to carbohydrate metabolism were significantly altered. Additionally, 319 metabolites were differentially expressed between the two groups, including trimethylamine N-oxide, sarsasapogenin, tyrosol, brinzolamide, and cis-3-hexenyl acetate. Multiple pathways, including mTOR signaling pathway, were significantly enriched by differential metabolites. Furthermore, close associations between differential microbiota and metabolites were observed, and numerousmicrobiota-metabolite-pathway axes were identified, such as Pseudodesulfovibrio mercurii/Desulfovibrionaceae bacterium-cis-3-hexenyl acetate-alpha-linolenic acid metabolism. Our findings revealed that abemaciclib alters the gut microbiota composition, plasma metabolite profiles, and their related metabolic pathways in SD rats, and these changes are closely associated with the occurrence of diarrhea. However, this association does not establish a causal relationship, and further in-depth mechanistic studies are required for validation.}, }
@article {pmid41552936, year = {2026}, author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y}, title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.}, journal = {Food &amp; function}, volume = {17}, number = {3}, pages = {1451-1464}, doi = {10.1039/d5fo04604a}, pmid = {41552936}, issn = {2042-650X}, mesh = {Animals ; Male ; Mice ; *Insulin Resistance ; *Dietary Advanced Glycation End Products/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Rutin/pharmacology ; *Glycation End Products, Advanced/adverse effects ; Bacteria/classification/genetics/isolation &amp; purification ; Fatty Acids, Volatile/metabolism ; }, abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.}, }
@article {pmid41554846, year = {2026}, author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A}, title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5761}, pmid = {41554846}, issn = {2045-2322}, support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; *Larva/microbiology/drug effects ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; *Ovum/microbiology/drug effects ; *Fishes/microbiology ; *Disinfection/methods ; Disinfectants/pharmacology ; Bacteria/genetics/drug effects/classification ; }, abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.}, }
@article {pmid41556662, year = {2026}, author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H}, title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0142725}, pmid = {41556662}, issn = {2379-5077}, support = {2022YFC2302700, 2023YFC2305900//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Kenya ; *Microbiota/genetics ; Virome ; Bacteria/genetics/classification/isolation &amp; purification ; *Culex/microbiology/virology/genetics ; *Aedes/microbiology/virology/genetics ; Phylogeny ; Transcriptome ; Metagenomics ; Geography ; }, abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.}, }
@article {pmid41558030, year = {2026}, author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E}, title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.}, journal = {Blood advances}, volume = {10}, number = {6}, pages = {1979-1991}, pmid = {41558030}, issn = {2473-9537}, mesh = {Humans ; *Feces/microbiology ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism ; Hematopoietic Stem Cell Transplantation/adverse effects ; Incidence ; *Gastrointestinal Diseases/etiology/microbiology/epidemiology ; *Gastrointestinal Microbiome ; }, abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.}, }
@article {pmid41558076, year = {2026}, author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S}, title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106427}, pmid = {41558076}, issn = {1525-3171}, mesh = {Animals ; *Chickens/immunology/microbiology ; *Triterpenes/administration &amp; dosage/metabolism/pharmacology ; Ursolic Acid ; *T-Lymphocytes, Regulatory/immunology/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Th17 Cells/immunology/drug effects ; *Intestines/drug effects/physiology ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; Random Allocation ; Intestinal Barrier Function ; Dose-Response Relationship, Drug ; Male ; }, abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.}, }
@article {pmid41560354, year = {2026}, author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S}, title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {17}, pages = {e17596}, pmid = {41560354}, issn = {2198-3844}, support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science &amp; Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Mice ; *Thiamine/metabolism ; *Gastrointestinal Microbiome/physiology ; *Fatty Liver/metabolism/microbiology ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Liver/metabolism ; Prebiotics/administration &amp; dosage ; Diet, High-Fat ; *Eubacteriales/metabolism ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.}, }
@article {pmid41560360, year = {2026}, author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q}, title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {18}, pages = {e18502}, pmid = {41560360}, issn = {2198-3844}, support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Animals ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism/genetics ; *Kynurenine/metabolism ; *Fibrosis/metabolism ; Mice ; *Receptors, Aryl Hydrocarbon/metabolism ; *Uracil/analogs &amp; derivatives/metabolism/pharmacology ; *Intestines/pathology/drug effects ; Gastrointestinal Microbiome ; Humans ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; }, abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.}, }
@article {pmid41561086, year = {2025}, author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX}, title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1740322}, pmid = {41561086}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Dysbiosis/therapy ; }, abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.}, }
@article {pmid41562094, year = {2025}, author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P}, title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1717935}, pmid = {41562094}, issn = {1664-3224}, mesh = {Animals ; *Phlebotomus/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics ; Female ; Insect Vectors/microbiology ; Metagenomics/methods ; *Leishmaniasis ; *Leishmania major ; }, abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.<br><br>METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.<br><br>RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).<br><br>DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.}, }
@article {pmid41562342, year = {2026}, author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J}, title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.}, journal = {Clinical and experimental rheumatology}, volume = {44}, number = {2}, pages = {186-193}, doi = {10.55563/clinexprheumatol/1b8sv1}, pmid = {41562342}, issn = {0392-856X}, mesh = {Humans ; *Myositis, Inclusion Body/microbiology/diagnosis ; Female ; Aged ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; *Bacteria/genetics/classification ; Feces/microbiology ; Case-Control Studies ; Ribotyping ; Severity of Illness Index ; Metagenomics ; }, abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.<br><br>METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.<br><br>RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (&#x2265; 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).<br><br>CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.}, }
@article {pmid41564488, year = {2026}, author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X}, title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128688}, doi = {10.1016/j.jenvman.2026.128688}, pmid = {41564488}, issn = {1095-8630}, mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Dissolved Organic Matter/analysis ; *Geologic Sediments/chemistry ; Carbon ; *Microbiota ; }, abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.}, }
@article {pmid41564978, year = {2026}, author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z}, title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.}, journal = {Microbial pathogenesis}, volume = {212}, number = {}, pages = {108285}, doi = {10.1016/j.micpath.2026.108285}, pmid = {41564978}, issn = {1096-1208}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; Toll-Like Receptor 4/metabolism ; Janus Kinase 2/metabolism ; STAT3 Transcription Factor/metabolism ; NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Acute Lung Injury/drug therapy ; Male ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice ; Lung/pathology/drug effects ; *Inflammation/drug therapy ; Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Intestinal Barrier Function ; Lipopolysaccharides ; }, abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&amp;E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.}, }
@article {pmid41565402, year = {2026}, author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G}, title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.}, journal = {Life sciences in space research}, volume = {48}, number = {}, pages = {204-215}, doi = {10.1016/j.lssr.2025.11.011}, pmid = {41565402}, issn = {2214-5532}, mesh = {Animals ; *Exosomes/transplantation/metabolism ; Humans ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Lung/pathology/metabolism ; *Umbilical Cord/cytology ; Male ; *Pulmonary Fibrosis/etiology/therapy ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Radiation Pneumonitis/therapy ; Intestinal Barrier Function ; }, abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.<br><br>METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (&#x3b1;-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1&#x3b2;) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.<br><br>RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.<br><br>CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.}, }
@article {pmid41565669, year = {2026}, author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J}, title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {45}, pmid = {41565669}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; }, mesh = {*Trichuriasis/parasitology/microbiology/epidemiology ; Humans ; Animals ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification ; Cote d'Ivoire ; Tanzania ; Trichuris ; Feces/microbiology/parasitology ; Mucins/metabolism ; }, abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.}, }
@article {pmid41565819, year = {2026}, author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N}, title = {Baby-to-baby strain transmission shapes the developing gut microbiome.}, journal = {Nature}, volume = {651}, number = {8104}, pages = {191-200}, pmid = {41565819}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Metagenomics ; }, abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.}, }
@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, Innovaci&#xf3;n y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Spain/ ; No 818368//European Commission under the European Union&#xb4;s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {Animals ; Swine/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Acinetobacter/isolation &amp; purification/genetics ; Abattoirs ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Food Storage ; Metagenome ; Food Handling ; Food, Processed ; Pseudomonas/isolation &amp; purification/genetics ; Brochothrix/isolation &amp; 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.<br><br>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.<br><br>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.}, }
@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 &amp; 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.}, }
@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.}, }
@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.<br><br>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&#xa0;weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.<br><br>MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.<br><br>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.<br><br>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.}, }
@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 &amp; 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.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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.<br><br>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&#x2013;metabolic biomarkers of MDD.<br><br>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).<br><br>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.<br><br>CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.}, }
@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.<br><br>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.<br><br>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 (&#x2191; 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (&#x2191; 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (&#x2193; 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (&#x2193; 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).<br><br>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.}, }
@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.<br><br>METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n&#x2009;=&#x2009;8) and without ICIs-TCP (n&#x2009;=&#x2009;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.<br><br>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.<br><br>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.}, }
@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 &amp; purification ; Cattle/virology ; *Virome/genetics ; Genome, Viral ; *Picornaviridae/genetics/classification/isolation &amp; 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.<br><br>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.<br><br>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.<br><br>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.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@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 &amp; purification/genetics ; Aged ; Peptostreptococcus/isolation &amp; 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.<br><br>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.<br><br>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.<br><br>CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression. &#xa0; 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.}, }
@article {pmid41579151, year = {2026}, author = {Gan, T and Zhang, N and Liu, L and Li, W and Ding, M and Chen, J and Zhou, T and Mao, A}, title = {Lactobacillus plantarum CCFM639 Alleviates Hypertension by Reshaping Gut Microbiota and Regulating Key Metabolites.}, journal = {Probiotics and antimicrobial proteins}, volume = {18}, number = {5}, pages = {6878-6892}, pmid = {41579151}, issn = {1867-1314}, support = {82400481//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Hypertension/microbiology/metabolism/drug therapy ; *Lactiplantibacillus plantarum/physiology ; *Gastrointestinal Microbiome ; *Probiotics/administration &amp; dosage ; Metabolome ; Male ; Feces/microbiology ; Female ; Middle Aged ; Bacteria/classification/isolation &amp; purification/genetics ; Blood Pressure ; Adult ; }, abstract = {A strong association between the gut microbiome and hypertension has emerged. Our previous work demonstrated that supplementation with L. plantarum CCFM639 (CCFM639) reduced blood pressure (BP) in hypertensive mice involving inhibiting the growth of S. aureofaciens Tü117 and conducted an exploratory randomized trial in adults with prehypertension or stage 1 hypertension. Here, we evaluate the effects of CCFM639 supplementation (10[9] CFU/day for 8 weeks) on the gut microbiome and serum metabolome in a subset of these participants (n = 20). Untargeted metabolomic analysis was performed on serum samples, and stool microbiome composition was assessed via metagenomic sequencing. Mono-CCFM639 supplementation altered the metabolomic profile without affecting gut microbiota diversity but reshaped microbial composition. CCFM639 supplementation modulated both the gut microbiome and serum metabolome. Circulating gut-derived metabolites are likely to account for the improvements in BP, suggesting that CCFM639 supplementation could be a key component of nutritional interventions targeting the gut microbiota for hypertension management.}, }
@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 &amp; 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 &amp; 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.}, }
@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 &amp; 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.}, }
@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 &amp; 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.}, }
@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 &amp; 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.}, }
@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).<br><br>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 &#x3b1;-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.<br><br>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).<br><br>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.}, }
@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 = {//Fundaci&#xf3;n FERO and the Fundaci&#xf3;n para la Promoci&#xf3;n 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.}, }
@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 &amp; 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.<br><br>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&#x2009;g of soy protein (totalling 30&#x2009;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).<br><br>RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56&#x2009;&#xb1;&#x2009;0.22&#x2009;cm; Control, -0.91&#x2009;&#xb1;&#x2009;0.26&#x2009;cm, p(interaction)&#x2009;<&#x2009;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&#x2009;&#xb1;&#x2009;0.21%, Control: -0.06&#x2009;&#xb1;&#x2009;0.16, p(interaction)&#x2009;<&#x2009;0.05; Agathobaculum butyriciproducens, Intervention: 0.02&#x2009;&#xb1;&#x2009;0.007%, p(time)&#x2009;<&#x2009;0.01, Control: -0.04&#x2009;&#xb1;&#x2009;0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88&#x2009;&#xb1;&#x2009;0.40%, Control: 0.62&#x2009;&#xb1;&#x2009;0.63, p(interaction)&#x2009;<&#x2009;0.05; Eubacterium_sp_CAG_38, Intervention: -0.64&#x2009;&#xb1;&#x2009;0.28%, Control: 0.10&#x2009;&#xb1;&#x2009;0.22, p(interaction)&#x2009;<&#x2009;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&#x2009;&#xb1;&#x2009;0.002; Control: 0.001&#x2009;&#xb1;&#x2009;0.001, p(interaction)&#x2009;<&#x2009;0.05). Interaction (group&#x2009;&#xd7;&#x2009;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&#x2009;&#xb1;&#x2009;0.34&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05, Control: 0.12&#x2009;&#xb1;&#x2009;0.43&#x2009;mg/g; isobutyric acid, Intervention: 0.14&#x2009;&#xb1;&#x2009;0.08&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05, Control: 0.08&#x2009;&#xb1;&#x2009;0.10&#x2009;mg/g; isovaleric acid, Intervention: 0.27&#x2009;&#xb1;&#x2009;0.14&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05; Control: 0.16&#x2009;&#xb1;&#x2009;0.20&#x2009;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.<br><br>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.}, }
@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 &amp; 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.<br><br>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.<br><br>RESULTS: Although &#x3b1;-diversity did not differ significantly among severity groups, &#x3b2;-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.<br><br>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.}, }
@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.<br><br>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.}, }
@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.}, }
@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.}, }
@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 f&#xfc;r 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//&#xd6;sterreichische Forschungsf&#xf6;rderungsgesellschaft (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.}, }
@article {pmid41588320, year = {2026}, author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X}, title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41588320}, issn = {1471-2180}, support = {32402705//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cattle/growth &amp; development/microbiology ; *Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation &amp; purification ; Fatty Acids, Volatile/analysis/metabolism ; *Gastrointestinal Microbiome ; Archaea/classification/genetics/isolation &amp; purification ; *Host Microbial Interactions ; *Viruses/classification/genetics/isolation &amp; purification ; Rumen/microbiology ; Metagenomics ; Metagenome ; }, abstract = {BACKGROUND: The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing. RESULTS: The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups. CONCLUSIONS: These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.}, }
@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.<br><br>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.<br><br>RESULTS: One hundred infants (90 hospitalized) were enrolled (mean &#xb1; SD age, 3.2 &#xb1; 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.<br><br>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.}, }
@article {pmid41591600, year = {2026}, author = {Bilecen Şen, D and Ertürkmen, P and Alp Baltakesmez, D}, title = {Microbiota and quality profiling of fermented goat meat sausages (sucuk) under nitrite-reduced and mixed-culture strategies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {2}, pages = {64}, pmid = {41591600}, issn = {1573-0972}, mesh = {Animals ; Fermentation ; *Meat Products/microbiology/analysis ; Goats ; *Nitrites/metabolism ; *Lactobacillales/isolation &amp; purification/classification/genetics/metabolism ; *Microbiota ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The bioprotective activity of lactic acid bacteria (LAB) to modulate the microbiota and quality of nitrite-reduced fermented goat meat sucuk was investigated. Antagonistic activity of LAB strains against foodborne pathogens was evaluated using agar well diffusion, spot-on lawn, and cross-streak assays. Three LAB isolates affiliated with the genera Weissella, Limosilactobacillus, and Lactiplantibacillus, exhibiting inhibition zones > 18 mm, were selected and applied as a mixed culture (MC; 2:1:1). Sucuk formulations with 150, 75, and 0 ppm sodium nitrite were produced in the presence or absence of a MC and analyzed during fermentation (days 0 and 7) and refrigerated storage (days 7 and 14). Among the treatments, 75 ppm nitrite combined with MC (75-MC) exhibited the highest LAB counts, enhanced acidification (pH 4.7 on fermentation day 7), inhibited pathogens and spoilage microorganisms, and improved moisture and color stability (> 90% of initial L* and a*), with a significant treatment × day interaction (P < 0.05). Metagenomic analysis of the 16 S rRNA (V3–V4) and ITS2 regions revealed a LAB-dominated sucuk microbiota, characterized by Levilactobacillus (69.5%), Lactiplantibacillus (12.1%), Psychrobacter (8.8%), and Lacticaseibacillus (3.0%) among bacteria, and Yarrowia (46%), Kurtzmaniella (11.8%), Geotrichum (6.7%), and Cladosporium (5.5%) among fungi. This microbial composition was associated with enhanced microbial stability and technological quality, while mixed-culture strategies under nitrite-reduced conditions promoted a Lactobacillaceae-enriched microbiota, highlighting their potential role in bioprotection and product quality.}, }
@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 &amp; 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.}, }
@article {pmid41593136, year = {2026}, author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S}, title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3724}, pmid = {41593136}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Deer/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Diet ; Seasons ; Bacteria/genetics/classification ; *Animal Feed/analysis ; }, abstract = {Plant secondary compounds (PSCs) impose physiological and nutritional constraints on herbivores, yet many species continue to rely on PSC-rich forage during critical periods of the year. Moose (Alces alces) on Isle Royale National Park depend heavily on balsam fir (Abies balsamea) during winter, exposing them to a chemically defended and nutritionally limited diet. To investigate how this foraging strategy shapes both physiological responses and gut microbial communities, we integrated fecal diet composition, urinary markers of detoxification and nutritional status, 16S rRNA gene sequencing, and shotgun metagenomic profiling from free ranging moose of two separated populations from the western and eastern region of the island. Balsam fir consumption varied strongly by region and was positively associated with glucuronic acid to creatinine (GA:C) and urea nitrogen to creatinine (UN:C) ratios, indicating increased detoxification activity and reduced nutritional condition. Microbial alpha diversity declined with higher fir intake in nutritionally limited individuals, while beta diversity differed by region, balsam fir consumption, and UN:C. Several bacterial genera responded to PSC exposure, including increases in the butyrate-producing genus Roseburia and shifts in network prominence of Phascolarctobacterium. Metagenomic data revealed pathways involved in the degradation of aromatic and terpenoid PSCs, although pathway abundances did not differ significantly with balsam fir consumption after multiple testing correction. These results show that winter foraging on balsam fir produces coordinated dietary, physiological, and microbial patterns, with both host and gut microbial detoxification capacities interacting to accommodate the chemical and nutritional challenges of a PSC-rich winter diet.}, }
@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.}, }
@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 &amp; 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.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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.}, }
@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//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ci&#xea;ncia e Tecnologia, da Secretaria de Ci&#xea;ncia, Tecnologia, Inova&#xe7;&#xe3;o e Com-plexo da Sa&#xfa;de, do Minist&#xe9;rio da Sa&#xfa;de (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.}, }
@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//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; 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.}, }
@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.}, }
@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&amp;D ProgramNational Key R&amp;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.}, }
@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.}, }
@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.}, }
@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 ; }, }
@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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.}, }
@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.}, }
@article {pmid41604101, year = {2026}, author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R}, title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {47}, pmid = {41604101}, issn = {1678-4405}, support = {952583//H2020 European Research Council/ ; }, mesh = {Humans ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.}, }
@article {pmid41604220, year = {2026}, author = {Yao, ML and Lin, P and Hua, K and Zhang, W}, title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {53}, number = {}, pages = {}, pmid = {41604220}, issn = {1476-5535}, support = {R01 DE032732/DE/NIDCR NIH HHS/United States ; //University of California/ ; No. DGE2146752//National Science Foundation/ ; R01DE032732/NH/NIH HHS/United States ; }, mesh = {*Dental Caries/microbiology ; *Microbiota/genetics ; *Multigene Family ; Humans ; *Mouth/microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Biosynthetic Pathways/genetics ; }, abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and posttranslationally modified peptide, and nonribosomal peptide encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out >3,000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. These results demonstrate that BGCs can provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, can differentiate oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts. One-sentence summary Specialized metabolites in oral bacteria are differentially expressed in healthy and cavity-affected communities.}, }
@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 &amp; 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.}, }
@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 &amp; biotechnology}, volume = {42}, number = {2}, pages = {65}, pmid = {41606218}, issn = {1573-0972}, mesh = {Humans ; *Microbiota/genetics ; *Multigene Family ; Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation &amp; 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.}, }
@article {pmid41606550, year = {2026}, author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X}, title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41606550}, issn = {1471-2466}, support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; }, mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Aspergillus fumigatus/isolation &amp; purification ; *Respiration, Artificial/adverse effects ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Risk Factors ; China/epidemiology ; *Microbiota ; *Pneumonia/microbiology/mortality ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {AIM OF THE STUDY: Invasive aspergillosis is a life-threatening complication in mechanically ventilated patients with pneumonia, predominantly caused by Aspergillus fumigatus. However, its independent mortality risk and early-warning strategies in critically ill populations remain unclear. METHODS: In this multicenter retrospective cohort study, we enrolled 1567 mechanically ventilated patients with severe pneumonia who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) across 12 tertiary hospitals in China (January 2019–March 2023). Propensity score matching (1:1) balanced confounders, and Cox regression quantified the independent mortality risk of A. fumigatus infection. RESULTS: The A. fumigatus detection rate was 10.27% (161/1567). Post-matching, 28-day mortality was significantly higher in A. fumigatus-positive versus negative cohorts (66% vs 47%, p = 0.001). Multivariable analysis confirmed A. fumigatus as an independent mortality risk factor (HR = 1.79, 95%CI 1.49–2.17, p < 0.001), with significant associations to underlying renal disease (19% vs 12%, p = 0.005), connective tissue disease (7% vs 4%, p = 0.026), and multi-organ dysfunction (ep < 0.05). Microbial community analysis revealed co-colonization synergies with Enterococcus faecium, Enterococcus faecalis, Candida albicans, HSV-1, and EBV. CONCLUSIONS: A. fumigatus infection independently increases 28-day mortality risk in mechanically ventilated patients. Early intensified screening and intervention are warranted for individuals with ≥ 3 organ dysfunctions, underlying renal/connective tissue diseases, or respiratory co-colonization by synergistic microbes.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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 &amp; purification/pathogenicity ; RNA, Ribosomal, 16S/genetics ; *Swine Diseases/microbiology/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; Porcine respiratory and reproductive syndrome virus/genetics/isolation &amp; purification ; *Bacterial Infections/veterinary/microbiology ; Influenza A virus/genetics/isolation &amp; 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.}, }
@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 &amp; development/metabolism ; Male ; Animal Feed/analysis ; Diet/veterinary ; Dietary Supplements/analysis ; *Endo-1,4-beta Xylanases/administration &amp; 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 &amp; 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.}, }
@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 = {Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; *Fresh Water/microbiology ; Genes, Bacterial ; *Microbiota ; *Microplastics/analysis ; *Seawater/microbiology ; *Water Pollutants, Chemical/analysis/toxicity ; }, 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.}, }
@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&amp;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.}, }
@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.}, }
@article {pmid41612181, year = {2026}, author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X}, title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41612181}, issn = {1471-2180}, support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; }, mesh = {Humans ; *Altitude ; China/epidemiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology ; *Adenoma/microbiology ; Male ; Female ; Archaea/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; }, abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA). METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status. RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations. CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.}, }
@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 Innovaci&#xf3;n/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 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.<br><br>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.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.}, }
@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 = {*Ascomycota/genetics/physiology ; Genome, Bacterial ; *Genome, Fungal ; *Lichens/microbiology/genetics ; Metagenome ; *Microbiota ; *Symbiosis ; }, 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.}, }
@article {pmid41618136, year = {2026}, author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX}, title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41618136}, issn = {1471-2180}, support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Antelopes/microbiology ; *Gastrointestinal Microbiome/genetics ; Tibet ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Metagenome ; Amidohydrolases/genetics ; Genome, Bacterial ; }, abstract = {BACKGROUND: The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations. RESULTS: This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience. CONCLUSIONS: In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.}, }
@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, Innovaci&#xf3;n y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; EDU-1868-2022//Junta de Castilla y Le&#xf3;n/ ; }, 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.}, }
@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.<br><br>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.<br><br>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.<br><br>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.}, }
@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.}, }
@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.}, }
@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 &amp; 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.}, }
@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.}, }
@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 &amp; 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.}, }
@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.}, }
@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.<br><br>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.<br><br>METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&amp;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.<br><br>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-&#x3ba;B 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.<br><br>CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-&#x3ba;B-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-&#x3ba;B signaling pathway, which subsequently improves SDD in mice.}, }
@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 F&#xf6;rderung 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.}, }
@article {pmid41620643, year = {2026}, author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R}, title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2623356}, pmid = {41620643}, issn = {1949-0984}, mesh = {Humans ; Bacteria/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Socioeconomic Factors ; Socioeconomic Disparities in Health ; }, abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.}, }
@article {pmid41621514, year = {2026}, author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G}, title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.}, journal = {International journal of biological macromolecules}, volume = {346}, number = {}, pages = {150646}, doi = {10.1016/j.ijbiomac.2026.150646}, pmid = {41621514}, issn = {1879-0003}, mesh = {*Probiotics/administration &amp; dosage/chemistry/pharmacology ; *Mannans/chemistry ; *Chitosan/chemistry ; *Colon/microbiology/metabolism/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Cellulose/chemistry ; Humans ; Microspheres ; Oxidation-Reduction ; *Drug Delivery Systems ; Sulfhydryl Compounds/chemistry ; }, abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.}, }
@article {pmid41622335, year = {2026}, author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T}, title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.}, journal = {Journal of plant research}, volume = {139}, number = {2}, pages = {195-205}, pmid = {41622335}, issn = {1618-0860}, mesh = {*Lotus/growth &amp; development/microbiology ; Symbiosis ; *Soil Microbiology ; *Mesorhizobium/physiology/genetics ; Root Nodules, Plant/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rhizobium/physiology ; }, abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.}, }
@article {pmid41627460, year = {2026}, author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT}, title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.}, journal = {Archives of microbiology}, volume = {208}, number = {4}, pages = {167}, pmid = {41627460}, issn = {1432-072X}, support = {DTDLCN.63/22//Ministry of Science and Technology/ ; }, mesh = {Humans ; Infant ; Vietnam ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenome ; Virome ; Male ; }, abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.}, }
@article {pmid41628276, year = {2026}, author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E}, title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {2}, pages = {e0013576}, pmid = {41628276}, issn = {1935-2735}, mesh = {Animals ; *Virome ; *Triatominae/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Arizona ; Texas ; New Mexico ; Phylogeny ; Female ; Sequence Analysis, DNA ; Male ; Species Specificity ; }, abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.}, }
@article {pmid41628665, year = {2026}, author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM}, title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: A proof-of-concept placebo-controlled randomized trial.}, journal = {Osteoarthritis and cartilage}, volume = {34}, number = {6}, pages = {869-881}, doi = {10.1016/j.joca.2026.01.630}, pmid = {41628665}, issn = {1522-9653}, mesh = {Humans ; Female ; Middle Aged ; *Osteoarthritis/drug therapy/physiopathology/microbiology ; Delayed-Action Preparations ; Male ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid/therapeutic use/administration &amp; dosage/pharmacology ; Aged ; Hand ; Proof of Concept Study ; Double-Blind Method ; Intestinal Barrier Function ; Feces/microbiology ; Treatment Outcome ; }, abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.<br><br>METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600&#x202f;mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.<br><br>RESULTS: 35 participants (mean age 62.5&#xb1;6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.<br><br>CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.<br><br>TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.}, }
@article {pmid41628857, year = {2026}, author = {Theodosiou, AA and Bogaert, D and Cleary, DW and Fady, PE and Feehily, C and Gilbert, JA and Greenhough, B and Guardabassi, L and Hall, LJ and Harman, T and Kuijper, EJ and Lebeer, S and Lorimer, J and Spector, TD and Jones, CE}, title = {Microbiome research in practice: priorities for clinical translation and impact.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {32}, number = {6}, pages = {927-935}, doi = {10.1016/j.cmi.2026.01.021}, pmid = {41628857}, issn = {1469-0691}, mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical ; *Translational Science, Biomedical ; }, abstract = {BACKGROUND: Rapid advances in microbiome science have sparked clinical and commercial enthusiasm for interventions, yet translation into practice risks outpacing both mechanistic understanding and the infrastructure required for safe adoption.<br><br>OBJECTIVES: To outline a coordinated research, clinical, social, and policy agenda for advancing safe, effective, and equitable microbiome-based interventions.<br><br>SOURCES: We convened an interdisciplinary Royal Society-funded expert workshop (Leeds, UK, October 2024) with international leaders in microbiome science, clinical trials, regulation, and social science. Thematic analysis of workshop discussions and written contributions identified priority domains for translation.<br><br>CONTENT: Three intersecting priorities emerged: scientific credibility, practical viability, and stakeholder engagement. Scientific credibility demands investment in multiomic and strain-level characterization of host-microbiome interactions on a large scale, benchmarking of clinical and microbiological endpoints, and harmonization of trial conduct and reporting. Clinical adoption requires fit-for-purpose regulation, diversified investment to address funding bottlenecks, and coordinated capacity building. Meaningful stakeholder engagement with clinicians, patients, policymakers, and the public is essential to foster confidence, develop clinically relevant research questions, and ensure equitable implementation of any new technology.<br><br>IMPLICATIONS: To realize the clinical impact of microbiome interventions, sustained collaboration across disciplines is essential. This review offers a translational roadmap and actionable priorities to accelerate safe, effective, and equitable microbiome-based interventions-ensuring the field fulfils its clinical potential and delivers real-world impact.}, }
@article {pmid41629500, year = {2026}, author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y}, title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6991}, pmid = {41629500}, issn = {2045-2322}, support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; }, mesh = {Humans ; *Crohn Disease/microbiology/metabolism ; *Feces/microbiology/chemistry ; *Metabolic Networks and Pathways ; Female ; Male ; Biomarkers ; Adult ; Metabolomics/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolome ; Dysbiosis/microbiology/metabolism ; Metagenomics ; }, abstract = {Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.}, }
@article {pmid41629580, year = {2026}, author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N}, title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6983}, pmid = {41629580}, issn = {2045-2322}, support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration &amp; dosage/pharmacology ; *Chickens/microbiology/growth &amp; development ; *Salmonella typhimurium ; *Salmonella Infections, Animal/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome/drug effects ; *Poultry Diseases/microbiology/prevention &amp; control ; Dietary Supplements ; Pediococcus acidilactici ; Animal Feed ; Ligilactobacillus salivarius ; }, abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.}, }
@article {pmid41629813, year = {2026}, author = {Astudillo-Guerrero, C and Garrido, &#xc1; and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G}, title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).}, journal = {BMC geriatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629813}, issn = {1471-2318}, mesh = {Humans ; Double-Blind Method ; *Fecal Microbiota Transplantation/methods ; Aged ; *Aging/physiology ; Male ; Female ; Aged, 80 and over ; *Sarcopenia/therapy ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; }, abstract = {BACKGROUND: Sarcopenia, characterized by the progressive loss of skeletal muscle mass and strength in older adults, is a key determinant of frailty and functional decline. Affecting up to 15% of individuals aged 65–80 years and more than 50% of those over 80, sarcopenia not only compromises physical autonomy but also increases the risk of metabolic dysfunction and cognitive decline. Emerging evidence suggests that age-related gut microbiota dysbiosis contributes to these impairments by reducing microbial diversity and altering host metabolic signaling, leading to chronic inflammation and mitochondrial dysfunction. The present study aims to evaluate the safety, tolerability, and preliminary efficacy of oral fecal microbiota transplantation derived from young, physically active donors administered to older adults, focusing on outcomes related to functional autonomy, muscle performance, metabolism and cognition. METHODS: This is a double-blind, randomized, placebo-controlled clinical trial involving community-dwelling adults aged 65–84 years. Participants will be randomized 1:1 to receive either FMT capsules or placebo following a short course of oral rifaximin (or placebo). Assessments will be performed at baseline and at 4, 8, and 20 weeks post-intervention. The primary outcomes are safety and tolerability, as well as changes in the Global Index of Functional Autonomy (GDLAM battery) and muscle strength. Secondary outcomes include gait speed, body composition (DXA), metabolic biomarkers, gut microbiota composition (shotgun metagenomics), cognitive performance, and psychological well-being. EXPECTED IMPACT: By restoring microbial diversity and function, FMT from young, active donors may enhance muscle quality, cognitive resilience, and metabolic health in older adults. This study introduces a novel, non-invasive therapeutic approach based on lyophilized and encapsulated microbiota, offering a feasible and scalable strategy to promote healthy aging. TRIAL REGISTRATION: ClinicalTrials.gov NCT06649981. Date of registration October 21, 2024.}, }
@article {pmid41629888, year = {2026}, author = {Luo, M and Xiao, X and Wu, Y}, title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629888}, issn = {1471-2431}, support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; }, mesh = {Humans ; *Phototherapy ; *Hyperbilirubinemia, Neonatal/therapy/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Metagenomics ; Male ; Feces/microbiology ; Female ; }, abstract = {BACKGROUND: Phototherapy serves as the primary treatment for neonatal hyperbilirubinemia (NH). This research aims to investigate the impact of phototherapy on the gut microbiota of NH, and to provide reliable theoretical evidence for the clinical application of phototherapy in such cases. METHODS: In this self-controlled longitudinal study, 26 newborns diagnosed with NH were enrolled. Fecal samples were collected before (pre-treatment) and 48 h after (post-treatment) initiating phototherapy. The gut microbiota was profiled using high-throughput 16 S ribosomal RNA (rRNA) gene sequencing. Gut microbiota composition and diversity were analyzed using standard bioinformatics pipelines. Data were processed with standard bioinformatics tools for taxonomic annotation, diversity analysis, and functional prediction based on the COG, KEGG, and MetaCyc databases. Statistical significance was assessed using the Wilcoxon signed-rank test (P < 0.05). RESULTS: While no significant differences were observed at the species level, analysis at the genus level revealed significant alterations in the gut microbiota. The genera Clostridium and Megamonas were identified as significantly increased post-phototherapy. Linear discriminant analysis effect size (LEfSe) analysis further confirmed distinct microbial signatures between the two groups: pre-treatment samples were enriched with families such as Porphyromonadaceae, Lachnospiraceae, Alcaligenaceae, Ruminococcaceae, Moraxellaceae, and the order Pseudomonadales. In contrast, post-treatment samples were predominantly characterized by the class Erysipelotrichi and its associated taxa (Erysipelotrichales and Erysipelotrichaceae). α-diversity indices (Sobs, Chao, Shannon, Simpson) showed no significant differences between the two groups, whereas β-diversity analysis indicated significant microbial community separation (P < 0.05). Predicted functional profiles (based on 16 S rRNA gene data using PICRUSt2) suggested predominant roles in metabolism, genetic information processing, and biosynthesis. However, no significant differences were observed between the pre- and post-treatment groups. CONCLUSIONS: Phototherapy significantly modulated the gut microbial composition of neonates with NH, notably increasing the abundance of Clostridium and Megamonas, and shifting the community towards Erysipelotrichi, while overall microbial functional capacity remained stable. These findings highlight the dynamic yet resilient nature of the neonatal gut microbiota under phototherapy and provide a foundation for microbiome-informed management strategies in neonatal hyperbilirubinemia.}, }
@article {pmid41633028, year = {2026}, author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y}, title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.}, journal = {Research in veterinary science}, volume = {203}, number = {}, pages = {106092}, doi = {10.1016/j.rvsc.2026.106092}, pmid = {41633028}, issn = {1532-2661}, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology/growth &amp; development/metabolism ; Multiomics ; Male ; Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; }, abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.}, }
@article {pmid41633137, year = {2026}, author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R}, title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.}, journal = {Forensic science international. Genetics}, volume = {83}, number = {}, pages = {103435}, doi = {10.1016/j.fsigen.2026.103435}, pmid = {41633137}, issn = {1878-0326}, mesh = {Animals ; Humans ; *Drowning/diagnosis ; *Lung/microbiology ; *Microbiota/genetics ; Mice ; *Metagenomics ; Postmortem Changes ; Immersion ; Biomarkers ; Real-Time Polymerase Chain Reaction ; Male ; }, abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.}, }
@article {pmid41633490, year = {2026}, author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS}, title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.}, journal = {The Journal of allergy and clinical immunology}, volume = {158}, number = {2}, pages = {408-420}, pmid = {41633490}, issn = {1097-6825}, support = {U01 AI110397/AI/NIAID NIH HHS/United States ; F32 AI194859/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI178155/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Child ; *Microbiota ; Female ; *Respiratory Tract Infections/microbiology/epidemiology/virology ; Male ; *Asthma/microbiology/epidemiology/virology ; Prospective Studies ; *Virome ; *Virus Diseases/epidemiology/microbiology ; *Nose/microbiology ; Rhinovirus ; }, abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.<br><br>OBJECTIVE: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.<br><br>METHODS: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated multikingdom changes to the nasal microbiome during infection. A sparse partial least-squares discriminant analysis model identified microbial signatures associated with prospective viral infection risk.<br><br>RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus being the most prevalent. Cold and asthma symptoms within the previous 14 days had a sensitivity of 79% and 59%, respectively, for quantitative RT-PCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted odds ratio, 0.41 [95% CI, 0.25-0.67]; P < .001), whereas phageome profiles increased risk (adjusted odds ratio, 3.74 [95% CI, 1.85-7.55]; P < .001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.<br><br>CONCLUSIONS: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.}, }
@article {pmid41634308, year = {2026}, author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A}, title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {7016}, pmid = {41634308}, issn = {2045-2322}, support = {192514//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Switzerland ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Feces/microbiology ; Africa ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.}, }
@article {pmid41634410, year = {2026}, author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY}, title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.}, journal = {Inflammation}, volume = {49}, number = {1}, pages = {78}, pmid = {41634410}, issn = {1573-2576}, support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; }, mesh = {Animals ; *Colitis/chemically induced/microbiology/prevention &amp; control ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects/physiology ; *Imiquimod/toxicity ; *Metagenome ; *Skin/pathology/drug effects ; Akkermansia ; Male ; *Verrucomicrobia ; Feces/microbiology ; }, abstract = {A decreased abundance of fecal Akkermansia muciniphila (Akk) has been observed in patients with psoriasis and psoriatic arthritis. The potential beneficial effects of Akk in managing psoriasis have been proposed, yet results remain inconsistent and mechanisms unclear. Using imiquimod (IMQ)-treated C57BL/6 mice, we conducted a metagenomic association study of pasteurized Akk (pAkk) in the IMQ mice through whole-genome shotgun sequencing. We also performed a dextran sodium sulfate (DSS)-induced colitis experiment and an intestinal permeability test. The association among pAkk supplements, skin thickness, inflammatory profiles, fecal microbiota alterations, functional genetic predictions, intestinal epithelium inflammation, and barrier integrity was investigated. The study demonstrated that pAkk supplementation ameliorated IMQ-induced skin thickening, weight loss, spleen weight gain, serum IL-17A, TNF-α levels, and DSS-induced colitis. pAkk supplementation was linked to greater fecal microbial diversity and alterations in fecal microbiota composition, with increased prevalence of Muribaculaceae, Bifidobacterium pseudolongum, Desulfovirionaceae, Erysipelotrichaceae, and Alistipes ihumi, which have been implicated in the Gamma-Aminobutyric Acid (GABA) shunt, cholinergic synapse, cell cycle, and Mitogen-Activated Protein Kinase (MAPK) pathways. In conclusion, pAkk may mitigate IMQ-induced skin thickening and DSS-induced colitis, associated with reduced levels of TNF-α and IL-17A. pAkk supplementation alters fecal microbiota and metabolic pathways in IMQ-treated mice.}, }
@article {pmid41634542, year = {2026}, author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y}, title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41634542}, issn = {1471-2180}, support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; }, mesh = {*Zea mays/microbiology/metabolism/chemistry ; Fermentation ; *Probiotics/metabolism ; Metabolomics ; *Microbiota ; Laccase/metabolism ; *Enzymes/metabolism ; Lactobacillus/metabolism ; Peroxidases/metabolism ; Bacillus subtilis/metabolism ; Cellulose/metabolism ; Bacteria/metabolism/classification/genetics ; Cellulase/metabolism ; }, abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear. METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10[8] CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process. RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties. CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.}, }
@article {pmid41634815, year = {2026}, author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X}, title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41634815}, issn = {2049-2618}, mesh = {*Caragana/microbiology ; Drought Resistance ; *Plant Roots/microbiology ; *Triticum/microbiology/growth &amp; development/physiology ; Desert Climate ; *Microbiota ; Droughts ; Biofilms/growth &amp; development ; Quorum Sensing ; Pseudomonas/genetics/physiology ; Metagenomics ; }, abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.<br><br>RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.<br><br>CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.}, }
@article {pmid41636495, year = {2026}, author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC}, title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0226425}, pmid = {41636495}, issn = {2165-0497}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique F&#xe9;d&#xe9;rale de Lausanne), Lausanne, Switzerland/ ; }, mesh = {Humans ; *Dry Eye Syndromes/microbiology/metabolism/etiology ; Female ; *Tears/chemistry/metabolism/microbiology ; *Microbiota ; Male ; *Proteome/metabolism ; *Contact Lenses/adverse effects/microbiology ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; *Eye Proteins/metabolism ; *Eye/microbiology ; Young Adult ; }, abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.}, }
@article {pmid41636510, year = {2026}, author = {Anne Hallowell, H and Malogan, J and Suez, J}, title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0100225}, pmid = {41636510}, issn = {2379-5077}, mesh = {Humans ; *Virome/genetics ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Viruses/genetics/isolation &amp; purification ; Bacteriophages/genetics ; Metagenomics/methods ; Metagenome ; }, abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.}, }
@article {pmid41638014, year = {2026}, author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L}, title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {292}, number = {}, pages = {107742}, doi = {10.1016/j.aquatox.2026.107742}, pmid = {41638014}, issn = {1879-1514}, mesh = {Animals ; *Norfloxacin/toxicity ; *Bile Acids and Salts/metabolism ; Larva/drug effects/microbiology ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/toxicity ; Metabolomics ; }, abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.}, }
@article {pmid41639568, year = {2026}, author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X}, title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41639568}, issn = {2045-2322}, support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity &amp; Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; }, mesh = {Animals ; *Asthma/drug therapy/metabolism/microbiology ; Mice ; *Glutamine/metabolism ; *Gastrointestinal Microbiome/drug effects ; Multiomics ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Cytokines/metabolism ; Th17 Cells/immunology/drug effects ; Metabolomics ; Mice, Inbred BALB C ; Disease Models, Animal ; Th2 Cells/immunology/drug effects ; Ovalbumin ; Female ; Lung/drug effects/pathology ; }, abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.}, }
@article {pmid41640872, year = {2026}, author = {Chen, YX and Sun, NQ and Mo, SJ}, title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.}, journal = {World journal of gastroenterology}, volume = {32}, number = {4}, pages = {114468}, pmid = {41640872}, issn = {2219-2840}, mesh = {*NF-E2-Related Factor 2/metabolism ; *Parkinson Disease/complications/microbiology ; Animals ; Humans ; *Gastrointestinal Diseases/etiology/therapy/microbiology/drug therapy ; Gastrointestinal Microbiome/drug effects ; Mice ; Signal Transduction/drug effects ; Disease Models, Animal ; Fecal Microbiota Transplantation ; }, abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.}, }
@article {pmid41642002, year = {2026}, author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB}, title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.}, journal = {mBio}, volume = {17}, number = {3}, pages = {e0364525}, pmid = {41642002}, issn = {2150-7511}, support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01AI163413//National Institute of Allergy and Infectious Diseases/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; R01NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Female ; *Vagina/microbiology/immunology ; *Microbiota/immunology/genetics ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Gardnerella/genetics/classification/immunology ; Metagenome ; Algorithms ; }, abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.}, }
@article {pmid41644290, year = {2026}, author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y}, title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.}, journal = {Journal of cosmetic dermatology}, volume = {25}, number = {2}, pages = {e70714}, pmid = {41644290}, issn = {1473-2165}, support = {//Proya Cosmetics Co. Ltd/ ; }, mesh = {Humans ; Female ; *Sebum/metabolism/microbiology ; *Scalp/microbiology/metabolism ; *Lipidomics/methods ; Adult ; *Dermatitis, Seborrheic/microbiology/metabolism ; Skin Microbiome ; Young Adult ; *Scalp Dermatoses/microbiology/metabolism ; Dandruff/microbiology/metabolism ; China ; Metagenomics/methods ; *Lipids/analysis ; Lipid Metabolism ; Malassezia/isolation &amp; purification ; East Asian People ; }, abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.<br><br>AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.<br><br>METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.<br><br>RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).<br><br>CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.}, }
@article {pmid41644553, year = {2026}, author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J}, title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41644553}, issn = {2055-5008}, support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Depression/etiology/microbiology ; Mice ; Mice, Inbred BALB C ; *Echinococcosis/psychology/microbiology/complications ; Disease Models, Animal ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Fecal Microbiota Transplantation ; Behavior, Animal ; Chronic Disease ; Metabolomics ; Metagenomics/methods ; Multiomics ; Chemokine CCL2 ; Interleukin-6 ; Male ; Hippocampus/pathology ; }, abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.}, }
@article {pmid41644585, year = {2026}, author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E}, title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41644585}, issn = {2045-2322}, mesh = {*Composting/methods ; *Manure/microbiology ; *RNA, Ribosomal, 16S/genetics ; Animals ; *Metagenomics/methods ; *Microbiota/genetics ; Cattle ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; }, abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.}, }
@article {pmid41644796, year = {2026}, author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J}, title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.}, journal = {Nature microbiology}, volume = {11}, number = {3}, pages = {664-677}, pmid = {41644796}, issn = {2058-5276}, support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Glomerular Filtration Rate ; Humans ; Feces/microbiology ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Biomarkers ; Disease Progression ; Male ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; }, abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.}, }
@article {pmid41645054, year = {2026}, author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H}, title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41645054}, issn = {1471-2164}, support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&amp;D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; }, mesh = {Animals ; *Enterocytozoon/physiology ; *Gastrointestinal Microbiome ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; *Vitamin B Complex/biosynthesis ; Metagenome ; *Biosynthetic Pathways ; Animals, Wild/microbiology ; }, abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.}, }
@article {pmid41650276, year = {2026}, author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H}, title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eaeb6265}, pmid = {41650276}, issn = {2375-2548}, mesh = {Animals ; *Bacteriophages/genetics/physiology/classification ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Genome, Viral ; Phylogeny ; Bacteroides/virology ; }, abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.}, }
@article {pmid41651079, year = {2026}, author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L}, title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.}, journal = {Toxicology and applied pharmacology}, volume = {509}, number = {}, pages = {117754}, doi = {10.1016/j.taap.2026.117754}, pmid = {41651079}, issn = {1096-0333}, mesh = {Animals ; *Adenine/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology ; Multiomics ; Male ; Metabolomics ; Mice, Inbred C57BL ; Mice ; Disease Models, Animal ; Kidney/metabolism/pathology ; Metagenomics ; }, abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.}, }
@article {pmid41651131, year = {2026}, author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C}, title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.}, journal = {Brain, behavior, and immunity}, volume = {134}, number = {}, pages = {106479}, pmid = {41651131}, issn = {1090-2139}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; R03 HD101336/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; Pregnancy ; *Depression/microbiology/metabolism ; *Obesity/microbiology/metabolism ; *Inflammation/metabolism/microbiology ; Adult ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome/physiology ; Biomarkers/blood ; Body Mass Index ; Feces/microbiology ; Surveys and Questionnaires ; Pregnancy Trimester, Third ; }, abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.<br><br>METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI&#xa0;<&#xa0;25) or obese (BMI&#xa0;&#x2265;&#xa0;30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q&#xa0;<&#xa0;0.1 was considered statistically significant.<br><br>RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q&#xa0;=&#xa0;0.02) and positively associated with Bacteroides thetaiotaomicron (q&#xa0;=&#xa0;0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.<br><br>DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.}, }
@article {pmid41651389, year = {2026}, author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M}, title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.}, journal = {Developmental and comparative immunology}, volume = {176}, number = {}, pages = {105565}, doi = {10.1016/j.dci.2026.105565}, pmid = {41651389}, issn = {1879-0089}, mesh = {Animals ; *Penaeidae/microbiology/immunology ; *Vibrio parahaemolyticus/physiology ; *Vibrio Infections/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Virulence/genetics ; Host-Pathogen Interactions ; }, abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.}, }
@article {pmid41651883, year = {2026}, author = {Pantiukh, K and Org, E}, title = {Human gut archaea collection from Estonian population.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41651883}, issn = {2052-4463}, support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Estonia ; *Archaea/genetics/classification ; Humans ; *Metagenome ; *Microbiota ; *Genome, Archaeal ; Feces/microbiology ; }, abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.}, }
@article {pmid41652998, year = {2026}, author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I}, title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.}, journal = {Biological research for nursing}, volume = {28}, number = {3}, pages = {406-417}, doi = {10.1177/10998004261423546}, pmid = {41652998}, issn = {1552-4175}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Infant ; *Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use ; Pregnancy ; *Antidepressive Agents/adverse effects/therapeutic use ; Adult ; Infant, Newborn ; Feces/microbiology ; }, abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.}, }
@article {pmid41654194, year = {2026}, author = {Wei, P and Zhang, L and Hu, Q and Zhu, A and Zhuang, Z and Zhang, Z and Zhang, S and Chen, J and Xiong, X and Qu, B and Zhang, Y and Chen, L and Xu, Z and Chen, Z and Zhong, Q and Xing, X and Li, X and Gao, J and He, Y and Xie, G and Shang, J and Guo, X and Jiang, J and Shi, Y and Zhao, J and Wang, Y and Zhao, J and Jin, Y}, title = {Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {58-69}, pmid = {41654194}, issn = {1995-820X}, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; *Multiplex Polymerase Chain Reaction/methods ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Male ; Child, Preschool ; Infant ; *Microbiota/genetics ; Child ; *Bacteria/genetics/classification/isolation &amp; purification ; Nasopharynx/microbiology/virology ; Gene Expression Profiling ; Viruses/genetics/isolation &amp; purification/classification ; Metagenomics ; }, abstract = {Despite widespread use of multiple PCR, a substantial proportion of pediatric acute respiratory tract infections (ARTIs) lack identifiable pathogens and are classified as unknown etiology. The microbial characteristics and clinical relevance of these cases remain unclear. In this study, we compared the airway microbiomes of PCR-positive and PCR-negative ARTIs and examined their relationships with sampling site and disease severity. A total of 514 hospitalized children with ARTIs were enrolled. Nasopharyngeal swabs (NS) and bronchoalveolar lavage fluid (BALF) samples were tested using a 22-target multiplex PCR panel and subsequently stratified by pathogen status for pooled metatranscriptomic sequencing to profile active microbial communities, viral genotypes, and antibiotic resistance genes. PCR identified common respiratory pathogens in 77.0% of NS and 54.1% of BALF samples. Metatranscriptomic analysis showed that PCR-negative pools displayed markedly lower viral activity and comparatively higher bacterial transcript abundance, with notable enrichment of Pseudomonas. Microbial signatures differed between upper and lower airway samples and across clinical severity, with severe cases demonstrating increased bacterial burden and Pseudomonas enrichment, whereas mild infections exhibited relatively stronger viral signals. Under current thresholds, antibiotic resistance genes were detected in patient pools but not in healthy controls. Overall, PCR-negative pediatric ARTIs exhibited distinct, bacteria-enriched microbial profiles. Integrating metatranscriptomics with PCR enhances pathogen characterization and reveals site- and severity-related microbial patterns that may support diagnostic evaluation and clinical management.}, }
@article {pmid41654729, year = {2026}, author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J}, title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41654729}, issn = {1471-2180}, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Essential Hypertension/microbiology ; Sex Factors ; Middle Aged ; Cohort Studies ; China ; Fatty Acids, Volatile/metabolism ; Sex Characteristics ; Hypertension/microbiology ; Metagenomics ; Aged ; Eubacteriales ; }, abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.<br><br>METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.<br><br>RESULTS: Our study confirmed a statistically significant difference in the &#x3b2;-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.<br><br>CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.}, }
@article {pmid41654923, year = {2026}, author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY}, title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41654923}, issn = {1479-5876}, support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; }, mesh = {Humans ; Female ; *Cytokines/blood ; Pregnancy ; *Virome ; Infant, Newborn ; Infant ; *Syphilis/blood/virology ; Adult ; Infectious Disease Transmission, Vertical ; *Mothers ; Phylogeny ; Longitudinal Studies ; }, abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.}, }
@article {pmid41655211, year = {2026}, author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X}, title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {24}, pages = {e04247}, pmid = {41655211}, issn = {2198-3844}, support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; }, mesh = {Animals ; Mice ; *Pituitary Neoplasms/microbiology/genetics/metabolism ; *Receptors, Dopamine D2/deficiency/genetics/metabolism ; *Escherichia coli ; Humans ; *Bacterial Translocation ; *Adenoma/microbiology/metabolism/genetics ; Disease Models, Animal ; Female ; *Gastrointestinal Microbiome ; Prolactinoma/genetics ; Male ; }, abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.}, }
@article {pmid41655253, year = {2026}, author = {Shi, Y and He, S and Li, C and Chan, H and Liu, Z and Yang, B and Li, Q}, title = {Bifidobacterium Breve Yang08 Alleviates Atopic Dermatitis By Enriching Akkermansia Muciniphila and Inhibiting Neutrophil Extracellular Traps Formation In Mice.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {20}, pages = {e18588}, pmid = {41655253}, issn = {2198-3844}, support = {32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 82574001//National Natural Science Foundation of China/ ; 2025A04J4030//Guangdong Provincial Science and Technology Plan Project/ ; }, mesh = {Animals ; *Extracellular Traps/metabolism/immunology ; *Dermatitis, Atopic/microbiology/immunology/therapy ; Mice ; *Bifidobacterium breve/physiology ; Humans ; Disease Models, Animal ; *Neutrophils ; *Gastrointestinal Microbiome ; *Akkermansia ; *Probiotics ; *Verrucomicrobia ; Male ; }, abstract = {Atopic dermatitis (AD) is linked to gut microbiota dysbiosis, yet the mechanisms connecting specific commensals to cutaneous immunoregulation remain elusive. We observed reduced Bifidobacterium breve (B. breve) abundance in AD patients. A new B. breve strain was isolated from human stools and nomenclated as Yang08. In MC903-induced AD-like mouse models, Yang08 outperformed a standard strain, ameliorating disease severity, including reduced ear thickening, epidermal hyperplasia, and mast cell infiltration in a manner dependent on viable bacteria and an intact gut microbiota. Antibiotic-mediated microbiota depletion abrogated its efficacy, while fecal microbiota transfer from Yang08-treated mice conferred protection, confirming microbial remodeling as essential. Metagenomics revealed Yang08 specifically enriched Akkermansia muciniphila, which was required for therapeutic effects in germ-free mice. Mechanistically, Yang08 abolished both neutrophil influx and NET deposition in lesions, with ex vivo experiments showing blunted NETosis capacity. Its therapeutic benefits were reversed by neutrophil depletion, NET degradation, or PAD4 inhibition. Overall, Yang08 alleviates AD by enriching A. muciniphila and inhibiting skin NETosis, emerging as a promising prophylactic candidate prevention for AD prevention.}, }
@article {pmid41655417, year = {2026}, author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P}, title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.}, journal = {Water research}, volume = {294}, number = {}, pages = {125493}, doi = {10.1016/j.watres.2026.125493}, pmid = {41655417}, issn = {1879-2448}, mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Bacteria/genetics ; *Microbiota ; Nitrogen ; China ; }, abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.}, }
@article {pmid41660426, year = {2026}, author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K}, title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1754671}, pmid = {41660426}, issn = {2235-2988}, mesh = {*Androgens/biosynthesis/metabolism ; Humans ; *Databases, Genetic ; *Microbiota/genetics ; Biocuration ; Computational Biology/methods ; }, abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.}, }
@article {pmid41660616, year = {2025}, author = {Liu, H and Liang, L and Wang, C and Luo, R and Luo, Q and Huang, C}, title = {Gut mycobiota dysbiosis and an emergent state of "co-dysbiosis" are associated with IgE sensitization in children with comorbid allergic rhinitis and constipation.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1745580}, pmid = {41660616}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Immunoglobulin E/immunology/blood ; *Rhinitis, Allergic/immunology/microbiology/epidemiology ; Child, Preschool ; *Constipation/immunology/microbiology/epidemiology ; *Gastrointestinal Microbiome/immunology ; Child ; Female ; Male ; *Fungi/immunology/genetics ; Case-Control Studies ; Comorbidity ; Pilot Projects ; *Mycobiome/immunology ; }, abstract = {BACKGROUND: The comorbidity of allergic rhinitis (AR) and functional constipation (FC), termed ARFC, implies shared gut-immune pathways. Although bacterial dysbiosis has been implicated, the role of the gut mycobiota (fungal community) in this specific comorbidity remains unexplored.<br><br>METHODS: This pilot case-control study characterized the gut mycobiota in 19 ARFC and 17 healthy control (HC) children aged 3-6 years using metagenomic sequencing. Fungal community structure, taxonomic composition, and correlations with IgE levels were analyzed. Cross-kingdom bacterial-fungal interaction networks were constructed, and functional potential was predicted.<br><br>RESULTS: Alpha diversity was comparable, whereas beta diversity revealed significant structural shifts in the ARFC gut mycobiota. Key immunomodulatory fungi, including Cenococcum, Dentiscutata, Ambispora, and Saccharomyces, were markedly depleted in ARFC. These taxa served as top discriminators in random forest models and exhibited significant inverse correlations with total and allergen-specific IgE levels. Cross-kingdom network analysis identified dramatic ecological restructuring: the HC network was characterized by prevalent competitive interactions, whereas the ARFC network shifted exclusively to positive correlations, a state termed "co-dysbiosis." No significant differences were observed in predicted KEGG functional pathways.<br><br>CONCLUSION: This study provides the first evidence that gut mycobiota dysbiosis-marked by depletion of immunoregulatory fungi and an ecological shift toward cooperative interkingdom interactions ("co-dysbiosis")-is associated with IgE sensitization in ARFC children. These findings position the gut mycobiota as a novel element of the gut-nose axis in allergic disease, warranting further investigation.}, }
@article {pmid41661278, year = {2026}, author = {Zhang, H and Zhai, C and Hu, H and Qian, G and Mao, M}, title = {A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.}, journal = {Acta diabetologica}, volume = {63}, number = {5}, pages = {789-799}, pmid = {41661278}, issn = {1432-5233}, support = {XFCX-DMYH//Jiaxing Institute of Arteriosclerotic Disease/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications/metabolism ; *Myocardial Infarction/microbiology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenomics ; Middle Aged ; Male ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVE: This study aimed to investigate gut microbiota composition and metabolic functions in patients with type 2 diabetes mellitus (DM) complicated by myocardial infarction (MI) and to explore potential mechanisms linking the gut microbiome to MI development.<br><br>METHODS: Sixty patients with DM complicated by MI and 52 patients with DM alone were initially recruited. After quality control, 29 DM&#x2009;+&#x2009;MI patients and 33 DM patients were included in the final analysis. Gut microbial profiles were characterized using shotgun metagenomic sequencing and bioinformatics analyses. Microbial diversity, composition, and gene functions were compared between groups based on KEGG, COG, and CAZy annotations.<br><br>RESULTS: Overall microbial diversity and metabolic profiles were comparable between the two groups; however, significant differences were observed in specific taxa and functional genes. Taxa enriched in the DM&#x2009;+&#x2009;MI group included Bacteroidales, Prevotellaceae, and Lachnospiraceae. In total, 510 KEGG orthology (KO) units and 21 pathways-including ABC transporters, quorum sensing, and general metabolic pathways-differed significantly between groups. Carbohydrate transport and metabolism, as well as glycoside hydrolase activity, represented the most enriched functional categories. Random forest models based on selected microbial species, KO units, and KEGG pathways achieved areas under the curve (AUCs) of 0.868, 0.885, and 0.820, respectively.<br><br>CONCLUSION: Patients with DM complicated by MI exhibit distinct gut microbial compositions and functional gene signatures compared with patients with DM alone. These microbiome-based markers may contribute to early risk stratification and provide potential targets for microbiota-focused interventions to mitigate MI risk in patients with diabetes.}, }
@article {pmid41661326, year = {2026}, author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H}, title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.}, journal = {Surgery today}, volume = {56}, number = {7}, pages = {1351-1359}, pmid = {41661326}, issn = {1436-2813}, mesh = {Humans ; *Weight Loss ; *Gastrectomy/methods ; Female ; *Laparoscopy/methods ; Male ; Treatment Outcome ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Obesity, Morbid/surgery/microbiology/metabolism ; *Bariatric Surgery/methods ; *Mouth/microbiology ; }, abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.}, }
@article {pmid41663920, year = {2026}, author = {Qian, Y and Shi, C and Wang, Y and Han, Q and Yu, Q and Li, M and Li, H}, title = {Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663920}, issn = {1471-2180}, support = {32471575//National Natural Science Foundation of China/ ; 24JRRA458//Gansu Province Science and Technology Plan for Youth Science Fund/ ; lzuyxcx-2022-172//Medical Innovation and Development Project of Lanzhou University/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Carbon Cycle/genetics ; *Parks, Recreational ; Carbon/metabolism ; Water Microbiology ; Metagenome ; Sequence Analysis, DNA ; Phylogeny ; Soil/chemistry ; Microbiota/genetics ; }, abstract = {In the midst of increasing global warming and accelerated urbanization, urban parks, serving as significant carbon sinks, are increasingly recognized for their role in mitigating the urban heat island effect. However, limited research investigating the urban park carbon cycle hinders our full understanding and effective use of their carbon sink potential. This study employed metagenomics sequencing and 16S rRNA gene sequencing to characterize the carbon cycle and its influencing factors within soil and water from collected from nine city parks. Notably, the abundance and alpha diversity of carbon cycle microbes and genes were higher in soil compared to water. Specifically, soil samples exhibited enrichment of carbon cycling genes involved primarily in polysaccharide metabolism, particularly those associated with starch and cellulose metabolism. Conversely, water samples, revealed a greater prevalence of genes associated with chitin metabolism. The most important factor affecting soil carbon cycling genes was bacterial community, followed by non-nutritional factors and nutrient factors, while heavy metals demonstrated no effect on soil carbon cycling genes. The most important factor affecting water carbon cycling genes was only bacterial community. The analysis yielded 381 high-quality metagenomic assembled genomes (MAGs) containing carbon cycling genes, with significant covariation observed between the pta and carbon cycling genes ackA and acyP, which encode cellulose degradation functions. These findings contribute to a better understanding of microbial carbon metabolism within urban parks and offer a foundation for effective carbon emission management strategies.}, }
@article {pmid41663924, year = {2026}, author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y}, title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663924}, issn = {1471-2180}, support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; Sheep/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Gastrointestinal Microbiome ; Metabolomics ; *Eating ; Metabolome ; Metagenomics ; Digestion ; }, abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling. RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI. CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.}, }
@article {pmid41663943, year = {2026}, author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W}, title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663943}, issn = {1471-2180}, support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; }, mesh = {*Triticum/microbiology/growth &amp; development/physiology ; Drought Resistance ; *Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; *Microbiota ; *Streptomyces/physiology ; Droughts ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; }, abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance. RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings. CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.}, }
@article {pmid41664657, year = {2026}, author = {Chuckran, PF and Blazewicz, SJ and Ceja-Navarro, JA and Pett-Ridge, J and Schwartz, E and Dijkstra, P}, title = {The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20641}, pmid = {41664657}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Transcription, Genetic ; Codon Usage ; *Microbiota/genetics ; Glucose/metabolism ; Environment ; Codon ; }, abstract = {Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.}, }
@article {pmid41664846, year = {2026}, author = {Stolf, CS and Paz, HES and Paraluppi, MC and Miguel, MMV and Santamaria, MP and Monteiro, MF and Amgarten, DE and Franco, RRA and Branco-de-Almeida, LS and Shaddox, LM and Casarin, RCV}, title = {Molar-Incisor and Generalized Grade C Periodontitis: Distinct Microbiome-Immune Interactions Suggest Divergent Pathogenesis.}, journal = {Journal of periodontal research}, volume = {61}, number = {4}, pages = {382-395}, doi = {10.1111/jre.70077}, pmid = {41664846}, issn = {1600-0765}, support = {R01 DE019456/DE/NIDCR NIH HHS/United States ; 2021/14430-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; R01DE019456/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/immunology ; Biofilms ; Cross-Sectional Studies ; Female ; Gingival Crevicular Fluid/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Male ; Adult ; Middle Aged ; Treponema denticola/isolation &amp; purification ; Cytokines ; Tannerella forsythia/isolation &amp; purification ; Eubacteriales ; }, abstract = {AIM: Molar-Incisor (PerioC-MIP) and Generalized (PerioC-G) Grade C Periodontitis could have distinctive etiopathogenesis behind their unique clinical patterns. Thus, this study aimed to distinguish these two phenotypes by analyzing the subgingival metagenomic profile and the inflammatory markers levels.<br><br>METHODS: In this cross-sectional comparative study, Gingival Crevicular Fluid (GCF) and Subgingival Biofilm (SB) were collected from 18 PerioC-MIP North Americans and 14 periodontally healthy controls (HC) from the same location (HC-MIP) and 20 PerioC-G Brazilians and 20 controls (HC-G). From GCF, immunoenzymatic analysis was performed. SB functional and taxonomic bacterial content was determined using shotgun metagenomics sequencing.<br><br>RESULTS: Taxonomic results showed significantly different alpha- and beta-diversity profiles between disease groups (p&#x2009;<&#x2009;0.05). Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis were associated with PerioC-MIP; levels of Tannerella forsythia, Filifactor alocis, Porphyromonas gingivalis, Fretibacterium fastidiosum, and Treponema denticola were significantly enriched at PerioC-G (p&#x2009;<&#x2009;0.05). PerioC-G had the function for flagellar assembly enriched, while PerioC-MIP SB was associated with biofilm formation of Escherichia coli. Different GCF inflammatory marker levels for each pattern resulted in PerioC-G presenting higher levels of IL-1&#x3b2;, IL-6, and IL-10 than PerioC-MIP (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: PerioC-G and PerioC-MIP presented different taxonomical profiles and GCF cytokine levels, raising the hypothesis that they may represent two different stages/susceptibility patterns of Periodontitis Grade C.}, }
@article {pmid41666549, year = {2026}, author = {Kang, X and Zhao, Z and Zhu, X and Ju, F}, title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141398}, doi = {10.1016/j.jhazmat.2026.141398}, pmid = {41666549}, issn = {1873-3336}, mesh = {*Plasticizers/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation &amp; purification ; Phthalic Acids/metabolism ; Microbial Consortia ; }, abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.}, }
@article {pmid41666834, year = {2026}, author = {S, H and A, P}, title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.}, journal = {Marine environmental research}, volume = {216}, number = {}, pages = {107903}, doi = {10.1016/j.marenvres.2026.107903}, pmid = {41666834}, issn = {1879-0291}, mesh = {*Carbon Sequestration ; Seasons ; *Seawater/microbiology ; Metagenomics ; *Microbiota ; Bacteria/classification/genetics/metabolism ; *Environmental Monitoring ; Oceans and Seas ; *Water Microbiology ; }, abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.}, }
@article {pmid41666847, year = {2026}, author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110114}, doi = {10.1016/j.envint.2026.110114}, pmid = {41666847}, issn = {1873-6750}, mesh = {Seasons ; *Microbiota ; Serbia ; *Air Microbiology ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Air Pollution/statistics &amp; numerical data/analysis ; Air Pollutants/analysis ; Bacteria/genetics ; }, abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.}, }
@article {pmid41666920, year = {2026}, author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A}, title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {3}, pages = {379-392.e5}, doi = {10.1016/j.chom.2026.01.013}, pmid = {41666920}, issn = {1934-6069}, mesh = {Humans ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Health ; Vitamin B 12/biosynthesis ; }, abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.}, }
@article {pmid41666926, year = {2026}, author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P}, title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.}, journal = {Cell}, volume = {189}, number = {7}, pages = {2073-2091.e21}, doi = {10.1016/j.cell.2025.12.051}, pmid = {41666926}, issn = {1097-4172}, mesh = {*Microbiota/genetics ; *Ecosystem ; Humans ; *Gene Flow/genetics ; Metagenome/genetics ; Gene Transfer, Horizontal ; Metagenomics ; Bacteria/genetics/classification ; }, abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.}, }
@article {pmid41667397, year = {2026}, author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E}, title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2627692}, pmid = {41667397}, issn = {1949-0984}, mesh = {Humans ; *beta-Lactamases/genetics/metabolism ; *Ceftriaxone/therapeutic use/administration &amp; dosage ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Prospective Studies ; *Enterobacteriaceae Infections/microbiology/drug therapy ; *Enterobacteriaceae/genetics/enzymology/drug effects/isolation &amp; purification ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Third Generation Cephalosporins ; Middle Aged ; Aged ; Genetic Variation ; Second Generation Cephalosporins ; }, abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.}, }
@article {pmid41668418, year = {2026}, author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S}, title = {Recent Microbial Evolutionary Insights From Metagenomics.}, journal = {Genome biology and evolution}, volume = {18}, number = {3}, pages = {}, pmid = {41668418}, issn = {1759-6653}, support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; }, mesh = {*Metagenomics/methods ; *Evolution, Molecular ; *Microbiota/genetics ; *Biological Evolution ; Phylogeny ; Humans ; DNA, Ancient ; Genome, Microbial ; }, abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.}, }
@article {pmid41668731, year = {2025}, author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C}, title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1745848}, pmid = {41668731}, issn = {2235-2988}, mesh = {Animals ; Female ; *Culex/microbiology/genetics/physiology ; Male ; Multiomics ; *Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; *Smell/genetics ; Arthropod Antennae/physiology/metabolism ; Metagenomics ; Transcriptome ; Computational Biology ; }, abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.<br><br>METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.<br><br>RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the&#xa0;gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant&#xa0;genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that&#xa0;the gut&#xa0;microbial richness of male individuals was significantly higher than that of&#xa0;females, and the &#x3b2;-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of&#xa0;olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.<br><br>DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.}, }
@article {pmid41668733, year = {2025}, author = {Sui, Q and Yu, J and Cui, S}, title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1707599}, pmid = {41668733}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Atherosclerosis/microbiology/diagnosis ; Aged ; Middle Aged ; Retrospective Studies ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Female ; Male ; ROC Curve ; Risk Factors ; Random Forest ; Bacteria/classification/genetics/isolation &amp; purification ; *Cardiovascular Diseases/diagnosis/microbiology ; Predictive Learning Models ; Metagenomics ; Prediction Algorithms ; }, abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.<br><br>METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).<br><br>RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.<br><br>CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.}, }
@article {pmid41669550, year = {2026}, author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A}, title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20648}, pmid = {41669550}, issn = {2167-8359}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Stress, Physiological ; Phylogeny ; Nutrients/metabolism ; }, abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.}, }
@article {pmid41669888, year = {2026}, author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T}, title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.}, journal = {Journal of hypertension}, volume = {44}, number = {4}, pages = {673-681}, pmid = {41669888}, issn = {1473-5598}, mesh = {Humans ; Female ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; Male ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; }, abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.<br><br>AIM: This study assessed the association between gut microbiome and incident hypertension.<br><br>METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74 &#x200a;years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.<br><br>RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20&#x200a;years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.<br><br>CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.}, }
@article {pmid41670415, year = {2026}, author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A}, title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {67}, number = {2}, pages = {27}, pmid = {41670415}, issn = {1552-5783}, mesh = {Animals ; Humans ; *Retinitis Pigmentosa/microbiology/diagnosis/drug therapy ; Mice ; Female ; Disease Progression ; Male ; *Gastrointestinal Microbiome/physiology/genetics ; Phenotype ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Mice, Inbred C57BL ; Anti-Bacterial Agents ; Feces/microbiology ; *Bacteria/genetics ; Young Adult ; }, abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.<br><br>METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The &#x3b1; and &#x3b2; diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.<br><br>RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1&#x3b2;, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.<br><br>CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.}, }
@article {pmid41671864, year = {2026}, author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H}, title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141429}, doi = {10.1016/j.jhazmat.2026.141429}, pmid = {41671864}, issn = {1873-3336}, mesh = {Animals ; Dogs ; Humans ; *Pets/microbiology ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Feces/microbiology ; Microbiota ; }, abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.}, }
@article {pmid41672331, year = {2026}, author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M}, title = {The gut microbiome as a modulator of antibiotic resistance: Mechanisms, dynamics, and therapeutic interventions.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108357}, doi = {10.1016/j.micpath.2026.108357}, pmid = {41672331}, issn = {1096-1208}, mesh = {Humans ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects/physiology/genetics ; Probiotics ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Prebiotics ; Animals ; Bacteriophages ; }, abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.}, }
@article {pmid41672407, year = {2026}, author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW}, title = {Gestational diabetes, human milk oligosaccharide concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {4}, pages = {101235}, pmid = {41672407}, issn = {1938-3207}, support = {R00 HD113834/HD/NICHD NIH HHS/United States ; R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *Milk, Human/chemistry ; *Oligosaccharides/metabolism/chemistry ; *Diabetes, Gestational/metabolism/microbiology ; Infant ; Adult ; Pregnancy ; *Gastrointestinal Microbiome ; *Weight Gain ; United States ; Feces/microbiology ; Cohort Studies ; Infant, Newborn ; Child Development ; Male ; }, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.<br><br>OBJECTIVES: This study aimed to identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-mo of life.<br><br>METHODS: Human milk was collected at 1-mo postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high-performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q < 0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-mo infant fecal microbial abundances measured by metagenomic whole-genome sequencing.<br><br>RESULTS: Participants with GDM had &#x223c;1 SD higher milk 6'sialyllactose (6'SL) {[&#x3b2; (95% confidence interval): 0.58 (0.20, 0.96)] and lacto-N-fucopentaose III (LNFP III) III [95% CI: 0.55 (0.16, 0.94)]} compared with those without GDM and 6'SL concentration was also positively associated with weight and length gain. Although infants of mothers with GDM had lower 1-mo fecal &#x3b1;-diversity and altered abundances of 6 of 56 microbial species detected compared with those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.<br><br>CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome. This study was registered at clinicaltrials.gov as NCT03301753.}, }
@article {pmid41672513, year = {2026}, author = {Nishijima, S and Hattori, M and Nagata, N}, title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {102}, number = {2}, pages = {82-103}, pmid = {41672513}, issn = {1349-2896}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Health ; Japan ; Metagenomics ; Metagenome ; *Disease ; East Asian People ; }, abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.}, }
@article {pmid41673004, year = {2026}, author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C}, title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41673004}, issn = {2052-4463}, mesh = {*Metagenome ; *Geologic Sediments/microbiology ; Metagenomics ; *Microbiota ; Bacteria/classification/genetics ; }, abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.}, }
@article {pmid41673107, year = {2026}, author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG}, title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41673107}, issn = {2045-2322}, mesh = {Animals ; Mice ; *Lupus Erythematosus, Systemic/pathology/immunology/microbiology/genetics ; *Gastrointestinal Microbiome ; *Inflammation/pathology ; Mice, Knockout ; Dysbiosis ; Disease Models, Animal ; Female ; Autoimmunity ; Efferocytosis ; Autoimmune Diseases ; }, abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.}, }
@article {pmid41673713, year = {2026}, author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ}, title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {65}, pmid = {41673713}, issn = {2049-2618}, support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Biofilms/growth &amp; development ; *Ice Cover/microbiology ; *Droughts ; *Rivers/microbiology ; Diatoms/genetics/physiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; Multiomics ; Switzerland ; Cyanobacteria/genetics/classification ; }, abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.<br><br>RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103&#xa0;days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6&#xa0;h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24&#xa0;h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24&#xa0;h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.<br><br>CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.}, }
@article {pmid41674272, year = {2026}, author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K}, title = {An ensemble binning approach to identify functional diversity in cleanroom environments.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {384}, number = {2314}, pages = {}, doi = {10.1098/rsta.2024.0438}, pmid = {41674272}, issn = {1471-2962}, support = {//UK Space Agency/ ; }, mesh = {*Environment, Controlled ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; Metagenomics/methods ; *Ecological Systems, Closed ; Spacecraft ; }, abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.}, }
@article {pmid41678593, year = {2026}, author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH}, title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.}, journal = {Circulation research}, volume = {138}, number = {4}, pages = {e326978}, pmid = {41678593}, issn = {1524-4571}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; Multiomics ; *Heart Diseases/metabolism/therapy/microbiology ; }, abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.}, }
@article {pmid41679417, year = {2026}, author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J}, title = {Female reproductive microbiome in fertility care.}, journal = {Fertility and sterility}, volume = {125}, number = {4}, pages = {558-573}, doi = {10.1016/j.fertnstert.2026.02.015}, pmid = {41679417}, issn = {1556-5653}, mesh = {Humans ; Female ; *Microbiota/physiology ; *Fertility ; *Infertility, Female/microbiology/therapy/diagnosis/physiopathology ; *Genitalia, Female/microbiology ; *Bacteria/genetics/classification ; }, abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. Although conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of the methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multiomics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads vs. relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches on the basis of clinical context and discuss emerging technologies, including multiomics integration for implementing microbiome assessment in fertility care.}, }
@article {pmid41679496, year = {2026}, author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y}, title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {123973}, doi = {10.1016/j.envres.2026.123973}, pmid = {41679496}, issn = {1096-0953}, mesh = {*Microplastics/toxicity/analysis ; *Rivers/microbiology ; *Seawater/microbiology ; Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Biofilms ; *Water Microbiology ; }, abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.}, }
@article {pmid41679750, year = {2026}, author = {Lamont, RF and Jørgensen, JS}, title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {133}, number = {6}, pages = {1129-1146}, doi = {10.1111/1471-0528.70173}, pmid = {41679750}, issn = {1471-0528}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota ; *Vaginosis, Bacterial/microbiology/complications ; Pregnancy ; *Premature Birth/prevention &amp; control/microbiology ; *Dysbiosis/microbiology/complications ; Probiotics/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.<br><br>METHODOLOGY: A narrative review.<br><br>RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.}, }
@article {pmid41679819, year = {2026}, author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M}, title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124886}, doi = {10.1016/j.carbpol.2026.124886}, pmid = {41679819}, issn = {1879-1344}, mesh = {*Galactans/chemistry/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Solubility ; Probiotics ; }, abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.}, }
@article {pmid41680567, year = {2026}, author = {Chen, L and Hong, C and Xie, Y}, title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {76}, pmid = {41680567}, issn = {1720-8319}, mesh = {Aged ; Humans ; *Gastrointestinal Microbiome/physiology ; Muscle Strength ; Probiotics/therapeutic use ; *Sarcopenia/microbiology/therapy/physiopathology ; Systematic Reviews as Topic ; Meta-Analysis as Topic ; }, abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.}, }
@article {pmid41683205, year = {2026}, author = {Yu, W and Tang, K and An, R and Ma, S and Tan, H and Chen, M}, title = {Study on Association Between Gut Microbiota, Serum Metabolism and Gestational Diabetes Mellitus Based on Metagenomic and Metabolomics Analysis.}, journal = {Nutrients}, volume = {18}, number = {3}, pages = {}, pmid = {41683205}, issn = {2072-6643}, mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/blood/metabolism ; Pregnancy ; Case-Control Studies ; Adult ; *Metabolomics ; *Gastrointestinal Microbiome/physiology ; *Metagenomics ; Feces/microbiology ; Pregnancy Trimester, First ; }, abstract = {Background/Objectives: This study aimed to explore the association between maternal gut microbiota and metabolic profiles in the first trimester and the subsequent risk of gestational diabetes mellitus (GDM), as well as to characterize association patterns linking gut microbiota, serum metabolites, and metabolic traits. Methods: A nested case-control study was conducted among women with GDM (n = 47) and those without GDM (n = 94). Metagenomic sequencing was applied to analyze fecal microbiota, and liquid chromatography-mass spectrometry (LC-MS) was used for non-targeted plasma metabolomics. Differential microbiota and metabolites between groups were identified, and correlation analyses were conducted to assess their associations with clinical indicators. Results: Women who later developed GDM showed lower alpha diversity and higher beta diversity. Eleven differential species were identified, with Collinsella aerofaciens and Clostridium bartlettii enriched in GDM, while nine species such as Alistipes putredinis and Bacteroidales bacterium ph8 were enriched in controls. Sixty-four plasma metabolites differed between groups, including increased glycerol-3-phosphate, aromatic amino acids, and glycerophosphocholine, and decreased cysteine, tryptophan, niacinamide, and stearic acid. Correlation analyses revealed significant relationships between Alistipes putredinis, Eubacterium eligens, and Bacteroidales bacterium ph8 with metabolic and clinical indicators (e.g., TG, TC, LDL). Conclusions: In this nested case-control study, women who later developed GDM exhibited reduced gut microbial diversity and altered metabolic profiles during the first trimester of pregnancy. Several microbial taxa and microbiota-metabolite associations were observed in relation to subsequent GDM status, highlighting early-pregnancy microbial and metabolic features that may be relevant to GDM-related metabolic changes.}, }
@article {pmid41683346, year = {2026}, author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH}, title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.}, journal = {Nutrients}, volume = {18}, number = {3}, pages = {}, pmid = {41683346}, issn = {2072-6643}, mesh = {Humans ; Pilot Projects ; Adult ; Male ; Female ; Double-Blind Method ; *Dietary Supplements ; *Respiratory Tract Infections/prevention &amp; control/immunology ; *Exercise/physiology ; *Stress, Physiological/drug effects ; Young Adult ; *Immunoglobulins/administration &amp; dosage ; Gastrointestinal Microbiome/drug effects ; Biomarkers/blood ; }, abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.<br><br>METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.<br><br>RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.<br><br>CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.}, }
@article {pmid41684743, year = {2025}, author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL}, title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1729196}, pmid = {41684743}, issn = {2235-2988}, mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics ; Chile ; *Biofilms/growth &amp; development ; Female ; Microbiota ; DNA, Bacterial/genetics ; Male ; Middle Aged ; Sequence Analysis, DNA ; Aged ; Bone and Bones/microbiology ; }, abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.<br><br>METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and comple