@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.},
}

Humans
*Gout/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Metagenome
*Dysbiosis/microbiology
Bacteria/genetics/classification
Biodiversity

@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 & 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 & 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.

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.

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.},
}

Animals
Symbiosis
*Microbiota
*Gossypium/parasitology
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Hemiptera/microbiology/growth & development

@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 & 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.},
}

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 & derivatives
Mice, Transgenic
Middle Aged
Aged
Cyclic AMP Response Element Modulator/genetics/metabolism

@article {pmid42675564,
year = {2026},
author = {Akyol, CK and Bilaç, Ö 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.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology
Male
Pilot Projects
*Gastrointestinal Microbiome/physiology
Turkey
Female
Child
Feeding Behavior/physiology
Sleep/physiology

@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 & 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.

METHODS: In the present investigation, healthy participants (n = 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.

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.

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.},
}

Humans
*Probiotics/administration & 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

@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.},
}

*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

@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.},
}

*Multiomics
*Food Microbiology/methods
*Artificial Intelligence
*Food Preservation/methods
*Microbiota
Metabolomics
Metagenomics

@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.},
}

*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

@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.},
}

Animals
*Rumen/microbiology
*Methane/metabolism
Cattle
*Metabolome
*Pichia/physiology/metabolism
Female
*Microbiota
Lactation
Animal Feed/analysis
Bacteria/classification/genetics/metabolism
Multiomics

@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.},
}

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

@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 & 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.

METHODS: Mice were administered rabeprazole (Rab) for 4 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.

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-β-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.

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.},
}

Animals
*Proton Pump Inhibitors/adverse effects
*Stem Cells/pathology/drug effects
*Intestines/pathology/injuries
*Lithocholic Acid/analogs & 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

@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.},
}

*Denitrification/genetics
*Metagenome
Aquatic Organisms/genetics
Anaerobiosis
*Microbiota
*Bays/chemistry/microbiology
*Bacteria/genetics/metabolism
Seawater/chemistry/microbiology

@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 & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
mesh = {Humans ; *Zinc/administration & 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.},
}

Humans
*Zinc/administration & dosage
*Pennisetum/chemistry
Infant
*Iron
*Gastrointestinal Microbiome/drug effects
Female
Male
*Food, Fortified
*Infant Nutritional Physiological Phenomena
Dietary Supplements
Feces/microbiology

@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 & 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.},
}

*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Glucans/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Multiomics
Microbiota/genetics
Phylogeny
Glycoside Hydrolases/metabolism/genetics

@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.

METHODS: Preoperative stool samples were collected from 131 women (median age 59) with benign (n = 23), high-risk/non-invasive (n = 47), or malignant (n = 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.

RESULTS: α-diversity differed across diagnosis groups and inversely correlated with increasing BMI (Inverse Simpson p = 0.025). β-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.

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.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Female
*Breast Neoplasms/pathology/microbiology/etiology
*Body Mass Index
Middle Aged
*Gastrointestinal Microbiome
*Obesity/complications/microbiology
Aged
Adult
Metagenomics/methods
Metagenome

@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 & purification ; *Fungi/classification/genetics/isolation & 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.},
}

Animals
Bees/microbiology
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
Species Specificity
Metagenomics
Phylogeny
Biodiversity
*Mycobiome

@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. & 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.},
}

*Microbiota/physiology
*Kelp/microbiology
*Metabolome
*Coral Reefs
Ecosystem
Climate Change

@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 & 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 & Human Services | National Institutes of Health (NIH)/ ; P30 DK043351//U.S. Department of Health & 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.},
}

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

@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 & control/pathology ; Mice ; *Catechin/metabolism/analogs & 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.},
}

Animals
*Cholesterol/metabolism
*Sterol Regulatory Element Binding Protein 2/metabolism/genetics
*Colorectal Neoplasms/metabolism/microbiology/prevention & control/pathology
Mice
*Catechin/metabolism/analogs & derivatives
Humans
*Eubacteriales/metabolism/physiology
*Carcinogenesis/metabolism
Gastrointestinal Microbiome
Mice, Inbred C57BL
Feces/microbiology/chemistry

@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.},
}

*Soil Microbiology
*Nitrogen/analysis/metabolism
China
*Microbiota
*Biodiversity
Forests
Grassland
Metagenomics
Nitrogen Cycle
Soil/chemistry
Bacteria

@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.},
}

*Systems Biology/methods
*Lignin/metabolism/chemistry
Microbial Consortia
Bacteria/metabolism

@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 & purification/metabolism ; *Cultured Milk Products/microbiology/analysis ; Lactobacillales/metabolism/genetics/isolation & 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.},
}

Animals
Metagenomics
Fermentation
Metabolomics
*Microbiota
Horses
*Milk/microbiology/chemistry/metabolism
*Bacteria/genetics/classification/isolation & purification/metabolism
*Cultured Milk Products/microbiology/analysis
Lactobacillales/metabolism/genetics/isolation & purification/classification
Female
Antioxidants/metabolism/analysis

@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 & 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 & 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.},
}

Animals
Mice
Humans
*Programmed Cell Death 1 Receptor/antagonists & 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 & purification/metabolism
Cell Line, Tumor
Female
*Immune Checkpoint Inhibitors/therapeutic use
Mice, Inbred C57BL
CD8-Positive T-Lymphocytes/immunology

@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 & 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.},
}

Animals
*Carps/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & 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

@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//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César 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 & 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.

RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + 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 + 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 < 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.

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.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Feces/microbiology
Metagenomics/methods
French Guiana
*Metals/pharmacology
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
*Drug Resistance, Microbial/genetics
Metagenome

@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 & 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.},
}

Biodegradation, Environmental
*Microplastics/metabolism
*Composting
*Polymers/metabolism/chemistry
*Bacteria/metabolism/genetics/classification/isolation & purification
Polyesters/metabolism
*Microbiota
Soil Microbiology

@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&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.},
}

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

@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 & purification/metabolism ; Metagenomics ; *Fungi/genetics/classification/isolation & purification/metabolism ; Viruses/genetics/classification/isolation & 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.},
}

*Cacao/microbiology/virology
Colombia
Fermentation
*Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics
*Fungi/genetics/classification/isolation & purification/metabolism
Viruses/genetics/classification/isolation & purification
*Microbiota
Desiccation
*Metagenome
Food, Processed
Food Microbiology

@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 & 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.},
}

*Bacillus/genetics/isolation & purification/classification
Italy
Phylogeny
Microbiota
Humans
RNA, Ribosomal, 16S/genetics

@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 & 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.},
}

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 & purification

@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.},
}

*Polyethylene Terephthalates/metabolism
*Microbiota
*Hydrolases/metabolism/genetics
Metagenomics
Biodegradation, Environmental
*Bacteria/enzymology/genetics/metabolism
Biocatalysis
Protein Engineering

@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 & 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.

METHODS: Our data included 1,228 adults aged 25-64 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.

RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 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 (< 0.0001).

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.},
}

Humans
*Life Style
Female
*Colorectal Neoplasms/microbiology/epidemiology/etiology
Middle Aged
Male
Adult
*Gastrointestinal Microbiome/genetics
Risk Factors
Metagenomics/methods
Finland/epidemiology
Metagenome
Diet

@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.

OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.

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.

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 K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.

CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ 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.},
}

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

@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.},
}

*Estuaries
*Microplastics/analysis
*Microbiota
India
Metagenomics
*Water Pollutants, Chemical/analysis/toxicity
Environmental Monitoring
High-Throughput Nucleotide Sequencing
*Metagenome
Bacteria/genetics

@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//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2023-0380//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2025-02673//Vetenskapsrådet (Swedish Research Council)/ ; 2022-01460//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784//Vetenskapsrådet (Swedish Research Council)/ ; Strategic Research Area Exodiab 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00989//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; IRC-0067//Stiftelsen för 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.},
}

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

@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 & 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.

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.

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.},
}

Animals
*Gastrointestinal Microbiome/genetics/immunology
Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Animals, Wild/microbiology/immunology

@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.},
}

Humans
*Cholangiocarcinoma/diagnosis/microbiology
*Bile Duct Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome/genetics/physiology
*Bifidobacterium
Feces/microbiology
Male
Dysbiosis/microbiology
Female
Metagenomics
China
Middle Aged

@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.},
}

Animals
*Polysaccharides/pharmacology/metabolism
*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/drug effects/physiology
*Bacteriophages/physiology/genetics
Mice
*Bacteria/virology
Humans
Metagenome
Virome

@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 & 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.},
}

*Rivers/microbiology
Bacteria
Atmosphere
Fungi
*Microbiota

@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 & 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.},
}

Volatile Organic Compounds/analysis/metabolism
*Microbiota
*Cheese/microbiology/analysis
Multiomics
Gas Chromatography-Mass Spectrometry
Bacteria/classification/genetics/isolation & purification/metabolism

@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.},
}

*Triazoles/metabolism
Biodegradation, Environmental
*Microbiota
*Microbial Consortia
*Bacteria/metabolism/genetics
Bioreactors/microbiology
Sewage/microbiology

@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.

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.

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).

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.},
}

*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome
Humans
*Non-alcoholic Fatty Liver Disease/microbiology
*Fatty Liver/microbiology
Species Specificity
Bacteria/classification

@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 & 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.

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.

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.},
}

*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 & purification/metabolism
Fatty Acids, Volatile/metabolism

@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 & 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.},
}

*Seawater/microbiology
Metagenomics
Biodegradation, Environmental
*Bacteria/metabolism/classification/genetics
*Microbiota
*Biodegradable Plastics/metabolism
Gene Expression Profiling
*Plastics/metabolism
Cellulose/metabolism/analogs & derivatives

@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.},
}

Animals
*Oligochaeta/microbiology
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Soil Microbiology
*Metagenomics/methods
*Microbiota/genetics

@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& 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.

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.

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 ± 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).

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.},
}

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

@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.},
}

Anaerobiosis
Methane/biosynthesis/metabolism
Bioreactors/microbiology
*Microbial Consortia/physiology
Fatty Acids, Volatile/metabolism
Food Loss and Waste

@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 & 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.

OBJECTIVES: We aimed to determine whether soluble corn fiber (SCF) improved cognition and altered fecal microbiota and fermentation end products in adults.

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.

RESULTS: SCF improved reaction times (RT) during congruent (β = -9.8 ms, 95% confidence interval (CI): -18.4, -1.2, false discovery rate (FDR) P = 0.01) and incongruent (β = -14.2 ms, 95% CI: -22.8, -5.6, FDR P = 0.003) flanker trials and increased Parabacteroides (∼4-fold, β = 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 (ρ = -0.33) and propionate (ρ = -0.36), whereas Parabacteroides was marginally positively associated with acetate (ρ = 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.

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).},
}

Aged
Female
Humans
Male
Middle Aged
Cognition/drug effects
Cross-Over Studies
*Dietary Fiber/pharmacology/administration & dosage
Double-Blind Method
*Executive Function/drug effects
Feces/microbiology
Fermentation
*Gastrointestinal Microbiome/drug effects
*Zea mays/chemistry

@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.},
}

Humans
Female
*Amniotic Fluid/virology
Pregnancy
*Virome/genetics
Phylogeny
Adult
China
Metagenomics
*Maternal Health
Case-Control Studies
Health Status

@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 & 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.

RESULTS: We introduce Pilea (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.

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.},
}

*Bacteria/growth & development/genetics/classification
*Metagenome
Software
*Metagenomics/methods
*Computational Biology/methods
Microbiota

@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.},
}

Animals
Biotransformation
*Stress, Physiological
*Gastrointestinal Microbiome/physiology
Fermentation
Mice
*Metabolic Networks and Pathways
Metabolomics/methods
Lactiplantibacillus plantarum/metabolism

@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 & dosage ; Oryza ; Pea Proteins/administration & dosage ; *Plant Proteins/administration & 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.

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.

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.

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.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Dietary Supplements
Male
Whey Proteins/administration & dosage
Oryza
Pea Proteins/administration & dosage
*Plant Proteins/administration & dosage
Young Adult
*Athletes
Animals
Resistance Training
Adult
Bacteria/classification/metabolism
Soccer
RNA, Ribosomal, 16S/genetics
*Football

@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).},
}

Biodegradation, Environmental
*Pesticides/metabolism
*Microbial Consortia
*Soil Pollutants/metabolism
Soil Microbiology

@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 & 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.},
}

Metagenomics
*Microbiota
Superoxide Dismutase/metabolism
Food Microbiology
Glycosyltransferases/genetics/metabolism
Bacteria/genetics/classification/isolation & purification
Pseudomonas/genetics
Malondialdehyde/metabolism

@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 & 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.},
}

RNA, Ribosomal, 16S/genetics
*Microbiota
*Zea mays/microbiology
Soil Microbiology
Rhizosphere
Fusarium/physiology
*Stress, Physiological
*Bacteria/classification/genetics/isolation & purification
Plant Roots/microbiology
Plant Diseases/microbiology
Sequence Analysis, DNA
Metagenomics/methods
DNA, Bacterial/genetics
Plant Stems/microbiology

@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.

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.

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.

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.},
}

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

@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.

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.

RESULTS: The α-diversity and β-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the α-diversity (Shannon index) and β-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.

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.},
}

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

@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 & 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.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
Brazil
*Metagenomics
*Culicidae/virology
Phylogeny
Female
Genome, Viral
*Virome/genetics
High-Throughput Nucleotide Sequencing
*Mosquito Vectors/virology

@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.

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.},
}

Humans
*Metagenome
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Cohort Studies
Genetic Variation
*Bacteria/genetics/classification
Genome, Bacterial

@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.},
}

*Composting/methods
*Microbiota
*Drug Resistance, Microbial/genetics
Lignin/metabolism
Bacteria/metabolism/genetics

@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 Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
mesh = {Animals ; Bees/microbiology/classification ; *Gastrointestinal Microbiome ; Phylogeny ; *Bacteria/classification/genetics/isolation & 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.},
}

Animals
Bees/microbiology/classification
*Gastrointestinal Microbiome
Phylogeny
*Bacteria/classification/genetics/isolation & purification
Sympatry
RNA, Ribosomal, 16S/genetics

@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.

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-γ⁺ CD8⁺ 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⁺ CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.

CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8⁺ 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.},
}

*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

@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 & 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.

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 (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.

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.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
*Metabolome
Age Factors
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Police
Male
Aging
Metagenome
Female
Feces/microbiology

@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.

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 >95% completeness and <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 ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

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.},
}

*Metagenome
*Metagenomics/methods
*Metadata
Molecular Sequence Annotation
*Microbiota/genetics
*Databases, Genetic
*Bacteria/classification/genetics
Computational Biology/methods
Biocuration

@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 & 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.},
}

*Metagenomics/methods
Autoencoder
Humans
*Software
Microbiota/genetics
Generative Adversarial Networks
Algorithms
Generative Artificial Intelligence
Metagenome

@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 & 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.},
}

Animals
*Mucins/metabolism
Humans
*Gastrointestinal Microbiome
Metagenome
Feces/microbiology
Cell Cycle Proteins/metabolism
Cohesins
Bacterial Proteins/metabolism/genetics
*Eubacteriales/metabolism/genetics/isolation & purification/classification
Animals, Domestic/microbiology

@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 & 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.},
}

Humans
Female
*Candidiasis, Vulvovaginal/microbiology
*Microbiota
*Vagina/microbiology
Adult
Case-Control Studies
Lactobacillus/isolation & purification/genetics
Recurrence
Prevotella

@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 & 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.},
}

*Quaternary Ammonium Compounds/pharmacology
*Acinetobacter/drug effects/genetics/isolation & purification/physiology
*Disinfectants/pharmacology
Biofilms/drug effects
*Microbiota/drug effects
Seasons
Drug Resistance, Bacterial

@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 Spéciaux 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 Spéciaux de Recherche/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Actinobacteria/isolation & purification/genetics/classification ; *Corynebacterium/isolation & 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.},
}

Adult
Female
Humans
Male
Middle Aged
*Actinobacteria/isolation & purification/genetics/classification
*Corynebacterium/isolation & purification/genetics/classification
*COVID-19/microbiology/complications
Longitudinal Studies
Microbiota
*Nasopharynx/microbiology
*Post-Acute COVID-19 Syndrome/microbiology
SARS-CoV-2/physiology

@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.

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.

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.

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.},
}

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

@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.},
}

*Ammonia/metabolism
Animals
*Citric Acid Cycle
*Composting/methods
Chickens
Nitrogen/metabolism
Isocitrate Dehydrogenase/metabolism
*Microbiota

@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 & 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.},
}

India
*Wastewater/microbiology
*Metagenomics/methods
Cities
*Metagenome/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Interspersed Repetitive Sequences/genetics
*Drug Resistance, Microbial/genetics
Microbiota/genetics

@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.

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.

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.},
}

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

@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 & 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.

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.

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.},
}

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 & purification/metabolism
Fermentation

@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 & 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.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
Multiomics
Metagenomics
*Gastrointestinal Microbiome/physiology
Animals
Diet
Metabolomics
Bacteria/classification/genetics/isolation & purification/metabolism

@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.},
}

Animals
*Chickens/genetics/physiology/microbiology
*Hybrid Vigor
Female
*Oxidative Phosphorylation
Multiomics
*Gastrointestinal Microbiome
Animal Feed/analysis

@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.

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 mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10 mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.

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.

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.},
}

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

@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 & 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.

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-β1 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.

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-β1 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-β1 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-β1.

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-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.},
}

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

@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.},
}

Humans
*Artificial Intelligence
Proteomics
*Eating
*Diet
Gastrointestinal Microbiome
Nutrition Assessment

@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 & 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.},
}

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 & purification
Metagenomics
Middle Aged
Aged
Microscopy, Electron, Transmission
Anti-Bacterial Agents/pharmacology
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@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.

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.

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.

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.},
}

Humans
*Microbiota
*Urologic Diseases/microbiology/diagnosis
Dysbiosis/microbiology
Male
*Urinary Tract/microbiology
Metagenomics
RNA, Ribosomal, 16S/genetics
*Urine/microbiology

@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 & 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.},
}

*Ecosystem
*Fresh Water/microbiology
Metagenome
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
*Lakes/microbiology
Transcriptome
Water Microbiology

@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.},
}

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

@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.},
}

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

@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.},
}

Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
Bioreactors/microbiology
*Wastewater/microbiology/chemistry
Pharmaceutical Preparations/metabolism
*Bacteria/metabolism/genetics
Microbial Consortia
Waste Disposal, Fluid
Adaptation, Physiological

@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.},
}

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

@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.

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.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin 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.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

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

@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 & 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.

METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥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.

RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, P = 0.005); mucosal diversity showed no difference (P = 0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, P = 0.14; mucosal: 3.40 vs. 3.72, P = 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.

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.},
}

Humans
*Colitis, Ulcerative/microbiology
Feces/microbiology
Prospective Studies
*Klebsiella/isolation & purification/genetics/physiology
Female
Severity of Illness Index
Male
Adult
Middle Aged
*Gastrointestinal Microbiome
Intestinal Mucosa/microbiology

@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 & purification ; Metagenome ; *Mouth/microbiology ; Dysbiosis/microbiology ; Treponema/genetics/isolation & 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.},
}

Humans
Metagenomics
*Microbiota/genetics
*Noma/microbiology
*Saliva/microbiology
RNA, Ribosomal, 16S/genetics
Child
Female
Male
*Bacteria/classification/genetics/isolation & purification
Metagenome
*Mouth/microbiology
Dysbiosis/microbiology
Treponema/genetics/isolation & purification
Shotgun Sequencing
Child, Preschool

@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.},
}

Humans
*Biological Products/metabolism/chemistry
*Microbiota
*Mouth/microbiology
Peptide Synthases/metabolism/genetics
Polyketide Synthases/metabolism/genetics
Multigene Family
*Bacteria/metabolism/genetics

@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.},
}

*Sulfur/metabolism
*Microbiota
*Nitrogen Cycle
*Coral Reefs
Bacteria/genetics/metabolism
China
Archaea/genetics/metabolism
*Nitrogen/metabolism
Seawater/microbiology

@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.

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.

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 < 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.

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.},
}

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