@article {pmid41816992,
year = {2026},
author = {Rao, B and Jiang, J and Zhang, R and Zhang, D and Zhang, C and Li, A and Lu, H and Zhang, H and Zhou, L and Guo, W and Wen, P and Xue, J and Pan, J and Aji, T and Lan, Z and Jiang, X and Zheng, S and Yu, Z and Ren, Z},
title = {Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {27},
pages = {e17658},
doi = {10.1002/advs.202517658},
pmid = {41816992},
issn = {2198-3844},
support = {82470654//National Natural Science Foundation of China/ ; 232300421124//Natural Science Foundation Key Project of Henan Province/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; ZYYC202301ZD//Henan Zhongyuan Medical Science and Technology Innovation and Development Foundation/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Cholangiocarcinoma/diagnosis/microbiology ; Male ; Female ; *Bile Duct Neoplasms/diagnosis/microbiology ; Middle Aged ; Feces/microbiology ; *Bifidobacterium/genetics ; Aged ; China ; Dysbiosis/microbiology ; },
abstract = {Growing evidence suggests a role for the gut microbiome in progression of cholangiocarcinoma (CCA), however, its diagnostic and therapeutic potential remains incompletely characterized. Here, metagenomic sequencing was performed on fecal samples (n = 785) from individuals across East, Central, and Northwestern China. Gut microbial dysbiosis in CCA was characterized by depletion of short-chain fatty acids-producing species and enrichment of potential pathobionts (Klebsiella aerogenes, Clostridium symbiosum). Diagnostic models built using species-level markers demonstrated superior performance, compared to pathway-based models, achieving area under the curve (AUC) values of 98.63% and 99.42% in the discovery cohort, with robust cross-regional validation (AUC = 80.89% and 80.43%). The model effectively distinguished CCA from hepatocellular carcinoma (AUC = 97.86%) and liver fibrosis (AUC = 98.73%) and nonalcoholic fatty liver disease (mean AUC = 96.86%). Analysis of public datasets encompassing 6847 samples across 31 studies and 11 disease states revealed moderate disease specificity influenced by biomarker overlap across conditions. Mechanistically, depleted Bifidobacterium pseudocatenulatum suppressed CCA progression, associated with inhibition of the PI3K-AKT-mTOR pathway. Collectively, this study supports the potential of fecal metagenomic signatures as a complementary noninvasive aid for CCA detection, and provides functional evidence for a candidate protective microbe.},
}

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

@article {pmid41888223,
year = {2026},
author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K},
title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41888223},
issn = {2045-2322},
support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; },
mesh = {*Metagenome ; Metagenomics/methods ; Humans ; Microbiota/genetics ; *Bacterial Proteins/genetics ; },
abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.},
}

*Metagenome
Metagenomics/methods
Humans
Microbiota/genetics
*Bacterial Proteins/genetics

@article {pmid41928361,
year = {2026},
author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S},
title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41928361},
issn = {2049-2618},
support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; },
mesh = {Animals ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Sus scrofa/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenome ; Diet ; Animal Feed ; Animals, Wild/microbiology ; },
abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.

RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.

CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.},
}

Animals
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Sus scrofa/microbiology
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification/metabolism
Metagenome
Diet
Animal Feed
Animals, Wild/microbiology

@article {pmid42013836,
year = {2026},
author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and , and , and Korten, I and Xavier, RJ},
title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.},
journal = {Cell host & microbe},
volume = {34},
number = {5},
pages = {925-941.e6},
doi = {10.1016/j.chom.2026.03.019},
pmid = {42013836},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics/drug effects ; Infant ; Haemophilus influenzae/genetics/drug effects/growth & development ; *Cystic Fibrosis/microbiology/therapy ; *Nose/microbiology ; Metagenomics ; Female ; Male ; Fungi/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; },
abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.},
}

Humans
*Microbiota/genetics/drug effects
Infant
Haemophilus influenzae/genetics/drug effects/growth & development
*Cystic Fibrosis/microbiology/therapy
*Nose/microbiology
Metagenomics
Female
Male
Fungi/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects/classification

@article {pmid42023843,
year = {2026},
author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D},
title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.},
journal = {mBio},
volume = {17},
number = {5},
pages = {e0053426},
doi = {10.1128/mbio.00534-26},
pmid = {42023843},
issn = {2150-7511},
support = {R01 AI158527/AI/NIAID NIH HHS/United States ; R01 AI158527/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Ethiopia/epidemiology ; *Trachoma/microbiology/epidemiology ; Male ; *Phylogeny ; Female ; RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Microbiota ; Young Adult ; Adolescent ; Child ; Child, Preschool ; Aged ; Infant ; Metagenomics ; Chlamydia trachomatis/genetics ; },
abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.},
}

Humans
Ethiopia/epidemiology
*Trachoma/microbiology/epidemiology
Male
*Phylogeny
Female
RNA, Ribosomal, 16S/genetics
Adult
Middle Aged
Microbiota
Young Adult
Adolescent
Child
Child, Preschool
Aged
Infant
Metagenomics
Chlamydia trachomatis/genetics

@article {pmid42057740,
year = {2026},
author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM},
title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {18},
pages = {14335-14347},
doi = {10.1021/acs.jafc.5c17636},
pmid = {42057740},
issn = {1520-5118},
mesh = {Rhizosphere ; Soil Microbiology ; Zea mays/growth & development/microbiology/metabolism/drug effects ; *Microbiota/drug effects ; Bacteria/genetics/isolation & purification/drug effects/classification/metabolism ; Soil/chemistry ; *Soil Pollutants/chemistry/pharmacology/toxicity ; *Plastics/chemistry ; },
abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.},
}

Rhizosphere
Soil Microbiology
Zea mays/growth & development/microbiology/metabolism/drug effects
*Microbiota/drug effects
Bacteria/genetics/isolation & purification/drug effects/classification/metabolism
Soil/chemistry
*Soil Pollutants/chemistry/pharmacology/toxicity
*Plastics/chemistry

@article {pmid42116470,
year = {2026},
author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W},
title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119200},
doi = {10.1016/j.foodres.2026.119200},
pmid = {42116470},
issn = {1873-7145},
mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Indoles/metabolism ; *Oligosaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Mice ; *Propionates/metabolism ; *Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy ; *Receptors, Aryl Hydrocarbon/metabolism ; *Anti-Bacterial Agents/adverse effects ; Humans ; Male ; Female ; Prospective Studies ; Dysbiosis/chemically induced ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.

OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.

METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.

RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.

CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.},
}

*NF-E2-Related Factor 2/metabolism
Animals
*Indoles/metabolism
*Oligosaccharides/pharmacology
Gastrointestinal Microbiome/drug effects
Mice
*Propionates/metabolism
*Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy
*Receptors, Aryl Hydrocarbon/metabolism
*Anti-Bacterial Agents/adverse effects
Humans
Male
Female
Prospective Studies
Dysbiosis/chemically induced
Oxidative Stress/drug effects
Multiomics

@article {pmid42116511,
year = {2026},
author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W},
title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119274},
doi = {10.1016/j.foodres.2026.119274},
pmid = {42116511},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; },
abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.},
}

*Fermentation
*Microbiota
*Metabolome
Food Microbiology
Taste
Volatile Organic Compounds/analysis
Bacteria/metabolism/classification/genetics
*Wine/microbiology/analysis
Fungi/metabolism/classification
Metabolomics
Flavoring Agents
China

@article {pmid42118429,
year = {2026},
author = {Tekin, B and Gurbanov, R},
title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42118429},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Aging/physiology
Biomarkers/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
Animals
Host Microbial Interactions
Fatty Acids, Volatile/metabolism

@article {pmid42119293,
year = {2026},
author = {Li, H and Xu, Y and Lin, T and Hu, C and Yang, Z and Su, H},
title = {Overwintering waterbirds are important reservoirs for the spread of antibiotic resistance genes (ARGs): Shared patterns at the waterbird-environment interface and the risk of horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142298},
doi = {10.1016/j.jhazmat.2026.142298},
pmid = {42119293},
issn = {1873-3336},
abstract = {The global spread of antibiotic resistance genes (ARGs) has become a critical challenge to public health. Long-distance migratory waterbirds are recognized as important biological vectors in the transregional spread of ARGs. However, the sharing patterns of ARGs and the horizontal transfer risks between these birds and their habitats during the wintering period remain poorly understood. This limits a comprehensive understanding of their role in ARG transmission. This study investigated a typical wintering wetland in southwestern China along the East Asian-Australasian Flyway, using metagenomic approaches to systematically characterize the distribution patterns, sharing profiles, and horizontal transfer risks of ARGs in the guts of overwintering waterbirds and their associated aquatic and terrestrial habitats. The results show that multidrug resistance genes are the predominant type of resistance observed both in the guts of overwintering waterbirds and in their habitats. Extensive sharing of ARGs occurs between the guts of overwintering waterbirds and their habitats, with approximately 50% of the 1250 identified ARG subtypes shared by both. We detected 55 high-risk ARG subtypes belonging to 10 resistance categories. Among these, β-lactam resistance genes (e.g., blaNDM-5 and blaCTX-M-15) were the predominant types. In addition, the co-localization of ARGs with mobile genetic elements (MGEs) (e.g., transposons and plasmids) suggests that the gut of waterbirds and aquatic environments may represent potential hotspots for horizontal transfer of ARGs. This study highlights the high connectivity of ARGs between overwintering waterbirds and their habitats, offering important insights into ecological and public health risks related to ARG spread.},
}

@article {pmid42119482,
year = {2026},
author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS},
title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.},
journal = {Chemosphere},
volume = {405},
number = {},
pages = {144948},
doi = {10.1016/j.chemosphere.2026.144948},
pmid = {42119482},
issn = {1879-1298},
abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.},
}

@article {pmid42120383,
year = {2026},
author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW},
title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42120383},
issn = {2041-1723},
support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; },
abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Carrageenan/metabolism
*Ruminants/microbiology
Rumen/microbiology
Glycoside Hydrolases/metabolism/genetics
Feces/microbiology
Bacteria/metabolism/genetics/classification/isolation & purification
Seaweed/metabolism
Bacteroides/metabolism/genetics/isolation & purification
Metagenomics
Phylogeny

@article {pmid40265464,
year = {2026},
author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q},
title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and Their Differences Compared to Other Ruminants.},
journal = {Integrative zoology},
volume = {21},
number = {3},
pages = {667-683},
doi = {10.1111/1749-4877.12984},
pmid = {40265464},
issn = {1749-4877},
support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Animals ; Cattle/microbiology ; *Rumen/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Bacteria/classification/genetics ; *Metagenome ; },
abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.},
}

Animals
Cattle/microbiology
*Rumen/microbiology
*Gastrointestinal Microbiome
Metagenomics
*Bacteria/classification/genetics
*Metagenome

@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {75},
number = {6},
pages = {1136-1146},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; Longitudinal Studies ; Middle Aged ; *Diet/adverse effects ; Inflammation/microbiology ; Diet, Mediterranean ; Case-Control Studies ; Feces/microbiology ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.

OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.

DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.

RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.

CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}

Humans
*Colitis, Ulcerative/microbiology
*Crohn Disease/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Adult
Longitudinal Studies
Middle Aged
*Diet/adverse effects
Inflammation/microbiology
Diet, Mediterranean
Case-Control Studies
Feces/microbiology

@article {pmid41794383,
year = {2026},
author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G},
title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.},
journal = {The Journal of nutritional biochemistry},
volume = {154},
number = {},
pages = {110327},
doi = {10.1016/j.jnutbio.2026.110327},
pmid = {41794383},
issn = {1873-4847},
mesh = {Humans ; *Metabolic Syndrome/microbiology/metabolism/blood ; Male ; *Metabolomics/methods ; Female ; Middle Aged ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Aged ; Dopamine/analogs & derivatives/blood ; },
abstract = {Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains an opportunity for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden. We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45). Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population. Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.},
}

Humans
*Metabolic Syndrome/microbiology/metabolism/blood
Male
*Metabolomics/methods
Female
Middle Aged
*Metagenomics/methods
*Gastrointestinal Microbiome
Adult
Feces/microbiology
Aged
Dopamine/analogs & derivatives/blood

@article {pmid41861946,
year = {2026},
author = {Wang, ST and Li, L and Yang, Q and Zhang, GF},
title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124314},
doi = {10.1016/j.envres.2026.124314},
pmid = {41861946},
issn = {1096-0953},
mesh = {*Sulfur/metabolism ; *Microbiota ; *Coral Reefs ; Nitrogen/metabolism ; Archaea/genetics ; *Nitrogen Cycle ; China ; Bacteria/genetics/metabolism ; Seawater/microbiology ; },
abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.},
}

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

@article {pmid41882035,
year = {2026},
author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK},
title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41882035},
issn = {2045-2322},
support = {2020//Centre for Agricultural Bioinformatics/ ; },
mesh = {*Triticum/microbiology/genetics/growth & development ; *Rhizosphere ; *Soil Microbiology ; Genotype ; *Microbiota/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; India ; Phylogeny ; },
abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.},
}

*Triticum/microbiology/genetics/growth & development
*Rhizosphere
*Soil Microbiology
Genotype
*Microbiota/genetics
*Soil/chemistry
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
India
Phylogeny

@article {pmid41905742,
year = {2026},
author = {Wu, Z and Duan, A and Liu, Y and Chen, R and Md Din, MF and Sanjaya, EH and Ali, EAE and Saad, A and Liu, Z and Chen, H},
title = {Mechanistic insights into sulfate-driven performance adaptation and membrane fouling in a UASB-SBR-AXMBR system: metabolic network reconstruction and microbial community succession.},
journal = {Environmental research},
volume = {299},
number = {},
pages = {124374},
doi = {10.1016/j.envres.2026.124374},
pmid = {41905742},
issn = {1096-0953},
mesh = {*Bioreactors/microbiology ; *Sulfates/metabolism ; *Waste Disposal, Fluid/methods ; Membranes, Artificial ; Metabolic Networks and Pathways ; Wastewater ; Nitrogen/metabolism ; *Microbiota ; Bacteria ; },
abstract = {Sulfate-rich wastewater poses considerable challenges to the operational stability of biological treatment systems. This study investigated the long-term (294 days) response of a combined UASB-SBR-AXMBR process to stepwise increases in sulfate concentration from 100 to 2000 mg/L. The system maintained stable carbon and nitrogen removal performance under sulfate stress, with COD removal exceeding 90.3% and total nitrogen removal stabilizing at 85.5% via a partial nitritation-anammox (PN/A) pathway. However, high sulfate loading significantly intensified membrane fouling, with the primary driving factor likely being the co-deposition of elemental sulfur (S[0]) and soluble extracellular polymeric substances (S-EPS). Microbial analysis revealed persistent enrichment of Bacteroidota and Proteobacteria in the SBR, alongside a marked increase in Anammoxoglobus (from 17.1% to 51.2%) in the Anaerobic Ammonia Oxidation Membrane Bioreactor (AXMBR), underpinning system resilience. Metagenomic profiling further indicated adaptive shifts in key nitrogen-cycling genes (hao, amoA) and sulfur metabolism pathways. Notably, sulfate-reducing bacteria (SRB) outcompeted methanogens, redirecting carbon flow from methanogenesis to sulfur reduction, while niche diversification in the AXMBR expanded nitrogen removal pathways. These findings provide new mechanistic insights into the adaptive responses of integrated bioprocesses under sulfate stress and provide practical guidance for the treatment of high-sulfate industrial wastewaters such as monosodium glutamate effluent.},
}

*Bioreactors/microbiology
*Sulfates/metabolism
*Waste Disposal, Fluid/methods
Membranes, Artificial
Metabolic Networks and Pathways
Wastewater
Nitrogen/metabolism
*Microbiota
Bacteria

@article {pmid41950533,
year = {2026},
author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X},
title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128511},
doi = {10.1016/j.micres.2026.128511},
pmid = {41950533},
issn = {1618-0623},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/drug therapy/diagnosis ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Metabolomics/methods ; Metagenomics/methods ; Feces/microbiology ; Proteomics/methods ; Drug Monitoring/methods ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/therapy/drug therapy/diagnosis
*Gastrointestinal Microbiome/genetics
Dysbiosis/microbiology
Metabolomics/methods
Metagenomics/methods
Feces/microbiology
Proteomics/methods
Drug Monitoring/methods
Multiomics

@article {pmid41968748,
year = {2026},
author = {Hilpert, K},
title = {Peptidomics: A New Dimension in Microbiome Research.},
journal = {Protein and peptide letters},
volume = {33},
number = {2},
pages = {488-496},
doi = {10.2174/0109298665436241260327111926},
pmid = {41968748},
issn = {1875-5305},
mesh = {Humans ; *Proteomics/methods ; *Gastrointestinal Microbiome ; *Peptides/metabolism ; Metabolomics/methods ; *Microbiota ; },
abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.},
}

Humans
*Proteomics/methods
*Gastrointestinal Microbiome
*Peptides/metabolism
Metabolomics/methods
*Microbiota

@article {pmid42035799,
year = {2026},
author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K},
title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {408},
number = {},
pages = {121858},
doi = {10.1016/j.jad.2026.121858},
pmid = {42035799},
issn = {1573-2517},
mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; Young Adult ; Feces/microbiology ; Case-Control Studies ; },
abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.

METHODS: Fecal samples were collected from 121 first-episode, drug-naïve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.

RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.

CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.},
}

Humans
*Major Depressive Disorder/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Male
Female
Adult
Young Adult
Feces/microbiology
Case-Control Studies

@article {pmid42068598,
year = {2026},
author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J},
title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128530},
doi = {10.1016/j.micres.2026.128530},
pmid = {42068598},
issn = {1618-0623},
mesh = {Animals ; *Anthozoa/microbiology/genetics ; *Vibrio/pathogenicity/genetics ; Metagenomics ; Symbiosis ; *Rhodobacteraceae/genetics/physiology ; Coral Reefs ; Gene Expression Profiling ; Transcriptome ; Virulence/genetics ; Microbiota ; Microalgae/genetics ; Photosynthesis/genetics ; Vibrio Infections ; },
abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.},
}

Animals
*Anthozoa/microbiology/genetics
*Vibrio/pathogenicity/genetics
Metagenomics
Symbiosis
*Rhodobacteraceae/genetics/physiology
Coral Reefs
Gene Expression Profiling
Transcriptome
Virulence/genetics
Microbiota
Microalgae/genetics
Photosynthesis/genetics
Vibrio Infections

@article {pmid42108291,
year = {2026},
author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Metagenomic Assembly and Gene Prediction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {63-89},
pmid = {42108291},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.},
}

*Metagenomics/methods
*Metagenome
*Computational Biology/methods
Molecular Sequence Annotation
Contig Mapping/methods
Software
Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid42108292,
year = {2026},
author = {Guo, JX and Gao, YZ},
title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {91-103},
pmid = {42108292},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.},
}

*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Humans
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid42108295,
year = {2026},
author = {Peng, B and Chang, X},
title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {147-164},
pmid = {42108295},
issn = {1940-6029},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; },
abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.},
}

Humans
*Gastrointestinal Microbiome
*Lung/metabolism
*Metabolomics/methods
Lung Diseases/metabolism/microbiology
Metagenomics/methods
Dysbiosis
Animals
*Genomics/methods
Proteomics/methods

@article {pmid42112348,
year = {2026},
author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H},
title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1782828},
pmid = {42112348},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; },
abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.},
}

Humans
*Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology
Dysbiosis/immunology
Animals
*Microbiota/immunology
*Gastrointestinal Microbiome/immunology
Autoimmunity

@article {pmid42112890,
year = {2026},
author = {Sorokin, DY and Khot, V and Merkel, AY and Mosier, D and Bale, NJ and Koenen, M and Strous, M},
title = {Physiology, functional genomics, and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., the first isolated haloalkaliphile within Verrucomicrobiota, representing a new family, Verruconatronumaceae fam. nov.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0047526},
doi = {10.1128/aem.00475-26},
pmid = {42112890},
issn = {1098-5336},
abstract = {Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1[T] (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch, and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose, and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1[T] features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1[T] (JCM 35393[T]=UQM 41574[T]) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.IMPORTANCEAlkaline soda lakes and soils are extreme habitats dominated by obligate haloalkaliphic prokaryotes, some of which can produce alkali- and salt-stable polysaccharide-degrading exoenzymes useful for industrial and domestic applications. However, so far, little was known about the microbial potential for mineralization of acidic polysaccharides, such as alginate, in these habitats. The described isolates are the first representatives of a new family within the phylum Verrucomicrobiota specializing in the degradation of alginate and related polysaccharides. We present the key enzymatic machinery for alginate breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example, in washing powders and biomass waste recycling. Furthermore, the new family is one of the most abundant taxa in alkaline environments, and these environments are not known to harbor signature alginate producing biota, such as brown algae. This way, our study opens a new window on polysaccharide turnover in alkaline environments.},
}

@article {pmid42113811,
year = {2026},
author = {Mussa, AJ and Ruboha, JO and Kabota, SA and Martin, MJ and Mwatawala, MW},
title = {Elevation and land use shape soil entomopathogenic fungal communities in the Uluguru mountains, Tanzania: Insights from metagenomic and culture-based approaches.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348781},
pmid = {42113811},
issn = {1932-6203},
mesh = {Tanzania ; *Soil Microbiology ; Animals ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Biodiversity ; Soil/chemistry ; Metagenomics/methods ; *Mycobiome ; },
abstract = {BACKGROUND: Soil-borne entomopathogenic fungi (EPFs) support ecological regulation of pests, yet their distribution across tropical mountain agroecosystems is poorly characterized. The study conducted between April and December 2024, evaluated diversity and distribution of soil EPF along the Uluguru Mountains slopes in Morogoro, Tanzania.

METHODS: Twenty-four soil samples were collected from cultivated and fallow soils at low (518 m), medium (1100 m), and high (1700 m) elevations on the Uluguru slopes (Morogoro, Tanzania). Amplicon sequencing of the ITS region profiled fungal communities, and selective isolation with ITS barcoding confirmed cultivable taxa. Diversity indices, Bray-Curtis dissimilarity, Principal Coordinate Analysis (PCoA), and PERMANOVA evaluated patterns across elevation and land use.

RESULTS: Fourteen EPF species in 12 genera were detected, dominated by Ophiocordycipitaceae (56.1%) and Clavicipitaceae (37.8%). Purpureocillium lilacinum, Metarhizium anisopliae, Clonostachys rosea, and Pochonia chlamydosporia were widespread. Cultivated soils at medium- and high elevations showed greater richness and diversity (1.37 and 1.57) than fallows (0.64 and 0.48) respectively, while high-altitude fallows were strongly dominated by Metapochonia suchlasporia. Community composition clustered by land use, with elevation as a secondary driver (PERMANOVA p = 0.06). Selected P. lilacinum and C. rosea species caused 10-50% mortality of Spodoptera frugiperda larvae in preliminary laboratory assays.

CONCLUSIONS: Elevation and land use jointly structure EPF communities in the Uluguru Mountains. Some taxa showed preliminary pathogenicity in laboratory assays, indicating potential for future evaluation as biological control agents in smallholder farming systems. Public deposition of sequencing reads will facilitate reuse and benchmarking.},
}

Tanzania
*Soil Microbiology
Animals
*Fungi/genetics/classification/isolation & purification
*Altitude
Biodiversity
Soil/chemistry
Metagenomics/methods
*Mycobiome

@article {pmid42116123,
year = {2026},
author = {Zhou, J and Cheng, H and Zhang, Y and Liu, T and Chen, X and Lea-Smith, DJ and Todd, JD and Liu, J and He, X and Liu, R and Zhang, XH},
title = {Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00908-5},
pmid = {42116123},
issn = {2524-6372},
support = {BB/Y008332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/X014428//Natural Environmental Research Council/ ; NE/P012671//Natural Environmental Research Council/ ; RPG-2020-413//Leverhulme Trust/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2025YFF0516900&2025YFF0516903//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.

RESULTS: To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4[+] and SiO3[2-]) based on Pearson's correlation analysis.

CONCLUSION: This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.},
}

@article {pmid42116469,
year = {2026},
author = {Liu, D and Li, J and Zhang, J and Zhang, C},
title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {236},
number = {},
pages = {119201},
doi = {10.1016/j.foodres.2026.119201},
pmid = {42116469},
issn = {1873-7145},
mesh = {*Carbon Dioxide/chemistry ; *Taste ; *Microbiota ; *Vegetables/microbiology/metabolism/chemistry ; *Food Microbiology ; *Atmosphere ; Biogenic Amines/analysis/metabolism ; Food Handling/methods ; Volatile Organic Compounds/analysis ; },
abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.},
}

*Carbon Dioxide/chemistry
*Taste
*Microbiota
*Vegetables/microbiology/metabolism/chemistry
*Food Microbiology
*Atmosphere
Biogenic Amines/analysis/metabolism
Food Handling/methods
Volatile Organic Compounds/analysis

@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 ; *Photobacterium/physiology ; *Penaeidae/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Metagenome ; Muscles/microbiology ; },
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
*Photobacterium/physiology
*Penaeidae/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Gastrointestinal Microbiome
Metagenomics
*Metagenome
Muscles/microbiology

@article {pmid42104576,
year = {2026},
author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R},
title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70246},
doi = {10.1111/aji.70246},
pmid = {42104576},
issn = {1600-0897},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; },
abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.

METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.

RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.

CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).},
}

Humans
Female
Pregnancy
*Placenta/microbiology
*Premature Birth/microbiology/immunology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics

@article {pmid42104663,
year = {2026},
author = {Yang, KL and Zhai, JN and Ye, JW and Zhang, XN and Wei, QC and Wang, H and Wang, HM and Chu, LL and Yang, J},
title = {Dysbiosis of Gut Archaea is Associated with Obesity and Could be Recovered after Bariatric Surgery.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {4},
pages = {437-446},
doi = {10.3967/bes2026.019},
pmid = {42104663},
issn = {2214-0190},
mesh = {Humans ; *Bariatric Surgery ; *Gastrointestinal Microbiome ; *Obesity/microbiology/surgery ; Male ; Female ; *Archaea/physiology/genetics/classification ; Adult ; Middle Aged ; *Dysbiosis/microbiology ; },
abstract = {OBJECTIVE: Obesity is closely associated with an altered gut microbiota; however, the role of archaea in obesity remains unknown. We aimed to delineate the alterations in gut archaea in obese subjects and explore the changes in bariatric surgery-associated gut archaeal composition.

METHODS: Metagenomic sequencing data from 191 obese subjects and 184 lean controls were retrieved from three public cohorts. Of these, 23 obese patients who underwent bariatric surgery were followed up for 3 months.

RESULTS: The gut archaea of obese subjects showed significantly lower Shannon diversity index than those of lean controls. Principal component analysis of the gut archaea revealed distinct clusters in obese subjects and lean controls. A model using the 20 top archaeal genera discriminated obese from lean controls with an area under the receiver operating characteristic curve (AUC) of 0.79, 0.83, and 0.86 in three cohorts. Ecological analysis showed decreased trans-kingdom correlations between archaea and bacteria in obese subjects compared to those in lean controls, with partial restoration observed after bariatric surgery.

CONCLUSION: This is the first study to demonstrate that obesity is characterized by gut archaeal dysbiosis across multiple cohorts. Bariatric surgery-induced weight loss is associated with significant changes in the gut archaea.},
}

Humans
*Bariatric Surgery
*Gastrointestinal Microbiome
*Obesity/microbiology/surgery
Male
Female
*Archaea/physiology/genetics/classification
Adult
Middle Aged
*Dysbiosis/microbiology

@article {pmid42108288,
year = {2026},
author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L},
title = {A Brief Review of Microbial Omics: Methods and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {1-20},
pmid = {42108288},
issn = {1940-6029},
mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; },
abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.},
}

*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Microbiota/genetics
*Computational Biology/methods
Single-Cell Analysis/methods
Artificial Intelligence
Transcriptome
Metagenomics/methods

@article {pmid42000565,
year = {2026},
author = {Wan, X and Zhan, J and Chen, Z and Wu, B},
title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106196},
doi = {10.1016/j.rvsc.2026.106196},
pmid = {42000565},
issn = {1532-2661},
mesh = {Animals ; *Chickens/microbiology ; *Housing, Animal ; *Ventilation ; Public Health ; *Air Microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Animal Husbandry/methods ; *Drug Resistance, Microbial ; RNA, Ribosomal, 16S/genetics ; Microbiota ; },
abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.},
}

Animals
*Chickens/microbiology
*Housing, Animal
*Ventilation
Public Health
*Air Microbiology
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Animal Husbandry/methods
*Drug Resistance, Microbial
RNA, Ribosomal, 16S/genetics
Microbiota

@article {pmid42055201,
year = {2026},
author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M},
title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {306},
number = {},
pages = {110551},
doi = {10.1016/j.cbpc.2026.110551},
pmid = {42055201},
issn = {1532-0456},
mesh = {Animals ; *Zebrafish/physiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Fluoxetine/toxicity ; *Water Pollutants, Chemical/toxicity ; Homeostasis/drug effects ; Female ; *Feeding Behavior/drug effects ; *Intestines/drug effects ; *Selective Serotonin Reuptake Inhibitors/toxicity ; Intestinal Mucosa/drug effects/metabolism ; },
abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.},
}

Animals
*Zebrafish/physiology/microbiology
*Gastrointestinal Microbiome/drug effects
*Fluoxetine/toxicity
*Water Pollutants, Chemical/toxicity
Homeostasis/drug effects
Female
*Feeding Behavior/drug effects
*Intestines/drug effects
*Selective Serotonin Reuptake Inhibitors/toxicity
Intestinal Mucosa/drug effects/metabolism

@article {pmid42098796,
year = {2026},
author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V},
title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42098796},
issn = {2049-2618},
support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; *Vulva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; *RNA, Messenger/genetics ; Vagina/microbiology ; *Host Microbial Interactions/genetics ; *RNA-Seq/methods ; Transcriptome ; },
abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.},
}

Humans
Female
*Microbiota/genetics
*Vulva/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
*RNA, Messenger/genetics
Vagina/microbiology
*Host Microbial Interactions/genetics
*RNA-Seq/methods
Transcriptome

@article {pmid42100652,
year = {2026},
author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C},
title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799729},
pmid = {42100652},
issn = {2235-2988},
mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; },
abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.},
}

Animals
*Probiotics/administration & dosage
Rats, Wistar
Male
Metagenomics
Rats
Feces/microbiology/chemistry
Disease Models, Animal
*Gastrointestinal Microbiome
*Liver Failure
Cytokines
Ammonia/blood
Dysbiosis
Galactosamine

@article {pmid42100978,
year = {2026},
author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD},
title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.},
journal = {Journal of biosciences},
volume = {51},
number = {},
pages = {},
pmid = {42100978},
issn = {0973-7138},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Female ; Rats ; Pregnancy ; Rats, Wistar ; *Malnutrition/metabolism/microbiology ; Docosahexaenoic Acids/administration & dosage/pharmacology ; Metabolome ; Fetal Development ; Male ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; *Prenatal Exposure Delayed Effects/metabolism ; Xanthophylls ; },
abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
Female
Rats
Pregnancy
Rats, Wistar
*Malnutrition/metabolism/microbiology
Docosahexaenoic Acids/administration & dosage/pharmacology
Metabolome
Fetal Development
Male
Metabolomics
Maternal Nutritional Physiological Phenomena
Dietary Supplements
*Prenatal Exposure Delayed Effects/metabolism
Xanthophylls

@article {pmid42103708,
year = {2026},
author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J},
title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72757-2},
pmid = {42103708},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.},
}

@article {pmid42090957,
year = {2026},
author = {Kämpfer, P and Lipski, A and Lawrence, KS and Olive, WR and Newman, MM and McInroy, JA and Viver, T},
title = {Pseudomonas corni sp. nov., Pseudomonas oplopanacis sp. nov., Pseudomonas salicis sp. nov., Pseudomonas rosaeacicularis sp. nov., Pseudomonas artemisiae sp. nov., Pseudomonas imperatae sp. nov. and Zestomonas ipomoeae sp. nov., isolated from rhizospheres showing plant growth promoting potential.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126719},
doi = {10.1016/j.syapm.2026.126719},
pmid = {42090957},
issn = {1618-0984},
abstract = {Several bacterial strains affiliated with the genera Pseudomonas and Zestomonas were isolated from rhizosphere samples and screened for plant growth-promoting (PGP) traits. Nine strains were analyzed polyphasically, showing ANI and dDDH values below or near species thresholds, together with phenotypic and biochemical traits supporting their differentiation. Genomic analyses revealed a repertoire of PGP-associated functions, including vitamin and cofactor biosynthesis (riboflavin, cobalamin, and thiamin), and high-affinity nutrient acquisition systems as phosphate transporters and phosphonate utilization. All strains encoded traits relevant to the rhizosphere inferred from genome annotation, including genes involved in auxin and cytokinin biosynthesis, oxidative stress tolerance, dissimilatory nitrate reduction, sulfur assimilation, and siderophore production. Metagenomic screening showed that most species are globally distributed across plant-associated, soil, freshwater, and animal-associated habitats. Based on phylogenetic, genomic, and phenotypic evidence, the strains represent seven novel species: Pseudomonas rosaeacicularis sp. nov., with AK-381[T] as the type strain (= LMG 34445[T] = CCM 9596[T]); Pseudomonas corni sp. nov., with AK-10[T] as the type strain (= CCM 9599[T] = LMG 34325[T]); Pseudomonas oplopanacis sp. nov., with AK-188[T] as the type strain (= CCM 9593[T] = LMG 34326[T]); Pseudomonas salicis sp. nov., with AK-309[T] as the type strain (= CCM 9595[T] = LMG 34328[T]); Pseudomonas artemisiae sp. nov., with DT-100[T] as the type strain (= LMG 32880[T] = DSM 115114[T] = CCM 9281[T]); Pseudomonas imperatae sp. nov., with ST-212[T] as the type strain (CCM 9594[T] = LMG 34330[T]); and Zestomonas ipomoeae sp. nov., with ST-55[T] as the type strain (LMG 32881[T] = CCM 9283[T] = DSM 115239[T]).},
}

@article {pmid42092753,
year = {2026},
author = {Palanisamy, M and Babalola, OO and Ramalingam, S},
title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42092753},
issn = {2730-6844},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; },
abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.},
}

*Salvia officinalis/microbiology
*Plant Leaves/microbiology
*Metagenomics
*Endophytes/genetics/classification
*Microbiota
*Metagenome
Bacteria/genetics/classification
Fungi/genetics

@article {pmid42096157,
year = {2026},
author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM},
title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3046},
number = {},
pages = {171-187},
pmid = {42096157},
issn = {1940-6029},
mesh = {*Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism/chemistry ; Bacterial Adhesion ; Bioreactors/microbiology ; *Plankton ; Intestinal Mucosa/microbiology ; Hydrogels/chemistry ; Biofilms/growth & development ; },
abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.},
}

*Clostridioides difficile/physiology
*Gastrointestinal Microbiome
Humans
Mucins/metabolism/chemistry
Bacterial Adhesion
Bioreactors/microbiology
*Plankton
Intestinal Mucosa/microbiology
Hydrogels/chemistry
Biofilms/growth & development

@article {pmid41117699,
year = {2026},
author = {Xie, H and Zhang, X and Liu, X},
title = {The Co-Metabolic Bioremediation of Benzo[a]pyrene Contaminated Soil by Achromobacter xylosoxidans B-2 and Its Effect on Indigenous Microbial Community.},
journal = {Environmental toxicology},
volume = {41},
number = {6},
pages = {330-340},
doi = {10.1002/tox.24576},
pmid = {41117699},
issn = {1522-7278},
support = {2023YFC3709000//National Key Research and Development Program of China/ ; 2018YFC1800600//National Key Research and Development Program of China/ ; 21677093//National Natural Science Foundation of China/ ; 21806100//National Natural Science Foundation of China/ ; },
mesh = {*Achromobacter denitrificans/metabolism/genetics/growth & development ; *Soil Pollutants/metabolism ; *Benzo(a)pyrene/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; Microbiota ; },
abstract = {Benzo[a]pyrene (BaP) is a persistent polycyclic aromatic hydrocarbon (PAH) that poses significant environmental and health risks. Co-metabolic bioremediation, which uses additional carbon sources to enhance microbial degradation, offers a promising approach for BaP removal. This study investigated the effects of different co-metabolic carbon sources on the growth of Achromobacter xylosoxidans B-2 and its efficiency in degrading BaP in both mineral salt medium (MSM) and BaP-contaminated soil. The addition of supplementary carbon sources, particularly starch and salicylic acid, significantly enhanced strain B-2 growth and BaP removal in MSM (p < 0.05), with the highest degradation rate reaching 46.35% in the starch-supplemented group. In soil, salicylic acid and starch also markedly improved BaP degradation, achieving 47.99% and 23.53% removal (both p < 0.01) after 30 days, respectively, compared to only 9.78% in the BaP-only group. Metagenomic analysis revealed that co-substrate amendments significantly altered soil microbiota, enriching PAH-degrading genera such as Achromobacter, especially the introduced A. xylosoxidans. This enrichment was accompanied by reduced overall microbial diversity, indicating strong selective pressure from the amendments. Functional gene profiling based on metagenomic data indicated an increased abundance of key PAH-degrading enzymes, including dioxygenases and dehydrogenases, in response to co-substrate addition. Redundancy analysis further indicated that environmental factors such as pH, organic matter, and phosphorus were significantly correlated with microbial community composition and BaP degradation efficiency. These findings demonstrate that co-metabolism not only enhances BaP removal but also drives functional and ecological changes in soil microbiota, providing mechanistic insight and practical guidance for improved bioremediation strategies.},
}

*Achromobacter denitrificans/metabolism/genetics/growth & development
*Soil Pollutants/metabolism
*Benzo(a)pyrene/metabolism
Biodegradation, Environmental
*Soil Microbiology
Microbiota

@article {pmid41742841,
year = {2026},
author = {Wang, Y and Wu, H and Qu, M and Zhang, C and Xu, Z and Pei, Y and Zhao, C and Wang, J and Ma, S and Lyu, N and Xu, X and Bi, Y and Zhu, B and Gao, GF},
title = {A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {26},
pages = {e74581},
doi = {10.1002/advs.74581},
pmid = {41742841},
issn = {2198-3844},
support = {2023YFC2307101//National Key Research and Development Program of China/ ; 235200810058//Project for Young Scientists of the Joint Funds of Science and Technology Research and Development Plan of Henan Province, China/ ; 30501278//Young TopNotch Talents Foundation of Henan Agricultural University/ ; },
mesh = {Animals ; China ; *Birds/microbiology/genetics ; *Animal Migration/physiology ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Ecosystem ; Animals, Wild/microbiology ; *Microbiota/genetics ; Genomics/methods ; },
abstract = {Migratory birds play an important role in the spread of antimicrobial resistance (AMR); however, gaps in surveillance data from vital regions along migratory flyways across China limit the detection of emergent threats. Here, we assembled 340 metagenomes from 52 bird species covering 11 provincial administrative districts in China, presenting a specialized migratory microbial genome and gene catalog to archive the genomic and functional diversity of gut microbiomes in wild birds. This comprehensive migratory bird microbial genome and gene (MBGG) catalog includes 5823 metagenome-assembled genomes (MAGs), 13 072 plasmid sequences, and 44 974 viral genomes, which represent 1709 candidate species spanning 36 phyla. The catalog also contains over 20 million non-redundant protein-encoding genes, the use of which is confirmed by the mining of 15 678 secondary metabolite biosynthetic gene clusters, 1814 known antibiotic resistance genes, and 7219 virulence factors. The number of clinically critical ARGs identified in Grus japonensis was the highest, followed by Cygnus cygnus and Sibirionetta formosa, which indicated that these species are hotspot species of clinically critical AMR dissemination. Moreover, we mapped the profile of bacterial zoonotic/opportunistic pathogens carried by wild birds and evaluated their associations with publicly available genomes. Finally, the precise migratory movements for 10 bird species using a global positioning system tracking system help to assess the movement of microorganisms and AMR risk. Collectively, this valuable resource provides the basis for the integration and unification of global wild bird microbiomes, timely sharing, and assessing the uncertainty of migratory microbiomes in the future.},
}

Animals
China
*Birds/microbiology/genetics
*Animal Migration/physiology
Metagenome/genetics
*Gastrointestinal Microbiome/genetics
Ecosystem
Animals, Wild/microbiology
*Microbiota/genetics
Genomics/methods

@article {pmid41747414,
year = {2026},
author = {Zhang, Q and Bao, C and Wang, K and Liu, L and Huang, H and Cai, S and Lu, H and Zheng, S and Luo, J and Kong, J},
title = {The impact of bronchiectasis on the lung microbiota of community-acquired pneumonia patients: An mNGS-based study.},
journal = {Computational biology and chemistry},
volume = {123},
number = {},
pages = {108948},
doi = {10.1016/j.compbiolchem.2026.108948},
pmid = {41747414},
issn = {1476-928X},
mesh = {Humans ; Male ; Female ; *Bronchiectasis/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Middle Aged ; Aged ; Retrospective Studies ; *Lung/microbiology ; *Pneumonia/microbiology/complications ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Changes in lung microbiota are associated with bronchiectasis and its clinical parameters. However, it is unclear whether distinct microbiota patterns reflect the characteristic lung status in bronchiectasis.

OBJECTIVE: This study aimed to identify key microbiota associated with community-acquired pneumonia (CAP) complicated with bronchiectasis and explore its relationship with clinical features.

METHODS: A single-center retrospective study enrolled 59 CAP patients who underwent bronchoscopy. Bronchoalveolar lavage samples were analyzed using metagenomic next-generation sequencing. The top 10 bacterial species and α- and β-diversity indices were compared between patients with and without bronchiectasis. Linear discriminant analysis was used to identify distinctive microbes. Spearman was used to analyze the correlation between the distinctive microbes and clinical characteristics.

RESULTS: The CAP with bronchiectasis group was dominated by Pseudomonas, while Prevotella dominated the non-bronchiectasis group. The bronchiectasis group had significantly lower α-diversity and distinct β-diversity compared to the non-bronchiectasis group. Stutzerimonas was identified as a key microbe in the bronchiectasis group, positively correlated with lymphocyte percentage and count, and negatively correlated with neutrophil percentage. Pseudomonas aeruginosa and Nocardia pneumoniae were key species in the bronchiectasis group.

CONCLUSION: The composition and diversity of lung microbiota in patients with CAP combined with bronchiectasis are significantly different. The genus Stutzerimonas can serve as a key marker to distinguish bronchiectasis from non-bronchiectasis patients to reflect the characteristic lung microbiota status. This study provides a potential basis for disease stratification and personalized management.},
}

Humans
Male
Female
*Bronchiectasis/microbiology/complications
*Community-Acquired Infections/microbiology/complications
*Microbiota
Middle Aged
Aged
Retrospective Studies
*Lung/microbiology
*Pneumonia/microbiology/complications
Community-Acquired Pneumonia

@article {pmid41763967,
year = {2026},
author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC},
title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.},
journal = {Annals of the rheumatic diseases},
volume = {85},
number = {5},
pages = {806-817},
doi = {10.1016/j.ard.2026.01.018},
pmid = {41763967},
issn = {1468-2060},
mesh = {Humans ; *Leukocyte L1 Antigen Complex/analysis ; Male ; *Feces/chemistry/microbiology ; Female ; *Arthritis, Psoriatic/microbiology/immunology/diagnosis ; *Gastrointestinal Microbiome ; Phenotype ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Adult ; Biomarkers/analysis ; Cytokines/blood ; Metagenomics ; },
abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.},
}

Humans
*Leukocyte L1 Antigen Complex/analysis
Male
*Feces/chemistry/microbiology
Female
*Arthritis, Psoriatic/microbiology/immunology/diagnosis
*Gastrointestinal Microbiome
Phenotype
Middle Aged
*Inflammatory Bowel Diseases/microbiology/diagnosis
Adult
Biomarkers/analysis
Cytokines/blood
Metagenomics

@article {pmid41825740,
year = {2026},
author = {Alvarado, DA and Holthaus, TA and Martell, S and Southey, NL and Atallah, M and Sarma, R and Revilla, D and Brown, M and Mehta, T and Khan, NA and Holscher, HD},
title = {Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.},
journal = {The Journal of nutrition},
volume = {156},
number = {5},
pages = {101473},
doi = {10.1016/j.tjnut.2026.101473},
pmid = {41825740},
issn = {1541-6100},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Cross-Over Studies ; *Dietary Fiber/administration & dosage/pharmacology ; Middle Aged ; Male ; Female ; *Zea mays/chemistry ; Aged ; Double-Blind Method ; *Executive Function/drug effects ; Feces/microbiology ; Cognition/drug effects ; },
abstract = {BACKGROUND: Dietary fiber may support cognition through gastrointestinal-microbiota mechanisms, but clinical evidence is limited.

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

METHODS: In a randomized, double-blind, crossover trial, 42 healthy adults (45-75 y) consumed SCF (18 g/d) or a maltodextrin placebo control (CON: 22 g/d) for 4 wk, separated by a washout. Cognitive outcomes included executive function with event-related potentials, relational memory, neuropsychological performance, and mood. Secondary outcomes included fecal microbiota, metabolomics, and gastrointestinal tolerance. Tertiary analyses related microbial and metabolite changes to cognitive improvements using correlation, mediation, and moderation models, and explored SCF fermentation pathways with 16S-predicted functional profiling, shotgun metagenomics, and in vitro culturing.

RESULTS: SCF improved reaction times (RT) during congruent (β = -9.8 ms, 95% confidence interval (CI): -18.4, -1.2, false discovery rate (FDR) P = 0.01) and incongruent (β = -14.2 ms, 95% CI: -22.8, -5.6, FDR P = 0.003) flanker trials and increased Parabacteroides (∼4-fold, β = 1.44 log, 95% CI: 1.01, 1.88, FDR P < 0.001). At the SCF endpoint, congruent RT tended to be inversely associated with fecal acetate (ρ = -0.33) and propionate (ρ = -0.36), whereas Parabacteroides was marginally positively associated with acetate (ρ = 0.34) (all FDR P < 0.1). Moderation analyses indicated that SCF-RT relation varied by Parabacteroides magnitude change. At endpoint, SCF increased the predicted functional potential of carbohydrate-related KEGG Orthologs and pathways (FDR P < 0.05). In vitro culturing confirmed Parabacteroides distasonis ferments SCF.

CONCLUSIONS: SCF consumption improved attentional inhibition, altered the gut microbiota, and selectively enriched Parabacteroides. Although mediation analyses did not support a direct microbiota-to-cognition pathway, moderation analyses suggested that SCF-related cognitive effects may depend in part on Parabacteroides abundance. Collectively, these findings suggest that certain cognitive benefits of SCF consumption may be partly underpinned by the gut microbiota. This study was registered at clinicaltrials.gov as NCT05066425 (https://clinicaltrials.gov/study/NCT05066425).},
}

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

@article {pmid41882673,
year = {2026},
author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C},
title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41882673},
issn = {1479-5876},
mesh = {Humans ; *Psoriasis/microbiology/virology ; Biomarkers/metabolism ; *Gastrointestinal Microbiome ; *Virome ; Male ; Female ; Case-Control Studies ; Adult ; Middle Aged ; *Environment ; Feces/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.

METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.

RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.

CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.

TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.},
}

Humans
*Psoriasis/microbiology/virology
Biomarkers/metabolism
*Gastrointestinal Microbiome
*Virome
Male
Female
Case-Control Studies
Adult
Middle Aged
*Environment
Feces/microbiology
Metagenomics

@article {pmid42019232,
year = {2026},
author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X},
title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.},
journal = {International journal of food microbiology},
volume = {456},
number = {},
pages = {111785},
doi = {10.1016/j.ijfoodmicro.2026.111785},
pmid = {42019232},
issn = {1879-3460},
mesh = {*Quorum Sensing ; *Homoserine/analogs & derivatives/metabolism ; *Lactones/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Carbon-Sulfur Lyases/metabolism/genetics ; Fermentation ; Bacterial Proteins/metabolism/genetics ; Microbiota ; },
abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.},
}

*Quorum Sensing
*Homoserine/analogs & derivatives/metabolism
*Lactones/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
Carbon-Sulfur Lyases/metabolism/genetics
Fermentation
Bacterial Proteins/metabolism/genetics
Microbiota

@article {pmid42086823,
year = {2026},
author = {Ismaeil, M and Saeed, AM and Donia, SA and El-Sayed, WS},
title = {Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42086823},
issn = {2045-2322},
mesh = {*Hot Springs/microbiology ; *Sulfur/metabolism ; *RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Soil Microbiology ; Hot Temperature ; Proteobacteria/genetics/metabolism ; },
abstract = {Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.},
}

*Hot Springs/microbiology
*Sulfur/metabolism
*RNA, Ribosomal, 16S/genetics
Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Soil Microbiology
Hot Temperature
Proteobacteria/genetics/metabolism

@article {pmid42087721,
year = {2026},
author = {Pan, W and Tang, S and Wanek, W and Luo, Z and Chen, J and Yang, Y and Ge, T and Marsden, KA and Liang, G and Chadwick, DR and Chen, X and Gregory, AS and Wu, L and Liang, Y and Jones, DL and Ma, Q},
title = {Microbial Community Traits and Necromass Dynamics Shape Soil Carbon Accumulation.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70906},
doi = {10.1111/gcb.70906},
pmid = {42087721},
issn = {1365-2486},
support = {U24A20575//National Natural Science Foundation of China/ ; 32573140//National Natural Science Foundation of China/ ; 32402680//National Natural Science Foundation of China/ ; 2024M752818//China Postdoctoral Science Foundation/ ; 2026SNJF084//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 2025SNJF025//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 202303AC100013//Yunnan Key Research and Development Program/ ; 05//Smart Fertilization Project/ ; BBS/E/RH/23NB0007//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; //Lawes Agricultural Trust/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; Fertilizers/analysis ; *Microbiota ; *Carbon Sequestration ; },
abstract = {Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long-term response to fertilisation remains unclear. Using the 180-year Broadbalk Experiment (the world's longest-running fertilisation trial; Rothamsted, UK), combined with [14]C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource-limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no-fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy-intensive enzyme synthesis. This metabolic efficiency facilitated a dual-pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg[-1], while microbial assimilation and necromass accumulation concurrently increased mineral-associated organic carbon (MAOC) from 6.8 to 21.5 g kg[-1]. Conversely, inorganic fertilisation induced an oligotrophic 'mining' strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon-limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta-analysis of field experiments (0-120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time-dependent manner, reaching a 77% gain after 80 years (three-fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long-term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism/analysis
Fertilizers/analysis
*Microbiota
*Carbon Sequestration

@article {pmid42088021,
year = {2026},
author = {Wang, A and Wang, Q and Zhang, T and Qi, G and Ren, W and Tian, W and Chen, J},
title = {Integrated multi-omics profiling reveals phenotype- and tissue-specific host-microbiota interactions in paired tumor and peritumoral tissues of advanced gastric cancer patients from Northwest China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1763765},
pmid = {42088021},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; China ; Female ; Male ; Middle Aged ; Gene Expression Profiling ; Gastric Mucosa/microbiology/pathology ; Aged ; Phenotype ; *Host Microbial Interactions/genetics ; Metagenomics ; *Microbiota ; Transcriptome ; Adult ; Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Multiomics ; },
abstract = {BACKGROUND: Advanced gastric cancer (AGC) exhibits a high incidence in Northwest China, largely attributed to region-specific dietary patterns and environmental exposures. Its pathogenesis involves complex host-microbiota crosstalk, which has not yet been comprehensively elucidated through integrated multi-omics approaches. Herein, we employed trasncriptomic and shotgun metagenomic sequencing on paired tumoral and peritumoal mucosal tissues from 88 AGC patients in Northwest China. Our aim was to systematically characterize host gene expression profiles, the composition and functional potential of the gastric mucosal microbiota, and their intricate interrelationships.

RESULTS: Transcriptomic profiling clearly distinguished tumoral from peritumoral regions (PERMANOVA, R[2] = 0.24, P = 0.0001), with 8870 differentially expressed genes (DEGs) identified between the two tissue types. Tumor tissues harbored 8377 up-regulated DEG, which were enriched in extracellular matrix (ECM) organization, cell cycle regulation, signaling transduction, and inflammatory pathways (e.g., PI3K-Akt, IL-17 signaling). In contrast, peritumoral tissues showed 493 up-regulated DEGs primarily associated with metabolic processes. Host gene expression was significantly modulated by Lauren classification in tumoral mucosa (P = 0.025) and by Helicobacter pylori (Hp) infection in peritumoral tissues (P = 0.0424). Hp-infected tissues exhibited 65 up-regulated DEGs linked to transcriptional misregulation in cancer, inflammation, immune activation and mitochondrial pathways. Lauren subtypes displayed distinct transcriptomic signatures: intestinal-type AGC was enriched in metabolic processes, diffuse-type in immune and signal transduction pathways, and mixed-type in Ras/MAPK/ErbB and NF-κB signaling pathways. Correlation analysis between the 8870 DEGs and seven differentially abundant bacterial species (e.g., Serratia surfactantfaciens, Pseudomonas protegens, Prevotella jejuni, and Streptococcus infantis) revealed 13199 significant correlations. Among these, S. surfactantfaciens and P. protegens exhibited the strongest connectivity with host genes. Functionally, the correlated DEGs were involved in ECM structure, cell cycle progression, immune and inflammatory responses, cellular proliferation and differentiation, and metabolic processes.

CONCLUSIONS: Our findings demonstrated phenotype- and tissue-specific regulation of host gene expression in AGC and revealed extensive host-microbe interactions. This work fills a critical gap in multi-omics research on AGC in the Northwest Chinese population and suggests potential diagnostic and therapeutic targets for AGC.},
}

Humans
*Stomach Neoplasms/microbiology/pathology/genetics
China
Female
Male
Middle Aged
Gene Expression Profiling
Gastric Mucosa/microbiology/pathology
Aged
Phenotype
*Host Microbial Interactions/genetics
Metagenomics
*Microbiota
Transcriptome
Adult
Helicobacter Infections/microbiology
*Gastrointestinal Microbiome
Helicobacter pylori
Multiomics

@article {pmid41985316,
year = {2026},
author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P},
title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214878},
doi = {10.1016/j.bioadv.2026.214878},
pmid = {41985316},
issn = {2772-9508},
mesh = {Animals ; *Inulin/chemistry/pharmacology ; *Diet, High-Fat/adverse effects ; *Bentonite/chemistry/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Rats ; *Inflammation/drug therapy/metabolism/etiology ; Rats, Sprague-Dawley ; },
abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.},
}

Animals
*Inulin/chemistry/pharmacology
*Diet, High-Fat/adverse effects
*Bentonite/chemistry/pharmacology
Gastrointestinal Microbiome/drug effects
Male
Rats
*Inflammation/drug therapy/metabolism/etiology
Rats, Sprague-Dawley

@article {pmid42067917,
year = {2026},
author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q},
title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42067917},
issn = {2049-2618},
support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Capsaicin/pharmacology ; Fecal Microbiota Transplantation ; *Aminolevulinic Acid/metabolism ; Male ; TRPV Cation Channels/genetics/metabolism ; Bacteria/classification/metabolism/genetics ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Metagenomics ; Metabolomics ; Specific Pathogen-Free Organisms ; },
abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.

RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.

CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Capsaicin/pharmacology
Fecal Microbiota Transplantation
*Aminolevulinic Acid/metabolism
Male
TRPV Cation Channels/genetics/metabolism
Bacteria/classification/metabolism/genetics
*Blood Glucose/drug effects
Mice, Inbred C57BL
Metagenomics
Metabolomics
Specific Pathogen-Free Organisms

@article {pmid42084764,
year = {2026},
author = {Joshi, G and Khannam, KS},
title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42084764},
issn = {1432-072X},
mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.},
}

*Microbiota
*Biotechnology
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Biodegradation, Environmental

@article {pmid41412926,
year = {2026},
author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A},
title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.},
journal = {Trends in microbiology},
volume = {34},
number = {5},
pages = {472-484},
doi = {10.1016/j.tim.2025.11.016},
pmid = {41412926},
issn = {1878-4380},
mesh = {Humans ; *Noncommunicable Diseases/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Communicable Diseases/microbiology/therapy ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Dysbiosis/microbiology ; Computational Biology/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.},
}

Humans
*Noncommunicable Diseases/microbiology/therapy
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Communicable Diseases/microbiology/therapy
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Dysbiosis/microbiology
Computational Biology/methods
Feces/microbiology
Bacteria/genetics/classification/isolation & purification

@article {pmid41733350,
year = {2026},
author = {Bian, K and Busch, A and Norton, J and Bott, C and Gonzalez, R and Curtis, K and Tolofari, D and Khunjar, W and Graham, KE and Pinto, AJ},
title = {Quantitative metagenomics using a portable protocol.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0217925},
pmid = {41733350},
issn = {1098-5336},
support = {5100//Water Research Foundation/ ; DE-EE0009270//U.S. Department of Energy/ ; },
mesh = {*Metagenomics/methods ; *Microbiota ; *Wastewater/microbiology ; Nanopore Sequencing/methods ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; DNA/analysis/genetics/isolation & purification ; RNA, Ribosomal, 16S/analysis/genetics ; RNA, Ribosomal, 18S/analysis/genetics ; DNA Barcoding, Taxonomic ; Workflow ; },
abstract = {A field-deployable DNA sequencing approach for quantitative microbial community profiling can enable rapid responses for a range of applications in the water sector-from process control to wastewater surveillance. Current quantitative approaches require complex instrumentation and have long turnaround times for DNA recovery and absolute quantitation. In this study, we report a field-deployable rapid detection and rapid absolute quantitation (rD+rQ) workflow that leverages real-time Nanopore sequencing for quantitative metagenomics. This workflow integrates a high-molecular-weight DNA recovery protocol for diverse environmental matrices of relevance to the water sector, and multiplexed Nanopore sequencing with barcoded spike-in-based calibration (BSINC). BSINC using multispecies genomic spike-in controls exhibits significantly higher calibration accuracy compared to conventional approaches that utilize either a single DNA fragment or single organism spike-in controls. Dynamic detection and quantitation limits were established based on the coverage fraction of sequenced genomes and the coefficient of variation of genome copy numbers across replicates to enhance the accuracy and precision of microbial quantitation. The rD+rQ workflow achieves species-level identification and absolute quantitative results comparable to digital PCR in environmental samples. This portable laboratory and easy-to-use rD+rQ workflow should facilitate rapid decision-making for the water industry.IMPORTANCERapid and real-time monitoring of microbial communities is critical for a vast array of applications in environmental microbiology and biotechnology. While recent developments in portable sequencing technologies and associated workflows make onsite analysis possible, these approaches do not provide quantitative data on microbial concentrations. In this study, we present a sample and data processing workflow that enables nontargeted and quantitative microbial community profiling and demonstrate its validity on complex environmental samples. This approach for acquiring quantitative data can drive rapid decision-making from bioprocess control to wastewater-based epidemiology.},
}

*Metagenomics/methods
*Microbiota
*Wastewater/microbiology
Nanopore Sequencing/methods
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
DNA/analysis/genetics/isolation & purification
RNA, Ribosomal, 16S/analysis/genetics
RNA, Ribosomal, 18S/analysis/genetics
DNA Barcoding, Taxonomic
Workflow

@article {pmid41935918,
year = {2026},
author = {Lazarevic, V and Ruppé, E and Schrenzel, J},
title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.},
journal = {Trends in microbiology},
volume = {34},
number = {5},
pages = {449-453},
doi = {10.1016/j.tim.2026.03.008},
pmid = {41935918},
issn = {1878-4380},
mesh = {*Metagenomics/methods/trends ; Humans ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.},
}

*Metagenomics/methods/trends
Humans
Computational Biology/methods
Microbiota/genetics

@article {pmid42012901,
year = {2026},
author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T},
title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {17},
pages = {13990-13997},
doi = {10.1021/acs.jafc.5c16498},
pmid = {42012901},
issn = {1520-5118},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Sweetening Agents/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Thiazines/metabolism ; Caco-2 Cells ; *Intestinal Mucosa/metabolism/drug effects/microbiology ; Butyrates/metabolism ; Male ; *Intestines/microbiology/drug effects ; Child ; Intestinal Barrier Function ; },
abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Sweetening Agents/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Thiazines/metabolism
Caco-2 Cells
*Intestinal Mucosa/metabolism/drug effects/microbiology
Butyrates/metabolism
Male
*Intestines/microbiology/drug effects
Child
Intestinal Barrier Function

@article {pmid42033990,
year = {2026},
author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W},
title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.},
journal = {Biomaterials},
volume = {333},
number = {},
pages = {124234},
doi = {10.1016/j.biomaterials.2026.124234},
pmid = {42033990},
issn = {1878-5905},
mesh = {*Biofilms/drug effects ; *Oxygen/chemistry ; *Microbiota/drug effects ; Animals ; Indocyanine Green/chemistry/pharmacology ; Humans ; Molybdenum/chemistry/pharmacology ; Photochemotherapy ; *Periodontitis/microbiology/drug therapy ; Mice ; Photosensitizing Agents/pharmacology/chemistry ; *Nanoparticles/chemistry ; Oxides/chemistry/pharmacology ; },
abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.},
}

*Biofilms/drug effects
*Oxygen/chemistry
*Microbiota/drug effects
Animals
Indocyanine Green/chemistry/pharmacology
Humans
Molybdenum/chemistry/pharmacology
Photochemotherapy
*Periodontitis/microbiology/drug therapy
Mice
Photosensitizing Agents/pharmacology/chemistry
*Nanoparticles/chemistry
Oxides/chemistry/pharmacology

@article {pmid42080299,
year = {2026},
author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J},
title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.},
journal = {Molecular ecology},
volume = {35},
number = {9},
pages = {e70367},
doi = {10.1111/mec.70367},
pmid = {42080299},
issn = {1365-294X},
support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; },
abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.},
}

*Lakes/virology/microbiology
*Viruses/genetics/classification
Metagenomics
Fresh Water/virology
Microbiota/genetics
Ecosystem
Geologic Sediments/virology
Biodiversity
Metagenome

@article {pmid42084116,
year = {2026},
author = {Qi, J and Liang, C and Zhang, C and Wang, M and Wei, G and Jiao, S},
title = {Intensifying Aridity Undermines the Role of Soil Biodiversity in Supporting Ecosystem Stability.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70903},
doi = {10.1111/gcb.70903},
pmid = {42084116},
issn = {1365-2486},
support = {42477129//National Science Foundation of China/ ; JYB2025XDXM706//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Biodiversity ; *Soil Microbiology ; *Climate Change ; China ; *Soil/chemistry ; *Ecosystem ; *Desert Climate ; },
abstract = {Biodiversity is widely recognized for enhancing ecosystem stability, yet its contribution is highly sensitive to climate change. However, whether and how climatic factors, particularly aridity, modulate the role of soil biodiversity in stabilizing ecosystems remains poorly understood. Here, we integrated a comprehensive soil survey of 265 dryland agricultural fields along a 3800 km east-west transect in China with a global meta-dataset encompassing 996 sites across six continents. Our analysis revealed a positive association between soil biodiversity and ecosystem stability, quantified using 11-year Normalized Difference Vegetation Index (NDVI) data (2012-2022). Critically, both our field data and global synthesis revealed that increasing aridity significantly weakened this biodiversity-stability relationship. The decline in soil microbial network complexity with increasing aridity partially explains this decoupling. Metagenomic analyses further showed that as aridity increased, microbial life history strategies shifted toward greater investment in stress tolerance at the expense of growth yield and resource acquisition. Together, our findings represent a substantial advance in revealing how intensifying aridity undermines the role of soil biodiversity in supporting ecosystem stability, and highlight the importance of microbial network complexity and life history strategies as key predictors of biodiversity-stability relationships under global change.},
}

*Biodiversity
*Soil Microbiology
*Climate Change
China
*Soil/chemistry
*Ecosystem
*Desert Climate

@article {pmid42084497,
year = {2026},
author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD},
title = {Characterizing microbiomes of African fermented foods in a global context.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
pmid = {42084497},
issn = {1465-2080},
mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Food Microbiology ; Metagenome ; Fermentation ; Africa ; Kenya ; Burkina Faso ; Ghana ; },
abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.},
}

*Fermented Foods/microbiology
*Microbiota/genetics
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
*Food Microbiology
Metagenome
Fermentation
Africa
Kenya
Burkina Faso
Ghana

@article {pmid41417461,
year = {2026},
author = {Drew, G and Kraft, CS and Mehta, N},
title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.},
journal = {Clinical chemistry},
volume = {72},
number = {5},
pages = {554-563},
doi = {10.1093/clinchem/hvaf156},
pmid = {41417461},
issn = {1530-8561},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/therapy/prevention & control ; *Feces/microbiology/chemistry ; *Metabolomics/methods ; *Donor Selection ; Clostridioides difficile ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.

CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.

SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Clostridium Infections/therapy/prevention & control
*Feces/microbiology/chemistry
*Metabolomics/methods
*Donor Selection
Clostridioides difficile
Gastrointestinal Microbiome

@article {pmid41844673,
year = {2026},
author = {Singh, NK and Garg, P and Kumari, S and Banda, L and Patel, AM and Sindhuja, RH and Bhandari, Y and Khan, NA and Tandon, S and Jain, R and Rajesh, T and Qureshi, A and Vodapalli, A and Singha, B and Esari, D and Annan, MO and Nagabandi, T and Panda, A and Kapley, A and Nandicoori, VK and Mishra, RK and Sowpati, DT and Siva, AB and Tallapaka, KB},
title = {Metagenomic profiling of antimicrobial resistance in wastewater from metropolitan cities of India.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41844673},
issn = {2041-1723},
support = {2021 HTH 018//Rockefeller Foundation/ ; },
mesh = {India ; *Wastewater/microbiology ; *Metagenomics/methods ; Cities ; *Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; },
abstract = {Wastewater-based surveillance has emerged as a powerful tool for monitoring microbial diversity, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). In this study, wastewater samples collected from March 2022 to March 2024 from 19 locations in four metropolitan cities of India were profiled using shotgun metagenomics. Taxonomic abundance and beta diversity analyses revealed significant differences in microbial community compositions, with city-specific clustering; suggesting distinct local environmental influences. However, such distinct clusters were not evident with the ARGs. A high proportion of potentially novel metagenome-assembled genomes (MAGs) (53-70%) were identified on reconstructing the microbial genomes from the metagenomic data. ARGs conferring resistance to antibiotics such as tetracyclines and beta-lactams showed higher association with MGEs in contrast to macrolide resistance genes. Microbial co-occurrence network analysis revealed a city-specific structure and higher contribution of ARGs from specific communities of microbes. These findings underscore the complex interplay between microbial diversity, ARG dissemination, and MGEs in wastewater environments, emphasizing the need for continued surveillance, for designing appropriate mitigation strategies towards curbing the spread of antimicrobial resistance.},
}

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

@article {pmid41889037,
year = {2026},
author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS},
title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109518},
pmid = {41889037},
issn = {1875-595X},
mesh = {Humans ; Female ; Pilot Projects ; Middle Aged ; *Microbiota ; Adult ; Saliva/microbiology/chemistry ; Aged ; *Mouth/microbiology ; *Menopause/physiology ; *Nitrates/metabolism ; Cross-Sectional Studies ; Aged, 80 and over ; Retrospective Studies ; Young Adult ; Adolescent ; Estradiol/analysis/metabolism ; Oral Health ; },
abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.

METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.

RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.

CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.},
}

Humans
Female
Pilot Projects
Middle Aged
*Microbiota
Adult
Saliva/microbiology/chemistry
Aged
*Mouth/microbiology
*Menopause/physiology
*Nitrates/metabolism
Cross-Sectional Studies
Aged, 80 and over
Retrospective Studies
Young Adult
Adolescent
Estradiol/analysis/metabolism
Oral Health

@article {pmid41999333,
year = {2026},
author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG},
title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.},
journal = {Environmental science & technology},
volume = {60},
number = {17},
pages = {12853-12867},
doi = {10.1021/acs.est.6c02641},
pmid = {41999333},
issn = {1520-5851},
mesh = {*Soil Microbiology ; *Bacteriophages ; *Microbiota/drug effects ; Herbicides ; *Herbicide Resistance ; },
abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.},
}

*Soil Microbiology
*Bacteriophages
*Microbiota/drug effects
Herbicides
*Herbicide Resistance

@article {pmid42020953,
year = {2026},
author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL},
title = {Metabolic potential structures gill symbiont communities in two common shipworm species.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag089},
pmid = {42020953},
issn = {1751-7370},
mesh = {Animals ; *Symbiosis ; *Gills/microbiology ; Metagenome ; Phylogeny ; *Bivalvia/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification/enzymology ; Microbiota ; Nitrogen Fixation ; },
abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes representing seven distinct symbiont species. The metagenome of each host specimen contained between one and five symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.},
}

Animals
*Symbiosis
*Gills/microbiology
Metagenome
Phylogeny
*Bivalvia/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification/enzymology
Microbiota
Nitrogen Fixation

@article {pmid42044543,
year = {2026},
author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y},
title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129734},
doi = {10.1016/j.jenvman.2026.129734},
pmid = {42044543},
issn = {1095-8630},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Geologic Sediments/microbiology ; Kinetics ; Aerobiosis ; *Thiazines/metabolism ; },
abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.},
}

Biodegradation, Environmental
*Microbial Consortia
Geologic Sediments/microbiology
Kinetics
Aerobiosis
*Thiazines/metabolism

@article {pmid42075236,
year = {2026},
author = {Wang, Z and Ma, C and Huang, H and Ke, S and Lv, J and Hu, J and Wang, S and Bao, Z},
title = {Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040840},
pmid = {42075236},
issn = {2076-2607},
support = {2025B1111180001//Guangdong S&T Program/ ; 2025A04J3824//GCI Science & Technology (China)/ ; SOLZSKY2025013//Department of Science and Technology of Hainan Province/ ; },
abstract = {Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont-the host and its associated microbiota-remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies.},
}

@article {pmid42075353,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV},
title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081151},
pmid = {42075353},
issn = {2223-7747},
support = {22-74-10001-П//the Russian Science Foundation/ ; },
abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.},
}

@article {pmid42079557,
year = {2026},
author = {Kujala, K and Kinnunen, V},
title = {Lactic acid bacteria dominate urban Bokashi: a participatory, culture-independent pilot study of microbial diversity and functional potential in household-scale food waste fermentation.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag018},
pmid = {42079557},
issn = {2633-6685},
abstract = {In recent years, concerns over declining biodiversity in urban spaces have increased. Urban Bokashi composting (i.e. microaerobic or anaerobic fermentation of food waste indoors) has been suggested as a possibility to promote microbial diversity in the domestic environment. However, studies on microbial communities in household-scale Bokashi and their potential impacts on health and environment are lacking. Thus, the present pilot study investigated microbial communities in different stages of the Bokashi composting process in collaboration with six Bokashi practitioners by looking into physicochemical characteristics as well as microbial community composition (16S amplicon sequencing, 34 samples) and functional potential (shotgun metagenome sequencing, 11 samples). The collective results indicate that i) microbial communities in Bokashi compost differed between stages, but also between households, ii) microbial communities were dominated by lactic acid bacteria like Lentilactobacillus or Lacticaseibacillus, iii) metabolic pathways for the production of diverse organic acids were detected, iv) application of Bokashi ferment or leachate to soil can supply nutrients and organic acids to promote plant growth but does not substantially affect soil microbial community composition, and v) potentially pathogenic organisms were detected in extremely low abundances. Thus, urban Bokashi is likely not associated with increased health risks and positive impacts are feasible.},
}

@article {pmid42079638,
year = {2026},
author = {Han, X and Zang, D and Lin, M and Yin, Y and Liu, D and Sun, Q and Chen, J},
title = {Dynamic changes in gut microbiota and metabolites in advanced lung cancer patients with immune-related adverse events.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1731931},
pmid = {42079638},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lung Neoplasms/drug therapy/immunology/metabolism ; Aged ; *Immune Checkpoint Inhibitors/adverse effects ; *Metabolome ; Metabolomics/methods ; *Drug-Related Side Effects and Adverse Reactions/metabolism/etiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Immune-related adverse events (irAEs) represent an urgent clinical challenge. Although accumulating evidence suggests that irAEs are associated with the gut microbiota and its metabolites, our understanding of the dynamic alterations in the gut microbiota and related metabolic profiles throughout the onset and progression of irAEs remains limited.

METHODS: A total of 48 fecal samples were collected from 32 lung cancer patients treated with immune checkpoint inhibitors, including 16 patients who developed irAEs and 16 who did not. Fecal samples were collected at baseline and, in patients with irAEs, at the time of irAEs onset. Metagenomic sequencing and untargeted metabolomics analyses were performed to identify baseline differences in gut microbiota and metabolites, characterize longitudinal dynamic changes in gut microbiota and metabolite profiles in patients with irAEs, and construct a machine learning based random forest model to predict the occurrence of irAEs.

RESULTS: There were baseline differences in microbial communities and metabolites between the two groups. In the non-irAEs group, Phocaeicola coprocola was enriched and Micrococales decreased. At baseline, viomycin was positively correlated with irAEs, while metabolites such as calcitriol and L-isoleucine were negatively correlated with irAEs. The roles of valine, leucine and isoleucine metabolism and vitamin B6 metabolism pathways were downregulated in the irAEs group. Compared to baseline, there were significant changes in gut microbiota and metabolites during the onset of irAEs, and the abundance of Veillonella increased during irAEs onset. Dynamic monitoring of metabolic changes in irAEs revealed decreased levels of trypsin butylester, BQ 123, DL-o-tyrosine, and nicotinamide-beta-riboside during irAEs attacks. Lysine degradation, arachidonic acid metabolism, folate biosynthesis, nicotinate and nicotinamide metabolism, and C5-branched dibasic acid metabolism were downregulated during the progression of irAEs. A model for predicting the occurrence of irAEs based on differential microbiota and metabolites was constructed, and after robust validation, the model showed good performance and excellent discriminative power.

CONCLUSIONS: The occurrence and development of irAEs are associated with the composition of the gut microbiota and metabolites, as well as their dynamic changes over time. These findings highlight the potential of gut microbiota and metabolites as biomarkers for predicting the occurrence and progression of irAEs.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
Male
Female
Middle Aged
*Lung Neoplasms/drug therapy/immunology/metabolism
Aged
*Immune Checkpoint Inhibitors/adverse effects
*Metabolome
Metabolomics/methods
*Drug-Related Side Effects and Adverse Reactions/metabolism/etiology
Feces/microbiology

@article {pmid41707490,
year = {2026},
author = {Jian, Z and Zhao, R and Zi, X and He, S and He, X and Ye, Y and Wang, K and Ge, C and Jia, J and Hu, Y and Dou, T},
title = {Sustainable antibiotic reduction in poultry production with Pulsatilla saponins and herbal supplementation.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106562},
pmid = {41707490},
issn = {1525-3171},
mesh = {Animals ; *Saponins/administration & dosage/metabolism ; Animal Feed/analysis ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Diet/veterinary ; Dietary Supplements/analysis ; *Chickens/growth & development/immunology/microbiology ; *Pulsatilla/chemistry ; *Gastrointestinal Microbiome/drug effects ; Male ; },
abstract = {The prolonged use of antibiotics in poultry production promotes the accumulation and spread of antibiotic resistance genes (ARG), raising concerns for animal health and public safety. Developing effective antibiotic alternatives that support performance while limiting resistance risk is therefore a priority. Using broiler chickens as a model, this study evaluated the effects of Pulsatilla saponins, alone or combined with a compound herbal formulation, on growth performance, immune responses, cecal microbiota, and the intestinal resistome, with an antibiotic-treated group as reference. Growth and immune parameters were integrated with shotgun metagenomic sequencing to characterize microbial and ARG responses to dietary interventions. Compared with antibiotic supplementation, the combination of 0.5% herbal medicine and 0.6% Pulsatilla saponins (ZBZ) combination significantly enhanced immune traits, including spleen index and serum IgA and IgM levels, while increasing cecal microbial diversity and reshaping community composition. Metagenomic analyses showed that antibiotic treatment enriched efflux pump and target modification associated ARG, indicative of a multidrug resistance profile. In contrast, ZBZ markedly reduced the abundance and diversity of multidrug resistance-related ARG. Notably, ZBZ supplementation enriched short-chain fatty acid-producing taxa that were negatively correlated with multiple ARG classes, suggesting that improvements in the intestinal metabolic environment and colonization resistance constrained the expansion of resistant bacteria. Overall, the combined use of Pulsatilla saponins and a compound herbal formulation improved growth and immune performance while reducing intestinal ARG burden through coordinated modulation of the cecal microbiota-resistome axis, providing a sustainable nutritional strategy for antibiotic-reduced poultry production.},
}

Animals
*Saponins/administration & dosage/metabolism
Animal Feed/analysis
*Anti-Bacterial Agents/pharmacology/administration & dosage
Diet/veterinary
Dietary Supplements/analysis
*Chickens/growth & development/immunology/microbiology
*Pulsatilla/chemistry
*Gastrointestinal Microbiome/drug effects
Male

@article {pmid41762491,
year = {2026},
author = {Yan, S and Li, R and Shen, X and Li, Y and Zhang, L and Xu, M and Xie, S},
title = {Redox potential drives divergent microbial carbon fixation in mangrove wetland sediments, with ammonium exerting context-dependent effects.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119457},
doi = {10.1016/j.marpolbul.2026.119457},
pmid = {41762491},
issn = {1879-3363},
mesh = {*Wetlands ; *Geologic Sediments/microbiology/chemistry ; Oxidation-Reduction ; *Ammonium Compounds ; *Carbon Cycle ; Microbiota ; },
abstract = {Mangrove wetlands represent dynamic coastal interfaces where redox conditions and nutrient cycling shape microbial communities and their biogeochemical functions. However, tidal-driven siltation continuously transports sediment from low- to high-tide zones, altering sediment redox potential and nutrient content. The microbial responses to these changes, particularly the response mechanisms of carbon-fixing microorganisms, remain unclear. We integrated metagenomic and metatranscriptomic sequencing with [13]C and [15]N isotope labeling to examine how oxidation-reduction potential (ORP) and ammonium (NH4[+]) availability regulate microbial assembly and metabolism in mangrove sediments. ORP emerged as the primary determinant of microbial composition and diversity, while NH4[+] exerted variable effects on microbial traits. Under high ORP, CBBL-microorganisms predominantly utilized the cmmG CO2-concentrating mechanism, and carbon fixation rates decreased with increasing NH4[+] concentration. Under low ORP, CBBM-harboring genera dominated, primarily utilizing another mechanism cmmE, while NH4[+] had little effect and total organic carbon (TOC) exerted stronger control. ORP thus acts as the dominant environmental filter, with NH4[+] selectively affecting nitrifiers and carbon-fixing taxa. This was the first study to simultaneously measure ammonia oxidation and carbon fixation rate in mangrove sediments, revealing their mechanistic coupling. This work provides new mechanistic insights into the regulation of microbial metabolic potential in mangrove ecosystems and contributes to a broader understanding of their resilience and function in coastal biogeochemical cycles under fluctuating climate and environmental conditions.},
}

*Wetlands
*Geologic Sediments/microbiology/chemistry
Oxidation-Reduction
*Ammonium Compounds
*Carbon Cycle
Microbiota

@article {pmid41812751,
year = {2026},
author = {Prabhakar, S and Rajeev, AC and Sankappa, NM and Harsha, R},
title = {High-throughput metagenomic profiling of functional and resistome features in estuarine microplastic microbiomes.},
journal = {Environmental research},
volume = {298},
number = {},
pages = {124159},
doi = {10.1016/j.envres.2026.124159},
pmid = {41812751},
issn = {1096-0953},
mesh = {*Microbiota/genetics ; *Estuaries ; *Microplastics/analysis ; Metagenomics ; *Water Pollutants, Chemical/analysis ; India ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; },
abstract = {Microplastics (MPs) are now recognized as persistent pollutants in aquatic ecosystems, providing unique surfaces for microbial colonization and acting as vectors for the spread of pathogens, antibiotic resistance, and virulence factors. Estuarine systems, due to their dynamic hydrology and proximity to anthropogenic activity, are particularly vulnerable to MP accumulation and associated microbial risks. This study presents the first comprehensive metagenomic investigation of MP-associated microbial communities across five estuaries spanning the northern and southern coastal regions of Karnataka, India. MPs were isolated, characterized, and the extracted total DNA from the MPs was subjected to high-throughput sequencing and comprehensive bioinformatic analyses. Taxonomic, functional, and resistance gene profiling were performed to evaluate microbial diversity, ecological roles, and potential public health implications. The findings revealed distinct regional differences in microbial community structure and functional potential, with evidence of clinically relevant pathogens, antibiotic resistance genes, and virulence determinants within the plastisphere. These results highlight the role of MPs as reservoirs and vectors for microbial risks in estuarine ecosystems. By linking microbial diversity of MPs with environmental and anthropogenic influences, this work provides crucial baseline data for monitoring and managing estuarine health. It also underscores the urgent need for integrated strategies to mitigate plastic pollution and its cascading ecological and public health impacts.},
}

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

@article {pmid41819204,
year = {2026},
author = {Qi, Y and Zheng, X and He, X and Huang, K and Wang, D and Zhang, XX},
title = {Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.},
journal = {Environmental research},
volume = {298},
number = {},
pages = {124241},
doi = {10.1016/j.envres.2026.124241},
pmid = {41819204},
issn = {1096-0953},
mesh = {*Triazoles/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Microbial Consortia ; Bioreactors/microbiology ; *Water Pollutants, Chemical/metabolism ; Sewage/microbiology ; Bacteria/metabolism/genetics ; },
abstract = {The escalating prevalence of benzotriazole (BTR), an emerging refractory organic pollutant, has drawn significant attention for the development of efficient bioremediation solutions. Although the construction of microbial consortia represents a promising strategy, the intrinsic relationship between community succession and functional features during artificial selection remains poorly understood. To address this, this study engineered two distinct microbial consortia from activated sludge using a top-down selection strategy in sequencing batch reactors fed with increasing BTR concentrations. While the two consortia evolved along divergent taxonomic pathways, they exhibited remarkable functional convergence, maintaining consistently high BTR transformation (>96%) and chemical oxygen demand (>75%) removal efficiencies. This robust performance under the stringent condition of BTR as the sole carbon source highlighted their significant adaptive potential. Metagenomic analysis further attributed this functional stability to the principle of functional redundancy, wherein taxonomically distinct keystone species (e.g., Nocardioides and Methylobacterium) harbored functionally analogous gene clusters. Additionally, multiple congeneric species (e.g., MAG.480 and MAG.17) within the Bacteroidota phylum exhibited significant divergence in their degradation gene repertoires. These findings not only advance ecological understanding of microbiome-mediated BTR biodegradation but also provide a foundation for the rational design and optimization of high-performance bioremediation consortia.},
}

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

@article {pmid41865866,
year = {2026},
author = {Wang, Y and Wang, D and Wang, H},
title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {316},
number = {},
pages = {111996},
doi = {10.1016/j.cbpa.2026.111996},
pmid = {41865866},
issn = {1531-4332},
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; *Larva/microbiology/metabolism ; *Ranidae/microbiology/metabolism/growth & development ; Sympatry ; *Anura/microbiology/metabolism ; },
abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.},
}

Animals
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome
*Larva/microbiology/metabolism
*Ranidae/microbiology/metabolism/growth & development
Sympatry
*Anura/microbiology/metabolism

@article {pmid41886955,
year = {2026},
author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ},
title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158089},
doi = {10.1016/j.phymed.2026.158089},
pmid = {41886955},
issn = {1618-095X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hyperuricemia/drug therapy/complications ; *Drugs, Chinese Herbal/pharmacology ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; Male ; *Kidney Diseases/drug therapy ; Dysbiosis/drug therapy ; Kidney/drug effects ; Mice, Inbred C57BL ; Basic Helix-Loop-Helix Proteins ; },
abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.

OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.

METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.

RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.

CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Hyperuricemia/drug therapy/complications
*Drugs, Chinese Herbal/pharmacology
*Receptors, Aryl Hydrocarbon/metabolism
Mice
Male
*Kidney Diseases/drug therapy
Dysbiosis/drug therapy
Kidney/drug effects
Mice, Inbred C57BL
Basic Helix-Loop-Helix Proteins

@article {pmid41930813,
year = {2026},
author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S},
title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158039},
doi = {10.1016/j.phymed.2026.158039},
pmid = {41930813},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Diterpenes/pharmacology ; *Colitis, Ulcerative/drug therapy ; Animals ; NF-kappa B/metabolism ; *Macrophages/drug effects ; Humans ; Mice, Inbred C57BL ; Mice ; *Anti-Inflammatory Agents/pharmacology ; Male ; Dextran Sulfate ; Signal Transduction/drug effects ; Cytokines/metabolism ; Molecular Docking Simulation ; Disease Models, Animal ; THP-1 Cells ; },
abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.

PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.

METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-γ-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.

RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-κB signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-κB signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.

CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-κB signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.},
}

*Gastrointestinal Microbiome/drug effects
*Diterpenes/pharmacology
*Colitis, Ulcerative/drug therapy
Animals
NF-kappa B/metabolism
*Macrophages/drug effects
Humans
Mice, Inbred C57BL
Mice
*Anti-Inflammatory Agents/pharmacology
Male
Dextran Sulfate
Signal Transduction/drug effects
Cytokines/metabolism
Molecular Docking Simulation
Disease Models, Animal
THP-1 Cells

@article {pmid41955934,
year = {2026},
author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM},
title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.},
journal = {The Science of the total environment},
volume = {1030},
number = {},
pages = {181776},
doi = {10.1016/j.scitotenv.2026.181776},
pmid = {41955934},
issn = {1879-1026},
mesh = {Humans ; *Microbiota/drug effects ; *Respiratory System/microbiology ; *Inhalation Exposure/adverse effects ; *Air Pollutants/adverse effects ; },
abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.

METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.

RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.

CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.},
}

Humans
*Microbiota/drug effects
*Respiratory System/microbiology
*Inhalation Exposure/adverse effects
*Air Pollutants/adverse effects

@article {pmid42000510,
year = {2026},
author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S},
title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142094},
doi = {10.1016/j.jhazmat.2026.142094},
pmid = {42000510},
issn = {1873-3336},
mesh = {*Composting/methods ; Metagenomics ; Manure/microbiology ; *Drug Resistance, Microbial/genetics ; *Humic Substances/analysis ; Microbiota ; Soil Microbiology ; Animals ; Bacteria/genetics ; Electricity ; },
abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.},
}

*Composting/methods
Metagenomics
Manure/microbiology
*Drug Resistance, Microbial/genetics
*Humic Substances/analysis
Microbiota
Soil Microbiology
Animals
Bacteria/genetics
Electricity

@article {pmid42001834,
year = {2026},
author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A},
title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158119},
doi = {10.1016/j.phymed.2026.158119},
pmid = {42001834},
issn = {1618-095X},
mesh = {Animals ; *Catechin/analogs & derivatives/pharmacology ; Swine ; *Diarrhea/drug therapy/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Energy Metabolism/drug effects ; Escherichia coli ; Escherichia coli Infections/drug therapy ; Enteric Nervous System/drug effects ; Disease Models, Animal ; },
abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.

OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.

METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and typeⅡinnate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.

RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-α, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.

CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.},
}

Animals
*Catechin/analogs & derivatives/pharmacology
Swine
*Diarrhea/drug therapy/microbiology/veterinary
*Gastrointestinal Microbiome/drug effects
*Energy Metabolism/drug effects
Escherichia coli
Escherichia coli Infections/drug therapy
Enteric Nervous System/drug effects
Disease Models, Animal

@article {pmid42014006,
year = {2026},
author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W},
title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.},
journal = {International journal of biological macromolecules},
volume = {362},
number = {},
pages = {152109},
doi = {10.1016/j.ijbiomac.2026.152109},
pmid = {42014006},
issn = {1879-0003},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Cyclophosphamide/adverse effects/pharmacology ; *Spleen/metabolism/drug effects/immunology ; Mice ; *Metabolomics/methods ; *Polysaccharides/pharmacology ; Cytokines/metabolism ; Male ; Immunosuppression Therapy ; },
abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Cyclophosphamide/adverse effects/pharmacology
*Spleen/metabolism/drug effects/immunology
Mice
*Metabolomics/methods
*Polysaccharides/pharmacology
Cytokines/metabolism
Male
Immunosuppression Therapy

@article {pmid42030718,
year = {2026},
author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L},
title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142145},
doi = {10.1016/j.jhazmat.2026.142145},
pmid = {42030718},
issn = {1873-3336},
mesh = {*Arsenic/metabolism/analysis ; *Water Pollutants, Chemical/metabolism/analysis ; *Estuaries ; *Rivers/microbiology/chemistry ; Geologic Sediments/chemistry ; Spatio-Temporal Analysis ; China ; Microbiota ; Bacteria/metabolism/genetics ; Water Microbiology ; Environmental Monitoring ; },
abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.},
}

*Arsenic/metabolism/analysis
*Water Pollutants, Chemical/metabolism/analysis
*Estuaries
*Rivers/microbiology/chemistry
Geologic Sediments/chemistry
Spatio-Temporal Analysis
China
Microbiota
Bacteria/metabolism/genetics
Water Microbiology
Environmental Monitoring

@article {pmid42064333,
year = {2026},
author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA},
title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112758},
pmid = {42064333},
issn = {2352-3409},
abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.},
}

@article {pmid42068031,
year = {2026},
author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y},
title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665870},
doi = {10.1080/19490976.2026.2665870},
pmid = {42068031},
issn = {1949-0984},
mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth & development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth & development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; },
abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.},
}

Animals
*Syndecan-1/genetics/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Mice
*Intestinal Mucosa/microbiology/metabolism
Gastrointestinal Microbiome
*Biofilms/growth & development
Mice, Knockout
Humans
*Faecalibacterium prausnitzii/physiology/genetics/growth & development
Mice, Inbred C57BL
Homeostasis
Disease Models, Animal
Dextran Sulfate
Colitis/microbiology/chemically induced
Male
Fecal Microbiota Transplantation

@article {pmid42069941,
year = {2026},
author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I},
title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42069941},
issn = {1432-0991},
mesh = {Humans ; *Prebiotics/administration & dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; },
abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.},
}

Humans
*Prebiotics/administration & dosage
Animals
*Gastrointestinal Microbiome/drug effects
Probiotics
*Microbiota

@article {pmid42070688,
year = {2026},
author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L},
title = {Unveiling the Plant Growth-Promoting and Antifungal Potential of Melissa officinalis Endophytes: the Integrative Culture-Dependent and Metagenomic Approaches.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113182},
doi = {10.1016/j.plantsci.2026.113182},
pmid = {42070688},
issn = {1873-2259},
abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113% to 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.},
}

@article {pmid42070841,
year = {2026},
author = {Li, S and Yan, X and Ndayishimiye, JC and Smirnov, A and Tsyganov, AN and Nassonova, E and Mazei, NG and Mazei, YA and Yang, J},
title = {Urban park metagenomics highlights sediments as a potential hotspot for CH4 and N2O emission across diverse habitats.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {481-491},
doi = {10.1016/j.jes.2025.07.053},
pmid = {42070841},
issn = {1001-0742},
mesh = {*Methane/analysis ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; *Nitrous Oxide/analysis ; Ecosystem ; *Environmental Monitoring ; *Air Pollutants/analysis ; Greenhouse Gases/analysis ; Microbiota ; },
abstract = {Urban areas contribute the vast majority of greenhouse gas (GHG) emissions, and urban greenspaces, including urban parks, are being established to promote environmental health by mitigating GHG emissions. However, the diversity of CH4 and N2O cycling genes and microbiomes in urban park ecosystems remains poorly understood. Here, we sampled five types of habitats in subtropical urban parks, including moss, sediment, soil, tree hole, and water, to explore the microbial communities and microbially mediated CH4 and N2O cycling processes using metagenomic sequencing. We found strongly positive biodiversity-ecosystem-functioning (BEF) relationships in nitrogen cycling functions, as well as in CH4 cycling, except in sediment, indicating the microbial community in the sediment had reached function saturation for CH4 cycling. CH4 cycling was driven by a few specific microbial genera, whereas many microorganisms participated in the denitrification process. Microbes in sediment exhibited the highest CH4 and N2O metabolic potential among the five habitats, especially for methanogenesis and N2O production processes. Significant positive correlations were observed between the mcrA and N2O cycling genes, suggesting methanogenesis could be coupled with denitrification. Environmental factors, such as dissolved oxygen, total nitrogen, and total carbon greatly affected microbial community composition and functional gene families. These results highlight that pond sediments are an overlooked potential source of CH4 and N2O emissions, which may undermine the role of urban greenspace in reducing GHG emissions. Reducing nitrogen pollution and eutrophication is recommended to mitigate CH4 and N2O emissions from pond sediments in urban environments.},
}

*Methane/analysis
Metagenomics
*Geologic Sediments/microbiology/chemistry
Parks, Recreational
*Nitrous Oxide/analysis
Ecosystem
*Environmental Monitoring
*Air Pollutants/analysis
Greenhouse Gases/analysis
Microbiota

@article {pmid42071227,
year = {2026},
author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z},
title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.},
journal = {Clinical and translational medicine},
volume = {16},
number = {5},
pages = {e70667},
doi = {10.1002/ctm2.70667},
pmid = {42071227},
issn = {2001-1326},
support = {2022YFA1304000//National Key R&D Program of China/ ; 2024B1111150001//Guangdong S&T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; },
abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.},
}

*Colorectal Neoplasms/microbiology/genetics/pathology/etiology
Humans
Animals
*DNA Damage/drug effects
Mice
Male
*Lactates/metabolism/adverse effects
Gastrointestinal Microbiome
*Carcinogenesis
Female
Feces/microbiology
Middle Aged

@article {pmid42074337,
year = {2026},
author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X},
title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083699},
pmid = {42074337},
issn = {1422-0067},
support = {2025YFE0121200//National Key R&D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; },
mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth & development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth & development ; *Transcriptome ; *Microbiota ; Soil Microbiology ; Metagenomics ; *Hypocreales/physiology ; Gene Expression Profiling ; },
abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.},
}

*Bacillus subtilis/physiology
*Rhizosphere
*Vigna/growth & development/microbiology/genetics
*Plant Roots/microbiology/genetics/growth & development
*Transcriptome
*Microbiota
Soil Microbiology
Metagenomics
*Hypocreales/physiology
Gene Expression Profiling

@article {pmid41833938,
year = {2026},
author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L},
title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41833938},
issn = {2055-5008},
support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Rhizosphere ; *Plant Diseases/microbiology ; Fusarium/physiology ; Metagenomics ; Plant Roots/microbiology ; Stress, Physiological ; DNA, Bacterial/genetics ; Plant Stems/microbiology ; },
abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.},
}

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

@article {pmid41921236,
year = {2026},
author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X},
title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.},
journal = {Pathology, research and practice},
volume = {282},
number = {},
pages = {156456},
doi = {10.1016/j.prp.2026.156456},
pmid = {41921236},
issn = {1618-0631},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Legionella pneumophila/pathogenicity ; *Bacterial Translocation ; *Legionnaires' Disease/microbiology/immunology/pathology/complications ; Guinea Pigs ; Dysbiosis/microbiology ; Immunocompromised Host ; Disease Models, Animal ; Liver/microbiology/pathology/immunology ; Apoptosis ; Male ; },
abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Legionella pneumophila/pathogenicity
*Bacterial Translocation
*Legionnaires' Disease/microbiology/immunology/pathology/complications
Guinea Pigs
Dysbiosis/microbiology
Immunocompromised Host
Disease Models, Animal
Liver/microbiology/pathology/immunology
Apoptosis
Male