@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
mesh = {*Sulfamethoxazole/toxicity ; *Soil Microbiology ; *Herbicides/toxicity ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Agroecology ; Bacteria/drug effects/metabolism/genetics ; *Anti-Bacterial Agents ; },
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}

*Sulfamethoxazole/toxicity
*Soil Microbiology
*Herbicides/toxicity
*Nitrogen/metabolism
*Toluidines/toxicity
*Soil Pollutants/toxicity
*Drug Resistance, Microbial/genetics
*Microbiota/drug effects
Agroecology
Bacteria/drug effects/metabolism/genetics
*Anti-Bacterial Agents

@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3801},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Asian People ; Aged ; East Asian People ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
Female
Male
*Myositis/microbiology
Middle Aged
Adult
China
Feces/microbiology
Metagenomics/methods
Dysbiosis/microbiology
Bacteria/genetics/classification
Virome
Machine Learning
Case-Control Studies
Metagenome
Asian People
Aged
East Asian People

@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {56},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
mesh = {Animals ; *Heteroptera/microbiology/physiology/classification ; *Gastrointestinal Microbiome ; *Predatory Behavior ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Proteobacteria/isolation & purification/classification/genetics ; Adaptation, Physiological ; Biological Evolution ; Enterococcus/isolation & purification/genetics/classification ; Serratia/isolation & purification/genetics ; Bacillota/isolation & purification/genetics/classification ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

Animals
*Heteroptera/microbiology/physiology/classification
*Gastrointestinal Microbiome
*Predatory Behavior
*Bacteria/classification/genetics/isolation & purification
Symbiosis
Phylogeny
Proteobacteria/isolation & purification/classification/genetics
Adaptation, Physiological
Biological Evolution
Enterococcus/isolation & purification/genetics/classification
Serratia/isolation & purification/genetics
Bacillota/isolation & purification/genetics/classification

@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/analysis/metabolism ; *Seawater/microbiology/chemistry ; Metagenomics ; Pacific Ocean ; *Metagenome ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Photosynthesis ; Chlorophyll/analysis ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}

*Oxygen/analysis/metabolism
*Seawater/microbiology/chemistry
Metagenomics
Pacific Ocean
*Metagenome
*Microbiota/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Photosynthesis
Chlorophyll/analysis

@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Carbon/metabolism ; *Nitrogen/metabolism ; Iceland ; *Thermus/metabolism/genetics/growth & development ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}

*Hot Springs/microbiology
*Carbon/metabolism
*Nitrogen/metabolism
Iceland
*Thermus/metabolism/genetics/growth & development
Nitrogen Fixation
Carbon Dioxide/metabolism

@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/epidemiology/metabolism/etiology ; *Fatty Acids, Volatile/metabolism/analysis ; *Gastrointestinal Microbiome ; Indonesia/epidemiology ; *Liver Cirrhosis/complications ; *Brain/metabolism ; *Liver/metabolism ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}

Humans
*Hepatic Encephalopathy/epidemiology/metabolism/etiology
*Fatty Acids, Volatile/metabolism/analysis
*Gastrointestinal Microbiome
Indonesia/epidemiology
*Liver Cirrhosis/complications
*Brain/metabolism
*Liver/metabolism

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; *Dysbiosis/virology/complications/microbiology ; Animals ; *Primary Ovarian Insufficiency/microbiology/virology/therapy/etiology ; Humans ; *Gastrointestinal Microbiome ; Rats ; *Virome ; Adult ; Fecal Microbiota Transplantation ; Feces/virology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Ovary/physiopathology ; Young Adult ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
*Dysbiosis/virology/complications/microbiology
Animals
*Primary Ovarian Insufficiency/microbiology/virology/therapy/etiology
Humans
*Gastrointestinal Microbiome
Rats
*Virome
Adult
Fecal Microbiota Transplantation
Feces/virology/microbiology
Bacteria/classification/genetics/isolation & purification
Ovary/physiopathology
Young Adult

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Hyperuricemia/microbiology ; *Overweight/microbiology ; Female ; Male ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Adult ; Middle Aged ; *Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Hyperuricemia/microbiology
*Overweight/microbiology
Female
Male
Cross-Sectional Studies
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Adult
Middle Aged
*Metagenomics
Metagenome

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0305125},
pmid = {41504449},
issn = {2165-0497},
support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle/metabolism ; *Rumen/microbiology/metabolism ; Female ; *Dietary Fiber/metabolism ; *Animal Feed/analysis ; Fermentation ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Poaceae/metabolism ; Mongolia ; Metabolomics ; Digestion ; Fungi/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

Animals
Cattle/metabolism
*Rumen/microbiology/metabolism
Female
*Dietary Fiber/metabolism
*Animal Feed/analysis
Fermentation
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
*Poaceae/metabolism
Mongolia
Metabolomics
Digestion
Fungi/classification/genetics/isolation & purification/metabolism
Gastrointestinal Microbiome

@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}

*Methane/metabolism
*Plant Bark/microbiology
Australia
*Microbiota
*Forests
*Hydrogen/metabolism
Carbon Monoxide/metabolism
Metagenomics
*Trees/microbiology
*Bacteria/metabolism/genetics/classification
Anaerobiosis

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
mesh = {China ; *Geologic Sediments/microbiology ; *Wetlands ; Aquaculture ; *Microbiota ; Bacteria/classification/genetics ; *Environmental Restoration and Remediation ; Ponds/microbiology ; },
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}

China
*Geologic Sediments/microbiology
*Wetlands
Aquaculture
*Microbiota
Bacteria/classification/genetics
*Environmental Restoration and Remediation
Ponds/microbiology

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {415-428},
pmid = {41507585},
issn = {2058-5276},
support = {K99 AA031328/AA/NIAAA NIH HHS/United States ; R21 AA030654/AA/NIAAA NIH HHS/United States ; R01 AA020098/AA/NIAAA NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R00 AA031328/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Ethanol/metabolism ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metabolic Networks and Pathways/genetics ; Male ; Fermentation ; Female ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics/isolation & purification ; Metagenomics ; Middle Aged ; Metabolomics ; Adult ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

Humans
*Ethanol/metabolism
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/genetics
Cohort Studies
Metabolic Networks and Pathways/genetics
Male
Fermentation
Female
Fecal Microbiota Transplantation
Escherichia coli/metabolism/genetics/isolation & purification
Metagenomics
Middle Aged
Metabolomics
Adult

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {126},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Animal Husbandry/methods ; *Drug Resistance, Bacterial ; Farms ; *Anti-Infective Agents/pharmacology ; Soil Microbiology ; Shotgun Sequencing ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

Animals
*Chickens/microbiology
*Microbiota/drug effects/genetics
*Bacteria/drug effects/genetics/classification/isolation & purification
*Anti-Bacterial Agents/pharmacology
Animal Husbandry/methods
*Drug Resistance, Bacterial
Farms
*Anti-Infective Agents/pharmacology
Soil Microbiology
Shotgun Sequencing

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {130},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Retrospective Studies ; Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; *Lung/microbiology ; Aged ; Nontuberculous Mycobacteria/genetics/isolation & purification ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Middle Aged ; Mycobacterium tuberculosis/genetics/isolation & purification ; Bacilloscopy ; *Tuberculosis, Pulmonary/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

Retrospective Studies
Humans
*Bronchoalveolar Lavage Fluid/microbiology
Female
Male
*Lung/microbiology
Aged
Nontuberculous Mycobacteria/genetics/isolation & purification
*Microbiota
High-Throughput Nucleotide Sequencing
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Middle Aged
Mycobacterium tuberculosis/genetics/isolation & purification
Bacilloscopy
*Tuberculosis, Pulmonary/microbiology
Metagenomics

@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Feces/microbiology ; Female ; Prospective Studies ; *Gastrointestinal Microbiome/genetics ; Male ; Australia ; *Specimen Handling/methods ; Middle Aged ; Aged ; Occult Blood ; Surveys and Questionnaires ; Adult ; Metagenomics/methods ; *Neoplasms/microbiology ; Whole Genome Sequencing ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}

Humans
Pilot Projects
*Feces/microbiology
Female
Prospective Studies
*Gastrointestinal Microbiome/genetics
Male
Australia
*Specimen Handling/methods
Middle Aged
Aged
Occult Blood
Surveys and Questionnaires
Adult
Metagenomics/methods
*Neoplasms/microbiology
Whole Genome Sequencing

@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Geologic Sediments/virology ; *Lakes/virology ; Tibet ; *DNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; Metagenomics ; Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}

*Geologic Sediments/virology
*Lakes/virology
Tibet
*DNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
Metagenomics
Biodiversity
Metagenome

@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {1998-2011},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
mesh = {*Iron/metabolism/analysis ; *Plant Roots/microbiology/metabolism/growth & development/genetics ; *Microbiota ; *Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology ; *Citrus/microbiology/metabolism/growth & development/genetics ; Bacteria/genetics/isolation & purification/classification/metabolism ; Rhizosphere ; Fertilizers/analysis ; *Proline/analogs & derivatives/metabolism ; Soil Microbiology ; },
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}

*Iron/metabolism/analysis
*Plant Roots/microbiology/metabolism/growth & development/genetics
*Microbiota
*Azetidinecarboxylic Acid/analogs & derivatives/metabolism/pharmacology
*Citrus/microbiology/metabolism/growth & development/genetics
Bacteria/genetics/isolation & purification/classification/metabolism
Rhizosphere
Fertilizers/analysis
*Proline/analogs & derivatives/metabolism
Soil Microbiology

@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
support = {INV-044643/GATES/Gates Foundation/United States ; },
mesh = {Animals ; *Feces/microbiology ; *Marsupialia/microbiology ; Phylogeny ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}

Animals
*Feces/microbiology
*Marsupialia/microbiology
Phylogeny
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Metagenome
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics

@article {pmid41511111,
year = {2026},
author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M},
title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0140525},
pmid = {41511111},
issn = {2379-5077},
support = {82571963//National Natural Science Foundation of China/ ; 2025A1515012162, 2024A1515010590//Natural Science Foundation of Guangdong Province/ ; JCYJ20250604145739052 and JCYJ20240813144117023//Shenzhen Science and Technology Program/ ; Y2024001//Resear Initaion Fund of Longgang District Maternity & Child Healthcare Hospital of Shenzhen City/ ; Postdoctoral fellow stationed in Shenzhen second batch in 2022//Shenzhen Municipal Human Resources and Social Security Bureau/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/metabolism/etiology/virology/genetics ; Male ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; *Jaundice, Neonatal/metabolism/complications/genetics/virology ; *Machine Learning ; *Metagenome ; Bile Acids and Salts/metabolism ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Feces/microbiology ; Infant ; Multiomics ; Child, Preschool ; },
abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.

IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.},
}

Humans
*Autism Spectrum Disorder/metabolism/etiology/virology/genetics
Male
Female
Infant, Newborn
*Gastrointestinal Microbiome/genetics
*Jaundice, Neonatal/metabolism/complications/genetics/virology
*Machine Learning
*Metagenome
Bile Acids and Salts/metabolism
*Metabolome
RNA, Ribosomal, 16S/genetics
Metagenomics
Feces/microbiology
Infant
Multiomics
Child, Preschool

@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
pmid = {41512665},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; Cecum/microbiology ; *Poultry Diseases/microbiology/prevention & control ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Ligilactobacillus salivarius/physiology/chemistry ; Amoxicillin/pharmacology ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Random Allocation ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}

Animals
*Chickens
Cecum/microbiology
*Poultry Diseases/microbiology/prevention & control
*Salmonella Infections, Animal/microbiology/prevention & control
*Ligilactobacillus salivarius/physiology/chemistry
Amoxicillin/pharmacology
*Probiotics/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
Random Allocation
Anti-Bacterial Agents/pharmacology

@article {pmid41512751,
year = {2026},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
mesh = {*Biofilms ; *Ecosystem ; Gene Transfer, Horizontal ; *Ships ; *Water Microbiology ; Bacteria/genetics ; },
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}

*Biofilms
*Ecosystem
Gene Transfer, Horizontal
*Ships
*Water Microbiology
Bacteria/genetics

@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
mesh = {Animals ; Bees/drug effects/microbiology/genetics ; *Aflatoxin B1/toxicity ; Transcriptome/drug effects ; Metagenomics ; Oxidative Stress/drug effects ; Gene Expression Profiling ; Microbiota/drug effects ; Apoptosis/drug effects ; Pollen ; },
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}

Animals
Bees/drug effects/microbiology/genetics
*Aflatoxin B1/toxicity
Transcriptome/drug effects
Metagenomics
Oxidative Stress/drug effects
Gene Expression Profiling
Microbiota/drug effects
Apoptosis/drug effects
Pollen

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {39},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology/classification ; Metagenome ; Plant Roots/microbiology ; Soil Microbiology ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

*Plant Leaves/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Salt-Tolerant Plants/microbiology/classification
Metagenome
Plant Roots/microbiology
Soil Microbiology

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41514203},
issn = {1471-2180},
mesh = {Animals ; Cattle/microbiology/growth & development ; Male ; *Animal Feed/analysis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Fermentation ; *Bacteria/classification/genetics/isolation & purification ; *Diet/veterinary ; Metagenomics ; Feces/microbiology ; Weight Gain ; },
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

Animals
Cattle/microbiology/growth & development
Male
*Animal Feed/analysis
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Fermentation
*Bacteria/classification/genetics/isolation & purification
*Diet/veterinary
Metagenomics
Feces/microbiology
Weight Gain

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {60},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; Female ; *Rectum/microbiology ; Milk/metabolism/chemistry ; Lactation ; *Gastrointestinal Microbiome ; Metagenomics ; Purines/metabolism ; *Bacteria/classification/genetics/isolation & purification ; Metabolomics ; Dairying ; Longevity ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

Animals
*Rumen/microbiology
Cattle/microbiology
Female
*Rectum/microbiology
Milk/metabolism/chemistry
Lactation
*Gastrointestinal Microbiome
Metagenomics
Purines/metabolism
*Bacteria/classification/genetics/isolation & purification
Metabolomics
Dairying
Longevity

@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {61},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; Cattle ; Female ; *Stress, Physiological ; Oxidative Stress ; *Gastrointestinal Microbiome/physiology ; Metagenomics/methods ; Milk/metabolism ; Metabolomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Lipolysis ; Archaea/classification/genetics/isolation & purification ; Methanobrevibacter/isolation & purification/genetics ; *Microbiota ; Methane/metabolism ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

Animals
*Rumen/microbiology/metabolism
*Lactation/physiology
Cattle
Female
*Stress, Physiological
Oxidative Stress
*Gastrointestinal Microbiome/physiology
Metagenomics/methods
Milk/metabolism
Metabolomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Lipolysis
Archaea/classification/genetics/isolation & purification
Methanobrevibacter/isolation & purification/genetics
*Microbiota
Methane/metabolism

@article {pmid41514452,
year = {2026},
author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K},
title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {24},
pmid = {41514452},
issn = {2049-2618},
support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium für Forschung, Technologie & Raumfahrt/ ; },
mesh = {*Wastewater/microbiology/virology ; *Bacteria/genetics/classification ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; *Eukaryota/genetics/classification ; Metagenomics ; *Viruses/genetics/classification ; Seasons ; Genetic Variation ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.

RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.

CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.},
}

*Wastewater/microbiology/virology
*Bacteria/genetics/classification
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
*Eukaryota/genetics/classification
Metagenomics
*Viruses/genetics/classification
Seasons
Genetic Variation

@article {pmid41515159,
year = {2025},
author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR},
title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515159},
issn = {2072-6643},
support = {1R01CA291965/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1P30CA016672/NH/NIH HHS/United States ; na/MRA/Melanoma Research Alliance/United States ; R01 CA291965/CA/NCI NIH HHS/United States ; na//MD Anderson Melanoma Moon Shot/ ; na//Andrew Sabin Family Fellowship/ ; },
mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; *Patient Reported Outcome Measures ; Middle Aged ; Aged ; *Gastrointestinal Microbiome ; *Diet ; *Immunotherapy/adverse effects ; Quality of Life ; *Cancer Survivors ; Adult ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Anxiety ; Prospective Studies ; Depression ; Exercise ; },
abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.},
}

Humans
*Melanoma/therapy/drug therapy/psychology
Male
Female
*Patient Reported Outcome Measures
Middle Aged
Aged
*Gastrointestinal Microbiome
*Diet
*Immunotherapy/adverse effects
Quality of Life
*Cancer Survivors
Adult
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
Anxiety
Prospective Studies
Depression
Exercise

@article {pmid41515236,
year = {2025},
author = {Zhang, Z and Wang, S and Sun, G and Pan, D},
title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515236},
issn = {2072-6643},
support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Humans ; Blood Glucose/metabolism ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Dysbiosis ; *Fasting ; *Gastrointestinal Microbiome/physiology ; Intermittent Fasting ; *Probiotics/therapeutic use/administration & dosage ; },
abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.},
}

Animals
Humans
Blood Glucose/metabolism
*Diabetes Mellitus, Type 2/microbiology/therapy
Dysbiosis
*Fasting
*Gastrointestinal Microbiome/physiology
Intermittent Fasting
*Probiotics/therapeutic use/administration & dosage

@article {pmid41516078,
year = {2025},
author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD},
title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516078},
issn = {1422-0067},
support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy ; Multiomics ; Female ; Male ; Adult ; *Gastrointestinal Microbiome ; Biomarkers ; Feces/microbiology ; Middle Aged ; Treatment Outcome ; Micronutrients ; Inflammation/microbiology ; },
abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/therapy
Multiomics
Female
Male
Adult
*Gastrointestinal Microbiome
Biomarkers
Feces/microbiology
Middle Aged
Treatment Outcome
Micronutrients
Inflammation/microbiology

@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R + D + I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Aging ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; Comorbidity ; Aged, 80 and over ; Syndrome ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}

Humans
*Aging
*Gastrointestinal Microbiome/genetics
*Frailty/microbiology
Male
Female
Aged
Comorbidity
Aged, 80 and over
Syndrome

@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; Multiomics ; Bacteria/metabolism ; *Aniline Compounds/metabolism ; Triazines ; },
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}

*Water Pollutants, Chemical/metabolism
*Microbiota
Biodegradation, Environmental
Multiomics
Bacteria/metabolism
*Aniline Compounds/metabolism
Triazines

@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {119},
number = {2},
pages = {778-789},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; //The Boehringer Ingelheim Veterinary Scholars Program/ ; //Kansas State University College of Veterinary Medicine Office of Research/ ; //Kansas State University/ ; //USDA/ ; //Veterinary Research Scholars Programs/ ; },
mesh = {Animals ; *Microbiota ; *Animal Feed/microbiology ; *Bacteria/isolation & purification/classification ; *Calliphoridae/microbiology ; Farms ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}

Animals
*Microbiota
*Animal Feed/microbiology
*Bacteria/isolation & purification/classification
*Calliphoridae/microbiology
Farms

@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
mesh = {Animals ; *Liver/metabolism ; *Circadian Rhythm ; *Hyperlipidemias/metabolism/genetics ; Mice ; Male ; Gastrointestinal Microbiome ; Multiomics ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Transcriptome ; Lipid Metabolism ; Intestinal Mucosa/metabolism ; Circadian Clocks ; },
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.

RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.

DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.

CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.},
}

Animals
*Liver/metabolism
*Circadian Rhythm
*Hyperlipidemias/metabolism/genetics
Mice
Male
Gastrointestinal Microbiome
Multiomics
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
Transcriptome
Lipid Metabolism
Intestinal Mucosa/metabolism
Circadian Clocks

@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {49},
number = {6},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
mesh = {Animals ; *Penaeidae/microbiology ; *Photobacterium/physiology ; RNA, Ribosomal, 16S/analysis ; Muscles/microbiology ; *Metagenome ; Microbiota ; Metagenomics ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}

Animals
*Penaeidae/microbiology
*Photobacterium/physiology
RNA, Ribosomal, 16S/analysis
Muscles/microbiology
*Metagenome
Microbiota
Metagenomics

@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Azotobacter ; Bacteria/classification/genetics ; Fertilizers ; Azospirillum ; Plant Roots/microbiology/growth & development ; Basidiomycota ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}

*Rhizosphere
*Onions/microbiology/growth & development/physiology
*Soil Microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Azotobacter
Bacteria/classification/genetics
Fertilizers
Azospirillum
Plant Roots/microbiology/growth & development
Basidiomycota

@article {pmid41523161,
year = {2025},
author = {Sanchez, G and Simakov, O and Nyholm, S and Nishiguchi, M and McFall-Ngai, M and Lami, R and Heath-Heckman, E and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {351},
pmid = {41523161},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a specimen of Sepioteuthis lessoniana (bigfin reef squid; Mollusca; Cephalopoda; Myopsida; Loliginidae). The genome sequence has a total length of 5,056.23 megabases. Most of the assembly (86.4%) is scaffolded into 44 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 28,970 protein-coding genes.},
}

@article {pmid41524715,
year = {2026},
author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S},
title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41524715},
issn = {2050-084X},
support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; },
mesh = {Humans ; *Microbial Interactions ; *Dysbiosis/microbiology ; *Microbiota ; Metagenomics ; Models, Biological ; },
abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.},
}

Humans
*Microbial Interactions
*Dysbiosis/microbiology
*Microbiota
Metagenomics
Models, Biological

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {33},
number = {4},
pages = {3203-3213},
pmid = {41524878},
issn = {1534-4681},
mesh = {Humans ; *Esophageal Neoplasms/microbiology/therapy/pathology/mortality ; *Microbiota ; Male ; *Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality ; Female ; Prognosis ; Survival Rate ; *Neoadjuvant Therapy/mortality ; *Esophagectomy/mortality ; Middle Aged ; *Mouth/microbiology ; Aged ; RNA, Ribosomal, 16S/genetics ; Follow-Up Studies ; },
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

Humans
*Esophageal Neoplasms/microbiology/therapy/pathology/mortality
*Microbiota
Male
*Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality
Female
Prognosis
Survival Rate
*Neoadjuvant Therapy/mortality
*Esophagectomy/mortality
Middle Aged
*Mouth/microbiology
Aged
RNA, Ribosomal, 16S/genetics
Follow-Up Studies

@article {pmid41524921,
year = {2026},
author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M},
title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {133},
pmid = {41524921},
issn = {1432-0991},
mesh = {Animals ; *Wolbachia/genetics/isolation & purification/classification/physiology ; *Aedes/microbiology/classification ; Phylogeny ; Female ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Pakistan ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Symbiosis ; Electron Transport Complex IV/genetics ; *Metagenome ; Microbiota ; Mosquito Vectors/microbiology ; },
abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).},
}

Animals
*Wolbachia/genetics/isolation & purification/classification/physiology
*Aedes/microbiology/classification
Phylogeny
Female
RNA, Ribosomal, 16S/genetics
Metagenomics
Pakistan
DNA, Bacterial/genetics
Sequence Analysis, DNA
Symbiosis
Electron Transport Complex IV/genetics
*Metagenome
Microbiota
Mosquito Vectors/microbiology

@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; *Secondary Metabolism/genetics ; Phylogeny ; Multigene Family ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Seawater/microbiology ; Genome, Bacterial ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}

*Porifera/microbiology
Animals
*Metagenome
*Microbiota/genetics
*Secondary Metabolism/genetics
Phylogeny
Multigene Family
*Bacteria/genetics/classification/metabolism/isolation & purification
Seawater/microbiology
Genome, Bacterial

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
pmid = {41525322},
issn = {1553-7358},
support = {S10 OD032203/OD/NIH HHS/United States ; UH3 AG064704/AG/NIA NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Longevity/genetics ; Humans ; *Aging/genetics/physiology ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Feces/microbiology ; Metagenome/genetics ; },
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

*Metagenomics/methods
*Longevity/genetics
Humans
*Aging/genetics/physiology
*Gastrointestinal Microbiome/genetics
Computational Biology
Feces/microbiology
Metagenome/genetics

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {40},
pmid = {41526362},
issn = {2055-5008},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Virulence Factors/genetics ; Cohort Studies ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenome ; Drug Resistance, Bacterial ; },
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

*Colorectal Neoplasms/microbiology
Humans
Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Virulence Factors/genetics
Cohort Studies
*Bacteria/genetics/classification/drug effects/isolation & purification
Metagenome
Drug Resistance, Bacterial

@article {pmid41527012,
year = {2026},
author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P},
title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.},
journal = {Alzheimer's research & therapy},
volume = {18},
number = {1},
pages = {23},
pmid = {41527012},
issn = {1758-9193},
mesh = {Humans ; *Alzheimer Disease/microbiology ; Female ; Male ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged ; Aged, 80 and over ; Saliva/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.

METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.

RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.

CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.

TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.},
}

Humans
*Alzheimer Disease/microbiology
Female
Male
*Microbiota
*Dysbiosis/microbiology
*Mouth/microbiology
Aged
Aged, 80 and over
Saliva/microbiology
Metagenomics

@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; },
mesh = {Humans ; *Parkinson Disease/virology/diagnosis ; *Gastrointestinal Microbiome ; *Virome ; Female ; Male ; Aged ; Metagenomics ; Case-Control Studies ; },
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}

Humans
*Parkinson Disease/virology/diagnosis
*Gastrointestinal Microbiome
*Virome
Female
Male
Aged
Metagenomics
Case-Control Studies

@article {pmid41528122,
year = {2026},
author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW},
title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41528122},
issn = {2057-5858},
mesh = {*Intensive Care Units ; Humans ; *Bacteria/genetics/isolation & purification/classification ; Metagenomics/methods ; Queensland ; Drug Resistance, Bacterial/genetics ; *Environmental Monitoring/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.},
}

*Intensive Care Units
Humans
*Bacteria/genetics/isolation & purification/classification
Metagenomics/methods
Queensland
Drug Resistance, Bacterial/genetics
*Environmental Monitoring/methods
Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
mesh = {*Rivers/microbiology ; *Plastics/metabolism/analysis ; India ; *Microbiota ; *Bacteria/classification/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Waste Disposal Facilities ; *Soil Pollutants/metabolism/analysis ; Metagenome ; },
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}

*Rivers/microbiology
*Plastics/metabolism/analysis
India
*Microbiota
*Bacteria/classification/metabolism
Biodegradation, Environmental
*Soil Microbiology
*Waste Disposal Facilities
*Soil Pollutants/metabolism/analysis
Metagenome

@article {pmid41529381,
year = {2026},
author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R},
title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.},
journal = {Virology},
volume = {616},
number = {},
pages = {110789},
doi = {10.1016/j.virol.2026.110789},
pmid = {41529381},
issn = {1096-0341},
mesh = {Humans ; *Nanopore Sequencing/methods ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; *Metagenomics/methods ; *Virus Diseases/virology ; High-Throughput Nucleotide Sequencing/methods ; Virome ; },
abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.},
}

Humans
*Nanopore Sequencing/methods
*Viruses/genetics/classification/isolation & purification
Genome, Viral
*Metagenomics/methods
*Virus Diseases/virology
High-Throughput Nucleotide Sequencing/methods
Virome

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {25},
number = {2},
pages = {232-239},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Metagenomics/methods ; Child, Preschool ; Female ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; Microbiota ; Oropharynx/microbiology ; },
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

Humans
*Cystic Fibrosis/microbiology/diagnosis
*Metagenomics/methods
Child, Preschool
Female
Male
*Bronchoalveolar Lavage Fluid/microbiology
*Bronchoalveolar Lavage/methods
*Specimen Handling/methods
Microbiota
Oropharynx/microbiology

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1533},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Food Chain ; *Cobamides/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification ; Animals ; Phylogeny ; Soil/chemistry ; Microbiota ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

*Soil Microbiology
*Food Chain
*Cobamides/metabolism/biosynthesis
*Bacteria/metabolism/genetics/classification
Animals
Phylogeny
Soil/chemistry
Microbiota

@article {pmid41530170,
year = {2026},
author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S},
title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {29},
pmid = {41530170},
issn = {2052-4463},
support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; },
abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.},
}

Chile
France
Metagenomics
Ecosystem
*DNA Barcoding, Taxonomic
*Metagenome
Seawater/microbiology
Salinity
Microbiota

@article {pmid41530917,
year = {2026},
author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF},
title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611544},
pmid = {41530917},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; *Software ; *Big Data ; Humans ; *Metagenome ; Reproducibility of Results ; Microbiota/genetics ; Computational Biology/methods ; Colorectal Neoplasms/microbiology ; },
abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.},
}

*Metagenomics/methods
*Software
*Big Data
Humans
*Metagenome
Reproducibility of Results
Microbiota/genetics
Computational Biology/methods
Colorectal Neoplasms/microbiology

@article {pmid41532487,
year = {2026},
author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK},
title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2026.2614431},
pmid = {41532487},
issn = {1549-7828},
abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.},
}

@article {pmid41534755,
year = {2026},
author = {Liu, K and Peng, W and Yang, X and Zeng, Y and Liu, Y and Yu, K and Zhu, Y and Gou, H and Li, L and Zhang, C},
title = {Efficacy and multi-omics regulatory effects of Guilou Tongluo formula in patients with chronic obstructive pulmonary disease combined with pulmonary hypertension: A prospective, multicenter, randomized controlled trial.},
journal = {Journal of ethnopharmacology},
volume = {361},
number = {},
pages = {121204},
doi = {10.1016/j.jep.2026.121204},
pmid = {41534755},
issn = {1872-7573},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/drug therapy/complications/physiopathology ; *Drugs, Chinese Herbal/therapeutic use/adverse effects ; Male ; Female ; *Hypertension, Pulmonary/drug therapy/physiopathology ; Prospective Studies ; Aged ; Middle Aged ; Treatment Outcome ; Gastrointestinal Microbiome/drug effects ; Medicine, Chinese Traditional ; },
abstract = {Pulmonary hypertension (PH) is a serious and common complication in patients with chronic obstructive pulmonary disease (COPD), and this clinical gap has been newly emphasized in the GOLD 2025 guidelines. Guilou Tongluo Formula (GLTLF) is a traditional Chinese herbal prescription widely used in clinical practice for the treatment of COPD combined with PH (COPD-PH). However, there is a lack of high-quality clinical trials to support its efficacy, and the underlying mechanisms of action remain unclear.

AIM OF THE STUDY: This study aims to evaluate the efficacy and safety of GLTLF in the treatment of COPD-PH, and to explore the potential mechanisms underlying its therapeutic effects.

MATERIALS AND METHOD: A total of 104 patients with COPD-PH were randomized to receive either conventional therapy alone (Control group) or in combination with GLTLF (GLTLF group). Clinical efficacy was assessed by changes in traditional Chinese medicine (TCM) syndrome scores, pulmonary artery systolic pressure (PASP), pulmonary function, arterial blood gases, COPD Assessment Test (CAT), modified Medical Research Council (mMRC) grade, WHO functional class (WHO-FC), 6-min walk distance (6MWD), and laboratory parameters. Potential mechanisms were explored via gut metagenomic and metabolomic analyses.

RESULTS: Clinical efficacy evaluation indicated that the TCM syndrome scores were significantly reduced in both groups post-treatment (P < 0.001). PASP, FEV1, and FEV1/FVC improved significantly in the GLTLF group (P < 0.05), and were superior to the control group post-treatment (P < 0.05). PaO2, PaCO2, BNP, and D-dimer improved after GLTLF intervention (P < 0.05). Both groups had increased 6MWD (P < 0.001), with the GLTLF group performing better (P = 0.006). CAT score, mMRC grade, and WHO-FC improved in both groups (P < 0.05), with superior outcomes in the GLTLF group (P < 0.05). Metagenomic sequencing revealed that GLTLF altered the structure and function of the gut microbiota in patients with COPD-PH. Metabolomic analysis identified a total of 87 differential metabolites following GLTLF intervention, which were significantly enriched in 18 metabolic pathways.

CONCLUSION: GLTLF can effectively treat patients with COPD-PH, enhance clinical efficacy, and modulate both metabolic status and gut microbiota composition.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/drug therapy/complications/physiopathology
*Drugs, Chinese Herbal/therapeutic use/adverse effects
Male
Female
*Hypertension, Pulmonary/drug therapy/physiopathology
Prospective Studies
Aged
Middle Aged
Treatment Outcome
Gastrointestinal Microbiome/drug effects
Medicine, Chinese Traditional

@article {pmid41535300,
year = {2026},
author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC},
title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {36},
pmid = {41535300},
issn = {2055-5008},
support = {NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Autism Spectrum Disorder/microbiology/complications/psychology ; Male ; Child ; *Synbiotics/administration & dosage ; *Anxiety/therapy ; Female ; Feces/microbiology ; Metagenomics ; Gastrointestinal Microbiome ; Child, Preschool ; Pentanoic Acids ; Treatment Outcome ; },
abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.},
}

Humans
Pilot Projects
*Autism Spectrum Disorder/microbiology/complications/psychology
Male
Child
*Synbiotics/administration & dosage
*Anxiety/therapy
Female
Feces/microbiology
Metagenomics
Gastrointestinal Microbiome
Child, Preschool
Pentanoic Acids
Treatment Outcome

@article {pmid41535683,
year = {2026},
author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q},
title = {Identification of antimicrobial peptides from ancient gut microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1788},
pmid = {41535683},
issn = {2041-1723},
support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science & Technology)/ ; },
mesh = {Humans ; *Antimicrobial Peptides/pharmacology/isolation & purification/chemistry ; Animals ; Feces/microbiology ; Metagenome ; *Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.},
}

Humans
*Antimicrobial Peptides/pharmacology/isolation & purification/chemistry
Animals
Feces/microbiology
Metagenome
*Gastrointestinal Microbiome
Microbial Sensitivity Tests
Anti-Bacterial Agents/pharmacology

@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {36},
number = {2},
pages = {103-120},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Neoplasms/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Risk Factors ; Animals ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}

Humans
*Dysbiosis/immunology/microbiology
*Neoplasms/immunology/microbiology/therapy
*Gastrointestinal Microbiome/immunology
Risk Factors
Animals

@article {pmid41536169,
year = {2026},
author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM},
title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.},
journal = {Molecular oral microbiology},
volume = {41},
number = {3},
pages = {117-130},
doi = {10.1111/omi.70018},
pmid = {41536169},
issn = {2041-1014},
mesh = {Humans ; Animals ; *Periodontal Diseases/microbiology ; Microbiota ; *Periodontitis/microbiology ; Eubacteriales ; },
abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.},
}

Humans
Animals
*Periodontal Diseases/microbiology
Microbiota
*Periodontitis/microbiology
Eubacteriales

@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; Infant, Newborn ; Feces/microbiology ; Adult ; *Gastrointestinal Microbiome ; Pregnancy ; Longitudinal Studies ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Obesity/metabolism/microbiology ; Infant ; Mexico ; Body Mass Index ; Metagenomics ; Young Adult ; *Pregnancy in Obesity/metabolism/microbiology ; Mothers ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}

Humans
*Milk, Human/chemistry/metabolism
Female
*Oligosaccharides/metabolism/analysis
Infant, Newborn
Feces/microbiology
Adult
*Gastrointestinal Microbiome
Pregnancy
Longitudinal Studies
*Bacteria/classification/isolation & purification/genetics/metabolism
*Obesity/metabolism/microbiology
Infant
Mexico
Body Mass Index
Metagenomics
Young Adult
*Pregnancy in Obesity/metabolism/microbiology
Mothers

@article {pmid41537582,
year = {2026},
author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D},
title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.},
journal = {mSphere},
volume = {11},
number = {2},
pages = {e0084225},
pmid = {41537582},
issn = {2379-5042},
support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; *Acinetobacter/genetics/classification/physiology ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; },
abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.},
}

*Solanum lycopersicum/microbiology/growth & development
*Microbiota
Soil Microbiology
*Acinetobacter/genetics/classification/physiology
Rhizosphere
Metagenomics
Plant Roots/microbiology
Metagenome
High-Throughput Nucleotide Sequencing

@article {pmid41538522,
year = {2026},
author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S},
title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e250131},
pmid = {41538522},
issn = {1678-8060},
mesh = {Animals ; *Arboviruses/genetics/isolation & purification/classification ; Colombia ; *Mosquito Vectors/virology/classification ; Metagenomics ; *Culicidae/virology/classification ; Seasons ; Caribbean Region ; *Virome/genetics ; *RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.

OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.

METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across Córdoba, Sucre, Bolívar, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50™ platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.

FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.

MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.},
}

Animals
*Arboviruses/genetics/isolation & purification/classification
Colombia
*Mosquito Vectors/virology/classification
Metagenomics
*Culicidae/virology/classification
Seasons
Caribbean Region
*Virome/genetics
*RNA, Viral/genetics
*RNA Viruses/genetics/classification/isolation & purification

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Antihypertensive Agents/pharmacology ; Male ; Rats ; *Lipid Metabolism/drug effects ; Rats, Inbred SHR ; Blood Pressure/drug effects ; *Prehypertension/drug therapy/microbiology ; Fecal Microbiota Transplantation ; Dysbiosis ; Hypertension/drug therapy ; Disease Models, Animal ; },
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology
*Antihypertensive Agents/pharmacology
Male
Rats
*Lipid Metabolism/drug effects
Rats, Inbred SHR
Blood Pressure/drug effects
*Prehypertension/drug therapy/microbiology
Fecal Microbiota Transplantation
Dysbiosis
Hypertension/drug therapy
Disease Models, Animal

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
pmid = {41539238},
issn = {1525-3171},
mesh = {Animals ; *Bacillus subtilis/chemistry ; *Probiotics/pharmacology/administration & dosage ; *Clostridium butyricum/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Thailand ; Diet/veterinary ; Metabolic Networks and Pathways/drug effects ; Animal Feed/analysis ; Male ; Cecum/microbiology ; *Metagenome ; Metagenomics ; },
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

Animals
*Bacillus subtilis/chemistry
*Probiotics/pharmacology/administration & dosage
*Clostridium butyricum/chemistry
*Chickens/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Thailand
Diet/veterinary
Metabolic Networks and Pathways/drug effects
Animal Feed/analysis
Male
Cecum/microbiology
*Metagenome
Metagenomics

@article {pmid41539415,
year = {2026},
author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL},
title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111204},
doi = {10.1016/j.ygeno.2026.111204},
pmid = {41539415},
issn = {1089-8646},
mesh = {*Fermentation ; *Vegetables/metabolism/microbiology ; *Fruit/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Germination ; Lactuca/growth & development/microbiology ; },
abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.},
}

*Fermentation
*Vegetables/metabolism/microbiology
*Fruit/metabolism/microbiology
*Microbiota
*Fertilizers
Germination
Lactuca/growth & development/microbiology

@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Moringa oleifera/microbiology/chemistry ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; *Plant Leaves/microbiology/chemistry ; *Taste ; Odorants/analysis ; Multiomics ; Amino Acids/analysis ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Microbiota ; *Bacteria/metabolism/classification ; *Fermented Foods/microbiology ; Food, Processed ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}

*Moringa oleifera/microbiology/chemistry
*Fermentation
Gas Chromatography-Mass Spectrometry
*Plant Leaves/microbiology/chemistry
*Taste
Odorants/analysis
Multiomics
Amino Acids/analysis
Volatile Organic Compounds/analysis
*Food Microbiology
*Microbiota
*Bacteria/metabolism/classification
*Fermented Foods/microbiology
Food, Processed

@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
pmid = {41539854},
issn = {1738-8872},
mesh = {Animals ; *Clostridium Infections/microbiology/therapy/prevention & control ; *Clostridioides difficile ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Feces/microbiology ; Bile Acids and Salts/metabolism ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}

Animals
*Clostridium Infections/microbiology/therapy/prevention & control
*Clostridioides difficile
*Clostridium/physiology/genetics
Gastrointestinal Microbiome
Mice
Disease Models, Animal
Feces/microbiology
Bile Acids and Salts/metabolism

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41540332},
issn = {1471-2180},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; *Drug Resistance, Microbial/genetics ; Female ; Metagenome ; China ; Sequence Analysis, DNA ; },
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

Animals
*Gastrointestinal Microbiome/genetics/drug effects
Mice
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects/isolation & purification
Mice, Inbred C57BL
Anti-Bacterial Agents/pharmacology
Mice, Inbred BALB C
Specific Pathogen-Free Organisms
Cecum/microbiology
*Drug Resistance, Microbial/genetics
Female
Metagenome
China
Sequence Analysis, DNA

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Probiotics/pharmacology ; *Lactiplantibacillus plantarum/physiology ; Liver/metabolism/drug effects ; *Liver Diseases, Alcoholic/therapy/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects/physiology ; Oxidative Stress ; Dysbiosis ; Intestinal Barrier Function ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
Mice, Inbred C57BL
*Probiotics/pharmacology
*Lactiplantibacillus plantarum/physiology
Liver/metabolism/drug effects
*Liver Diseases, Alcoholic/therapy/microbiology
Mice
*Gastrointestinal Microbiome/drug effects/physiology
Oxidative Stress
Dysbiosis
Intestinal Barrier Function

@article {pmid41544440,
year = {2026},
author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X},
title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106373},
pmid = {41544440},
issn = {1525-3171},
mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Bacteriophages/drug effects/physiology ; Animal Feed/analysis ; *Chlortetracycline/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Virome/drug effects ; Dietary Supplements/analysis ; *Plant Extracts/administration & dosage/pharmacology ; Gastrointestinal Tract/virology ; Diet/veterinary ; },
abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.},
}

Animals
*Chickens/virology
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Bacteriophages/drug effects/physiology
Animal Feed/analysis
*Chlortetracycline/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Virome/drug effects
Dietary Supplements/analysis
*Plant Extracts/administration & dosage/pharmacology
Gastrointestinal Tract/virology
Diet/veterinary

@article {pmid41544986,
year = {2026},
author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z},
title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111205},
doi = {10.1016/j.ygeno.2026.111205},
pmid = {41544986},
issn = {1089-8646},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology/metabolism ; Fermentation ; Female ; *Metabolome ; Metagenome ; Pregnancy ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.},
}

Animals
*Rumen/microbiology/metabolism
Cattle/microbiology/metabolism
Fermentation
Female
*Metabolome
Metagenome
Pregnancy
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41547150,
year = {2026},
author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W},
title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111622},
doi = {10.1016/j.ijfoodmicro.2026.111622},
pmid = {41547150},
issn = {1879-3460},
mesh = {Animals ; *Milk/microbiology ; Horses ; *Lactobacillales/genetics/physiology ; Metagenomics ; Fermentation ; Female ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation & purification/classification ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.},
}

Animals
*Milk/microbiology
Horses
*Lactobacillales/genetics/physiology
Metagenomics
Fermentation
Female
*Microbiota
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/isolation & purification/classification

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; Metagenome ; Phylogeny ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA/methods
Metagenome
Phylogeny
Genome, Bacterial
High-Throughput Nucleotide Sequencing
Feces/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {31},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
mesh = {Animals ; *Prion Diseases/microbiology/drug therapy/prevention & control ; *Catechin/analogs & derivatives/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

Animals
*Prion Diseases/microbiology/drug therapy/prevention & control
*Catechin/analogs & derivatives/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice
Male

@article {pmid41548304,
year = {2026},
author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T},
title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141134},
doi = {10.1016/j.jhazmat.2026.141134},
pmid = {41548304},
issn = {1873-3336},
mesh = {*Rivers/microbiology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Water Microbiology ; Microbiota/genetics ; Bacteria/genetics ; },
abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.},
}

*Rivers/microbiology
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
*Water Microbiology
Microbiota/genetics
Bacteria/genetics

@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; Bacteria/metabolism ; *Microbial Consortia/physiology ; Bioreactors/microbiology ; Caproates/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}

*Sewage/microbiology
*Fatty Acids/biosynthesis
Bacteria/metabolism
*Microbial Consortia/physiology
Bioreactors/microbiology
Caproates/metabolism
Carbon Dioxide/metabolism

@article {pmid41549294,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {139},
pmid = {41549294},
issn = {1432-0991},
mesh = {*Lakes/virology ; *Viruses/classification/genetics/isolation & purification ; Genome, Viral ; *Virome ; Metagenomics ; India ; *Biodiversity ; Ecosystem ; Phylogeny ; Fresh Water/virology ; },
abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.},
}

*Lakes/virology
*Viruses/classification/genetics/isolation & purification
Genome, Viral
*Virome
Metagenomics
India
*Biodiversity
Ecosystem
Phylogeny
Fresh Water/virology

@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*Biodiversity ; Deoxyribonucleases/metabolism ; Animals ; Extrachromosomal DNA ; *DNA, Environmental/isolation & purification/genetics ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; Fishes/classification/genetics ; Rivers ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}

*Biodiversity
Deoxyribonucleases/metabolism
Animals
Extrachromosomal DNA
*DNA, Environmental/isolation & purification/genetics
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
Fishes/classification/genetics
Rivers

@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food & function},
volume = {17},
number = {3},
pages = {1451-1464},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
mesh = {Animals ; Male ; Mice ; *Insulin Resistance ; *Dietary Advanced Glycation End Products/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Rutin/pharmacology ; *Glycation End Products, Advanced/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Fatty Acids, Volatile/metabolism ; },
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}

Animals
Male
Mice
*Insulin Resistance
*Dietary Advanced Glycation End Products/adverse effects
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Rutin/pharmacology
*Glycation End Products, Advanced/adverse effects
Bacteria/classification/genetics/isolation & purification
Fatty Acids, Volatile/metabolism

@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {62},
number = {1},
pages = {25-43},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
mesh = {*Diatoms/classification/genetics/physiology ; Phylogeny ; Germany ; Sweden ; Algal Proteins/genetics ; DNA, Algal/analysis/genetics ; Sequence Analysis, DNA ; Species Specificity ; Ribulose-Bisphosphate Carboxylase/genetics ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}

*Diatoms/classification/genetics/physiology
Phylogeny
Germany
Sweden
Algal Proteins/genetics
DNA, Algal/analysis/genetics
Sequence Analysis, DNA
Species Specificity
Ribulose-Bisphosphate Carboxylase/genetics

@article {pmid41554846,
year = {2026},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A},
title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5761},
pmid = {41554846},
issn = {2045-2322},
support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; },
mesh = {Animals ; *Larva/microbiology/drug effects ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; *Ovum/microbiology/drug effects ; *Fishes/microbiology ; *Disinfection/methods ; Disinfectants/pharmacology ; Bacteria/genetics/drug effects/classification ; },
abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.},
}

Animals
*Larva/microbiology/drug effects
*Microbiota/drug effects
RNA, Ribosomal, 16S/genetics
*Ovum/microbiology/drug effects
*Fishes/microbiology
*Disinfection/methods
Disinfectants/pharmacology
Bacteria/genetics/drug effects/classification

@article {pmid41555453,
year = {2026},
author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M},
title = {Spatial and temporal patterns of public transit aerobiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {64},
pmid = {41555453},
issn = {2049-2618},
mesh = {*Bacteria/classification/genetics/isolation & purification ; *Air Microbiology ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Shotgun Sequencing ; Metagenomics/methods ; Cities ; Humans ; Aerosols/analysis ; Biodiversity ; Seasons ; Spatio-Temporal Analysis ; },
abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.

RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.

CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.},
}

*Bacteria/classification/genetics/isolation & purification
*Air Microbiology
*Fungi/classification/genetics/isolation & purification
*Microbiota
Shotgun Sequencing
Metagenomics/methods
Cities
Humans
Aerosols/analysis
Biodiversity
Seasons
Spatio-Temporal Analysis

@article {pmid41556507,
year = {2026},
author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M},
title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70704},
doi = {10.1111/gcb.70704},
pmid = {41556507},
issn = {1365-2486},
support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Microbiology ; *Stress, Physiological ; *Microbiota ; *Metagenome ; Biodiversity ; Metagenomics ; Bacteria/genetics/classification ; },
abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.},
}

*Soil Microbiology
*Stress, Physiological
*Microbiota
*Metagenome
Biodiversity
Metagenomics
Bacteria/genetics/classification

@article {pmid41556662,
year = {2026},
author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H},
title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0142725},
pmid = {41556662},
issn = {2379-5077},
support = {2022YFC2302700, 2023YFC2305900//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Kenya ; *Microbiota/genetics ; Virome ; Bacteria/genetics/classification/isolation & purification ; *Culex/microbiology/virology/genetics ; *Aedes/microbiology/virology/genetics ; Phylogeny ; Transcriptome ; Metagenomics ; Geography ; },
abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.},
}

Animals
Kenya
*Microbiota/genetics
Virome
Bacteria/genetics/classification/isolation & purification
*Culex/microbiology/virology/genetics
*Aedes/microbiology/virology/genetics
Phylogeny
Transcriptome
Metagenomics
Geography

@article {pmid41558030,
year = {2026},
author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E},
title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.},
journal = {Blood advances},
volume = {10},
number = {6},
pages = {1979-1991},
pmid = {41558030},
issn = {2473-9537},
mesh = {Humans ; *Feces/microbiology ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism ; Hematopoietic Stem Cell Transplantation/adverse effects ; Incidence ; *Gastrointestinal Diseases/etiology/microbiology/epidemiology ; *Gastrointestinal Microbiome ; },
abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.},
}

Humans
*Feces/microbiology
*Graft vs Host Disease/etiology/epidemiology/microbiology
*Carbohydrate Metabolism
*Bacteria/metabolism
Hematopoietic Stem Cell Transplantation/adverse effects
Incidence
*Gastrointestinal Diseases/etiology/microbiology/epidemiology
*Gastrointestinal Microbiome

@article {pmid41558076,
year = {2026},
author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S},
title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106427},
pmid = {41558076},
issn = {1525-3171},
mesh = {Animals ; *Chickens/immunology/microbiology ; *Triterpenes/administration & dosage/metabolism/pharmacology ; Ursolic Acid ; *T-Lymphocytes, Regulatory/immunology/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Th17 Cells/immunology/drug effects ; *Intestines/drug effects/physiology ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; Random Allocation ; Intestinal Barrier Function ; Dose-Response Relationship, Drug ; Male ; },
abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.},
}

Animals
*Chickens/immunology/microbiology
*Triterpenes/administration & dosage/metabolism/pharmacology
Ursolic Acid
*T-Lymphocytes, Regulatory/immunology/drug effects
*Gastrointestinal Microbiome/drug effects
*Th17 Cells/immunology/drug effects
*Intestines/drug effects/physiology
Diet/veterinary
Dietary Supplements/analysis
Animal Feed/analysis
Random Allocation
Intestinal Barrier Function
Dose-Response Relationship, Drug
Male

@article {pmid41558481,
year = {2026},
author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I},
title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.},
journal = {Current biology : CB},
volume = {36},
number = {3},
pages = {748-759.e5},
doi = {10.1016/j.cub.2025.12.046},
pmid = {41558481},
issn = {1879-0445},
mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/physiology/genetics ; Europe ; *Metagenome ; North America ; },
abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.},
}

*Symbiosis
*Lichens/microbiology
*Ascomycota/physiology/genetics
Europe
*Metagenome
North America

@article {pmid41560354,
year = {2026},
author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S},
title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {17},
pages = {e17596},
pmid = {41560354},
issn = {2198-3844},
support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science & Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Mice ; *Thiamine/metabolism ; *Gastrointestinal Microbiome/physiology ; *Fatty Liver/metabolism/microbiology ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Liver/metabolism ; Prebiotics/administration & dosage ; Diet, High-Fat ; *Eubacteriales/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.},
}

Animals
Mice
*Thiamine/metabolism
*Gastrointestinal Microbiome/physiology
*Fatty Liver/metabolism/microbiology
Male
Disease Models, Animal
Mice, Inbred C57BL
Liver/metabolism
Prebiotics/administration & dosage
Diet, High-Fat
*Eubacteriales/metabolism

@article {pmid41560360,
year = {2026},
author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q},
title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {18},
pages = {e18502},
pmid = {41560360},
issn = {2198-3844},
support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Animals ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism/genetics ; *Kynurenine/metabolism ; *Fibrosis/metabolism ; Mice ; *Receptors, Aryl Hydrocarbon/metabolism ; *Uracil/analogs & derivatives/metabolism/pharmacology ; *Intestines/pathology/drug effects ; Gastrointestinal Microbiome ; Humans ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; },
abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.},
}

Animals
*Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism/genetics
*Kynurenine/metabolism
*Fibrosis/metabolism
Mice
*Receptors, Aryl Hydrocarbon/metabolism
*Uracil/analogs & derivatives/metabolism/pharmacology
*Intestines/pathology/drug effects
Gastrointestinal Microbiome
Humans
Signal Transduction/drug effects
Mice, Inbred C57BL

@article {pmid41561086,
year = {2025},
author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX},
title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1740322},
pmid = {41561086},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Dysbiosis/therapy ; },
abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.},
}

Humans
*Gastrointestinal Diseases/therapy/microbiology
*Gastrointestinal Microbiome/physiology
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Gastrointestinal Tract/microbiology
Dysbiosis/therapy

@article {pmid41561096,
year = {2025},
author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C},
title = {The analysis of gut microbiota characteristics in children with global developmental delay.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1606453},
pmid = {41561096},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Developmental Disabilities/microbiology ; High-Throughput Nucleotide Sequencing ; Female ; Child, Preschool ; Male ; DNA, Bacterial/genetics ; Child ; China ; Biodiversity ; Infant ; },
abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.

METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.

RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R² = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.

CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
Prospective Studies
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Developmental Disabilities/microbiology
High-Throughput Nucleotide Sequencing
Female
Child, Preschool
Male
DNA, Bacterial/genetics
Child
China
Biodiversity
Infant

@article {pmid41562094,
year = {2025},
author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P},
title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1717935},
pmid = {41562094},
issn = {1664-3224},
mesh = {Animals ; *Phlebotomus/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics ; Female ; Insect Vectors/microbiology ; Metagenomics/methods ; *Leishmaniasis ; *Leishmania major ; },
abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.

METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.

RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).

DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.},
}

Animals
*Phlebotomus/microbiology/parasitology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics
Female
Insect Vectors/microbiology
Metagenomics/methods
*Leishmaniasis
*Leishmania major

@article {pmid41562342,
year = {2026},
author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J},
title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.},
journal = {Clinical and experimental rheumatology},
volume = {44},
number = {2},
pages = {186-193},
doi = {10.55563/clinexprheumatol/1b8sv1},
pmid = {41562342},
issn = {0392-856X},
mesh = {Humans ; *Myositis, Inclusion Body/microbiology/diagnosis ; Female ; Aged ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; *Bacteria/genetics/classification ; Feces/microbiology ; Case-Control Studies ; Ribotyping ; Severity of Illness Index ; Metagenomics ; },
abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.

METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.

RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (≥ 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).

CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.},
}

Humans
*Myositis, Inclusion Body/microbiology/diagnosis
Female
Aged
*Gastrointestinal Microbiome
Male
Middle Aged
*Bacteria/genetics/classification
Feces/microbiology
Case-Control Studies
Ribotyping
Severity of Illness Index
Metagenomics

@article {pmid41564488,
year = {2026},
author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X},
title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128688},
doi = {10.1016/j.jenvman.2026.128688},
pmid = {41564488},
issn = {1095-8630},
mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Dissolved Organic Matter/analysis ; *Geologic Sediments/chemistry ; Carbon ; *Microbiota ; },
abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.},
}

*Lakes/chemistry/microbiology
Seasons
*Dissolved Organic Matter/analysis
*Geologic Sediments/chemistry
Carbon
*Microbiota

@article {pmid41564978,
year = {2026},
author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z},
title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.},
journal = {Microbial pathogenesis},
volume = {212},
number = {},
pages = {108285},
doi = {10.1016/j.micpath.2026.108285},
pmid = {41564978},
issn = {1096-1208},
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; Toll-Like Receptor 4/metabolism ; Janus Kinase 2/metabolism ; STAT3 Transcription Factor/metabolism ; NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Acute Lung Injury/drug therapy ; Male ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice ; Lung/pathology/drug effects ; *Inflammation/drug therapy ; Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Intestinal Barrier Function ; Lipopolysaccharides ; },
abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.},
}

Animals
*Drugs, Chinese Herbal/pharmacology
Toll-Like Receptor 4/metabolism
Janus Kinase 2/metabolism
STAT3 Transcription Factor/metabolism
NF-kappa B/metabolism
*Gastrointestinal Microbiome/drug effects
*Acute Lung Injury/drug therapy
Male
Homeostasis/drug effects
Signal Transduction/drug effects
Mice
Lung/pathology/drug effects
*Inflammation/drug therapy
Colitis, Ulcerative/drug therapy/chemically induced
Cytokines/metabolism
Mice, Inbred C57BL
Disease Models, Animal
Intestinal Barrier Function
Lipopolysaccharides