@article {pmid41661278,
year = {2026},
author = {Zhang, H and Zhai, C and Hu, H and Qian, G and Mao, M},
title = {A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.},
journal = {Acta diabetologica},
volume = {63},
number = {5},
pages = {789-799},
pmid = {41661278},
issn = {1432-5233},
support = {XFCX-DMYH//Jiaxing Institute of Arteriosclerotic Disease/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications/metabolism ; *Myocardial Infarction/microbiology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenomics ; Middle Aged ; Male ; Aged ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {OBJECTIVE: This study aimed to investigate gut microbiota composition and metabolic functions in patients with type 2 diabetes mellitus (DM) complicated by myocardial infarction (MI) and to explore potential mechanisms linking the gut microbiome to MI development.

METHODS: Sixty patients with DM complicated by MI and 52 patients with DM alone were initially recruited. After quality control, 29 DM + MI patients and 33 DM patients were included in the final analysis. Gut microbial profiles were characterized using shotgun metagenomic sequencing and bioinformatics analyses. Microbial diversity, composition, and gene functions were compared between groups based on KEGG, COG, and CAZy annotations.

RESULTS: Overall microbial diversity and metabolic profiles were comparable between the two groups; however, significant differences were observed in specific taxa and functional genes. Taxa enriched in the DM + MI group included Bacteroidales, Prevotellaceae, and Lachnospiraceae. In total, 510 KEGG orthology (KO) units and 21 pathways-including ABC transporters, quorum sensing, and general metabolic pathways-differed significantly between groups. Carbohydrate transport and metabolism, as well as glycoside hydrolase activity, represented the most enriched functional categories. Random forest models based on selected microbial species, KO units, and KEGG pathways achieved areas under the curve (AUCs) of 0.868, 0.885, and 0.820, respectively.

CONCLUSION: Patients with DM complicated by MI exhibit distinct gut microbial compositions and functional gene signatures compared with patients with DM alone. These microbiome-based markers may contribute to early risk stratification and provide potential targets for microbiota-focused interventions to mitigate MI risk in patients with diabetes.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/complications/metabolism
*Myocardial Infarction/microbiology/metabolism/complications
*Gastrointestinal Microbiome/genetics
Female
Metagenomics
Middle Aged
Male
Aged
Bacteria/classification/genetics/isolation & purification

@article {pmid41664846,
year = {2026},
author = {Stolf, CS and Paz, HES and Paraluppi, MC and Miguel, MMV and Santamaria, MP and Monteiro, MF and Amgarten, DE and Franco, RRA and Branco-de-Almeida, LS and Shaddox, LM and Casarin, RCV},
title = {Molar-Incisor and Generalized Grade C Periodontitis: Distinct Microbiome-Immune Interactions Suggest Divergent Pathogenesis.},
journal = {Journal of periodontal research},
volume = {61},
number = {4},
pages = {382-395},
doi = {10.1111/jre.70077},
pmid = {41664846},
issn = {1600-0765},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2021/14430-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; R01DE019456/DE/NIDCR NIH HHS/United States ; R01DE019456/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/immunology ; Biofilms ; Cross-Sectional Studies ; Female ; Gingival Crevicular Fluid/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Male ; Adult ; Middle Aged ; Treponema denticola/isolation & purification ; Cytokines ; Tannerella forsythia/isolation & purification ; Eubacteriales ; },
abstract = {AIM: Molar-Incisor (PerioC-MIP) and Generalized (PerioC-G) Grade C Periodontitis could have distinctive etiopathogenesis behind their unique clinical patterns. Thus, this study aimed to distinguish these two phenotypes by analyzing the subgingival metagenomic profile and the inflammatory markers levels.

METHODS: In this cross-sectional comparative study, Gingival Crevicular Fluid (GCF) and Subgingival Biofilm (SB) were collected from 18 PerioC-MIP North Americans and 14 periodontally healthy controls (HC) from the same location (HC-MIP) and 20 PerioC-G Brazilians and 20 controls (HC-G). From GCF, immunoenzymatic analysis was performed. SB functional and taxonomic bacterial content was determined using shotgun metagenomics sequencing.

RESULTS: Taxonomic results showed significantly different alpha- and beta-diversity profiles between disease groups (p < 0.05). Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis were associated with PerioC-MIP; levels of Tannerella forsythia, Filifactor alocis, Porphyromonas gingivalis, Fretibacterium fastidiosum, and Treponema denticola were significantly enriched at PerioC-G (p < 0.05). PerioC-G had the function for flagellar assembly enriched, while PerioC-MIP SB was associated with biofilm formation of Escherichia coli. Different GCF inflammatory marker levels for each pattern resulted in PerioC-G presenting higher levels of IL-1β, IL-6, and IL-10 than PerioC-MIP (p < 0.05).

CONCLUSION: PerioC-G and PerioC-MIP presented different taxonomical profiles and GCF cytokine levels, raising the hypothesis that they may represent two different stages/susceptibility patterns of Periodontitis Grade C.},
}

Humans
*Microbiota/immunology
Biofilms
Cross-Sectional Studies
Female
Gingival Crevicular Fluid/microbiology/immunology
*Periodontitis/microbiology/immunology
Male
Adult
Middle Aged
Treponema denticola/isolation & purification
Cytokines
Tannerella forsythia/isolation & purification
Eubacteriales

@article {pmid41689625,
year = {2026},
author = {Hayashi, T and Iida, N and Yasuda, K and Yoshio, T and Terashima, T and Takatori, H and Moriyama, H and Takeshita, Y and Takamura, T and Yamashita, T},
title = {Escherichia coli as a gut microbial marker of obesity and its reduction following bariatric treatment.},
journal = {Journal of gastroenterology},
volume = {61},
number = {6},
pages = {741-749},
pmid = {41689625},
issn = {1435-5922},
support = {19K17394//Japan Society for the Promotion of Science/ ; 23K15036//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Escherichia coli/isolation & purification/genetics ; Cross-Sectional Studies ; Female ; Feces/microbiology ; *Bariatric Surgery/methods ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Middle Aged ; Male ; *Obesity, Morbid/microbiology/surgery ; Adult ; Biomarkers ; Dysbiosis/microbiology ; *Obesity/microbiology/surgery ; },
abstract = {BACKGROUND: Alterations in the gut microbiota have been implicated in obesity-related metabolic disorders; however, the disease-relevant microbial features that link gut dysbiosis to metabolic risk remain incompletely defined. In particular, whether quantitative expansion or strain-level divergence of specific taxa underlie metabolic dysfunction is unclear.

METHODS: We performed cross-sectional and longitudinal metagenomic analyses of fecal samples from 19 patients with severe obesity undergoing bariatric intervention and 30 healthy donors. Whole-genome shotgun sequencing was combined with quantitative PCR to assess both relative and absolute bacterial abundance. Cultured Escherichia coli isolates were further examined by whole-genome sequencing to evaluate strain-level diversity. Associations between microbial features and metabolic parameters were analyzed.

RESULTS: The gut microbiota of patients with severe obesity was taxonomically and functionally distinct from that of healthy donors. Among altered taxa, E. coli was significantly enriched in obesity and showed a consistent and marked reduction at 6 months post-intervention, irrespective of procedure type. Absolute E. coli abundance quantified by qPCR decreased significantly following intervention. In contrast, whole-genome analysis revealed no clear genotypic clustering of E. coli strains by host phenotype. Notably, E. coli abundance correlated positively with HbA1c and systolic blood pressure and negatively with serum albumin levels, whereas global microbial diversity and KEGG-based metabolic pathways showed limited longitudinal change.

CONCLUSIONS: Quantitative expansion of gut E. coli, rather than strain-specific genomic divergence, is associated with metabolic risk in severe obesity and is consistently reduced at 6 months after bariatric intervention. These findings suggest that microbial load-dependent effects of E. coli may be associated with obesity-related metabolic dysfunction and represent a potential biomarker. This exploratory, single-center study is hypothesis-generating and warrants further validation in larger, multi-center cohorts as well as interventional studies using preclinical animal models.},
}

Humans
*Escherichia coli/isolation & purification/genetics
Cross-Sectional Studies
Female
Feces/microbiology
*Bariatric Surgery/methods
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Middle Aged
Male
*Obesity, Morbid/microbiology/surgery
Adult
Biomarkers
Dysbiosis/microbiology
*Obesity/microbiology/surgery

@article {pmid41846078,
year = {2026},
author = {Li, Q and Yuan, J and Sun, Y and Wang, Y and Li, Y and Ni, A and Zong, Y and Yang, H and Li, X and Huang, X and Ma, H and Chen, J},
title = {Multi-omics analysis revealed that oxidative phosphorylation contributed to the heterosis for feed efficiency in laying chickens.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106658},
pmid = {41846078},
issn = {1525-3171},
mesh = {Animals ; *Chickens/genetics/physiology/microbiology ; *Hybrid Vigor ; Female ; *Oxidative Phosphorylation ; Multiomics ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; },
abstract = {Improving feed efficiency has been the top priority in animal husbandry. Host genetics and gut microbiota synergistically regulate feed efficiency in laying chicken. However, the role of gut microbiota in heterosis for feed efficiency was rarely investigated. Herein, we used multi-omics data to elucidate the regulatory mechanisms of heterosis for feed efficiency in White Leghorn, Beijing-You chicken, and their reciprocal crosses. We observed divergent heterosis for residual feed intake (RFI) between two crossbreds during the laying period from 43 to 46 weeks of age. Metagenomic analysis showed the significant difference in richness and function of cecal microbiota among crossbreds and purebreds (P < 0.05), and the differential functional pathways were mainly related to metabolism. Most microorganisms (>90 %) were non-additive in crossbreds. Weighted gene co-expression network analysis and LDA effect size analysis revealed seven non-additive RFI-associated microorganisms, such as Leyella, Paraprevotella, and Zongyangia. We also identified 544 RFI-associted metabolites, which were mainly overrepresented in glycerophospholipid metabolism and oxidative phosphorylation. Integrative analysis further revealed the interactions among non-additive microorganisms, genes, and metabolites. Specifically, the non-additive expression of Zongyangia was positively correlated with UQCR10 and Ubiquinone-1 levels within the oxidative phosphorylation pathway. These factors were negatively correlated with RFI, contributing to the RFI heterosis. Our study highlighted that key microorganisms, genes, and metabolites involved in oxidative phosphorylation interact to regulate negative heterosis for RFI in laying hens. The findings established a theoretical and practical foundation for further exploring the molecular mechanisms that drive heterosis for feed efficiency.},
}

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

@article {pmid41863981,
year = {2026},
author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C},
title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106706},
pmid = {41863981},
issn = {1525-3171},
mesh = {Animals ; *Polyphenols/metabolism/administration & dosage ; *Antioxidants/metabolism ; Male ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Tea/chemistry ; *Geese/microbiology/physiology/metabolism ; Cecum/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Random Allocation ; *Intestines/drug effects/physiology/anatomy & histology ; *Camellia sinensis/chemistry ; },
abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.},
}

Animals
*Polyphenols/metabolism/administration & dosage
*Antioxidants/metabolism
Male
Diet/veterinary
Dietary Supplements/analysis
Animal Feed/analysis
*Tea/chemistry
*Geese/microbiology/physiology/metabolism
Cecum/microbiology/drug effects
*Gastrointestinal Microbiome/drug effects
Intestinal Barrier Function/drug effects
Random Allocation
*Intestines/drug effects/physiology/anatomy & histology
*Camellia sinensis/chemistry

@article {pmid41903463,
year = {2026},
author = {Rathnayake, M and Shaik, NA and Palkumbura, A and Ranaraja, A and Basnayake, Y and Basyouni, R and Taylor, A and Ambrose, N and Popowich, S and Ayalew, LE and Tikoo, S and Gomis, S},
title = {Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106823},
pmid = {41903463},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Infectious bursal disease virus/physiology ; *Jejunum/microbiology ; *Poultry Diseases/virology/microbiology ; *Birnaviridae Infections/veterinary/virology ; *Animal Husbandry/methods ; *Anti-Bacterial Agents/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; RNA, Ribosomal, 16S/analysis ; RNA, Bacterial/analysis ; },
abstract = {Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.},
}

Animals
*Chickens/microbiology
*Infectious bursal disease virus/physiology
*Jejunum/microbiology
*Poultry Diseases/virology/microbiology
*Birnaviridae Infections/veterinary/virology
*Animal Husbandry/methods
*Anti-Bacterial Agents/administration & dosage
*Gastrointestinal Microbiome/drug effects
Animal Feed/analysis
Diet/veterinary
RNA, Ribosomal, 16S/analysis
RNA, Bacterial/analysis

@article {pmid42101202,
year = {2026},
author = {Yashar, M and Thigale, UY and Karakus, S},
title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.},
journal = {Current opinion in ophthalmology},
volume = {37},
number = {4},
pages = {299-307},
doi = {10.1097/ICU.0000000000001228},
pmid = {42101202},
issn = {1531-7021},
mesh = {Humans ; *Microbiota/physiology ; *Eye Infections, Bacterial/microbiology ; },
abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus , Corynebacterium , and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.},
}

Humans
*Microbiota/physiology
*Eye Infections, Bacterial/microbiology

@article {pmid42199424,
year = {2026},
author = {Zhao, L and Wang, Q and Chen, J and Wang, J},
title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1767902},
pmid = {42199424},
issn = {1664-3224},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; },
abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.

METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.

RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.

CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/metabolism
Female
Multiomics
Male
*Gastrointestinal Microbiome
Child, Preschool
Metagenomics/methods
China/epidemiology
*Metabolome
Metabolomics/methods
Infant
Feces/microbiology
Bacteria/classification/genetics
Child

@article {pmid42200521,
year = {2026},
author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI},
title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
doi = {10.1099/mgen.0.001739},
pmid = {42200521},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; },
abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.},
}

*Metagenomics/methods
Humans
*Metagenome
*Bacteria/classification/genetics
Genome, Bacterial
Sequence Analysis, DNA/methods
Computational Biology/methods
Microbiota/genetics

@article {pmid42201143,
year = {2026},
author = {Zhang, W and Eleftherianos, I and Mohamed, A and Smagghe, G and Chakkalakkal, G and Al-Akeel, R and Toprak, U and Tettamanti, G and Keyhani, N and Renault, D},
title = {Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag137},
pmid = {42201143},
issn = {1751-7370},
abstract = {Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.},
}

@article {pmid42201863,
year = {2026},
author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI},
title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0340244},
doi = {10.1371/journal.pone.0340244},
pmid = {42201863},
issn = {1932-6203},
mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; },
abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.},
}

Humans
*Bone and Bones/microbiology/pathology
*Metagenomics/methods
*Archaeology
*Microbiota/genetics
Bacteria/genetics/classification
Fungi/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Norway
Phylogeny

@article {pmid41765175,
year = {2026},
author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C},
title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.},
journal = {Journal of endodontics},
volume = {52},
number = {6},
pages = {919-928},
doi = {10.1016/j.joen.2026.02.016},
pmid = {41765175},
issn = {1878-3554},
mesh = {Humans ; *Microbiota/genetics ; *Dental Pulp Cavity/microbiology ; *Virulence Factors/genetics ; Female ; Metagenomics ; Male ; Adult ; *Dental Pulp Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacterial Load ; },
abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8 mm) and 20 with small periapical lesions (<2 mm) were analyzed. Quantitative polymerase chain reaction, 16S next-generation and whole genome sequencing were used to assess microbial load, diversity, and composition. Functional predictions were performed using the Kyoto Encyclopedia of Genes and Genomes and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (P = .011), but comparable alpha diversity and number of species per group in 16S and whole genome analysis (P > .05). Lesion size showed significance by ANOSIM (P = .04) but not in PERMANOVA (P = .36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, P = .012; PERMANOVA R[2] = 0.063, P = .046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.},
}

Humans
*Microbiota/genetics
*Dental Pulp Cavity/microbiology
*Virulence Factors/genetics
Female
Metagenomics
Male
Adult
*Dental Pulp Diseases/microbiology
RNA, Ribosomal, 16S/genetics
Bacterial Load

@article {pmid41964024,
year = {2026},
author = {Sosef, NP and Boxman, ILA and Dirks, RAM},
title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {41964024},
issn = {1743-422X},
support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; },
mesh = {*Nucleic Acid Hybridization/methods ; *Food Safety/methods ; Animals ; Humans ; Ostreidae/virology ; *Virome ; Norovirus/genetics/isolation & purification ; Food Microbiology ; *Viruses/genetics/isolation & purification/classification ; },
abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.},
}

*Nucleic Acid Hybridization/methods
*Food Safety/methods
Animals
Humans
Ostreidae/virology
*Virome
Norovirus/genetics/isolation & purification
Food Microbiology
*Viruses/genetics/isolation & purification/classification

@article {pmid41965517,
year = {2026},
author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H},
title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41965517},
issn = {1471-2180},
support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Silicon Dioxide/adverse effects/toxicity ; *Arginine/metabolism ; Mice ; *Pulmonary Fibrosis/chemically induced/metabolism/microbiology ; *Dysbiosis/microbiology/metabolism ; Disease Models, Animal ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; Lung/pathology ; Akkermansia ; },
abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.

RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.

CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.},
}

Animals
*Silicon Dioxide/adverse effects/toxicity
*Arginine/metabolism
Mice
*Pulmonary Fibrosis/chemically induced/metabolism/microbiology
*Dysbiosis/microbiology/metabolism
Disease Models, Animal
*Tryptophan/metabolism
*Gastrointestinal Microbiome
Cytokines/metabolism
Mice, Inbred C57BL
Male
Lung/pathology
Akkermansia

@article {pmid42068877,
year = {2026},
author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G},
title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158256},
doi = {10.1016/j.phymed.2026.158256},
pmid = {42068877},
issn = {1618-095X},
mesh = {Animals ; *Apoptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Thyroid Gland/drug effects/metabolism ; Male ; Rats ; *Goiter/drug therapy/chemically induced/metabolism ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Propylthiouracil ; Thyroid Hormones/biosynthesis ; Disease Models, Animal ; },
abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.

METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.

RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.

CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.},
}

Animals
*Apoptosis/drug effects
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology
*Thyroid Gland/drug effects/metabolism
Male
Rats
*Goiter/drug therapy/chemically induced/metabolism
*Fatty Acids, Volatile/metabolism
Rats, Sprague-Dawley
Fecal Microbiota Transplantation
Propylthiouracil
Thyroid Hormones/biosynthesis
Disease Models, Animal

@article {pmid42134644,
year = {2026},
author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X},
title = {Antibiotic-mediated gut microbiota depletion partially attenuates methamphetamine-induced reward and linoleic acid metabolic disturbance.},
journal = {Neuropharmacology},
volume = {296},
number = {},
pages = {111022},
doi = {10.1016/j.neuropharm.2026.111022},
pmid = {42134644},
issn = {1873-7064},
mesh = {Animals ; *Methamphetamine/pharmacology ; *Reward ; *Gastrointestinal Microbiome/drug effects/physiology ; *Linoleic Acid/metabolism ; Male ; *Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; Mice ; *Central Nervous System Stimulants/pharmacology ; },
abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of its oxidative metabolism could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.},
}

Animals
*Methamphetamine/pharmacology
*Reward
*Gastrointestinal Microbiome/drug effects/physiology
*Linoleic Acid/metabolism
Male
*Anti-Bacterial Agents/pharmacology
Mice, Inbred C57BL
Mice
*Central Nervous System Stimulants/pharmacology

@article {pmid42178569,
year = {2026},
author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T},
title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42178569},
issn = {2049-2618},
support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; },
abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.

RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67 mg CO2 per g dry weight in a year.

CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.},
}

Animals
*Porifera/microbiology
*Ammonia/metabolism
*Symbiosis
Oxidation-Reduction
*Archaea/metabolism/genetics/classification/isolation & purification
*Microbiota
*Carbon/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Autotrophic Processes
Carbon Cycle
Seawater/microbiology

@article {pmid42178714,
year = {2026},
author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP},
title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2676162},
pmid = {42178714},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; },
abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.},
}

Humans
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/genetics
Aged
Female
Male
*Cognition
Middle Aged
*Cognitive Dysfunction/microbiology
Aged, 80 and over
*Bacteria/classification/genetics/isolation & purification/metabolism
Cohort Studies
Metagenomics
Metabolic Networks and Pathways/genetics

@article {pmid42178721,
year = {2026},
author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M},
title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2675078},
pmid = {42178721},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/microbiology/immunology/etiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Immunoglobulin A, Secretory/immunology/genetics ; *Transplant Recipients ; Tacrolimus/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Adolescent ; Immunosuppressive Agents/adverse effects/therapeutic use ; *Organ Transplantation/adverse effects ; Feces/microbiology ; Child, Preschool ; Liver Transplantation/adverse effects ; },
abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.},
}

Humans
*Dysbiosis/microbiology/immunology/etiology
*Gastrointestinal Microbiome
Child
Male
Female
*Immunoglobulin A, Secretory/immunology/genetics
*Transplant Recipients
Tacrolimus/adverse effects
Bacteria/classification/genetics/isolation & purification
Adolescent
Immunosuppressive Agents/adverse effects/therapeutic use
*Organ Transplantation/adverse effects
Feces/microbiology
Child, Preschool
Liver Transplantation/adverse effects

@article {pmid42184066,
year = {2026},
author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A},
title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42184066},
issn = {1573-0972},
support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration & dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Polyphenols/pharmacology/chemistry/administration & dosage
Rats, Sprague-Dawley
Male
Rats
*Chitosan/chemistry
*Tea/chemistry
*Metabolic Networks and Pathways/drug effects
Liver/metabolism/drug effects
*Nanoparticles/chemistry
*Ferric Compounds/chemistry
Proteome
Proteomics
Bacteria/classification/genetics/drug effects

@article {pmid42184767,
year = {2026},
author = {Chen, D and Ibrar, M and Yan, F and Sun, G and Xue, R and Jia, A and Zhou, J and Gao, Y and Ma, C and Wang, M and Zhang, J and Ma, Z and Liu, L},
title = {The rising power of females: Dioecious shrub enhances soil organic carbon sequestration via fungal necromass in chronosequence of desertified alpine grassland restoration.},
journal = {Journal of environmental management},
volume = {409},
number = {},
pages = {130022},
doi = {10.1016/j.jenvman.2026.130022},
pmid = {42184767},
issn = {1095-8630},
abstract = {Desertification-induced soil organic carbon (SOC) loss poses a major environmental threat to the alpine grasslands of the Qinghai-Tibet Plateau, jeopardizing ecological security and sustainability. While pioneer shrub introduction has yielded positive ecological outcomes, the mechanisms of SOC recovery remain poorly understood. We investigated the effects of a widely used dioecious shrub on rhizosphere SOC dynamics across a 20-year restoration chronosequence, employing a comprehensive framework that combined root exudation measurements, soil physicochemical analysis, metagenomics, and biomarker profiling to decipher the mechanism. Our results reveal that microbial-derived carbon dominated rhizosphere SOC accrual, contributing 20.1-22.0% to the total SOC pool, over 50 times more than plant-derived carbon (0.1-0.4%). The microbial pool was predominantly fungal necromass (>93%), correlated with declining root exudation and suppressed carbon-degrading gene abundance during restoration. In the 20th year after recovery, a striking divergence in the effects of male and female shrubs on rhizosphere SOC became apparent, with female shrubs sustaining 15% more microbial necromass and 47% more lignin phenols than males. Our findings highlight that SOC restoration in the rhizosphere of pioneer shrubs is predominantly driven by a fungal-mediated microbial carbon pump. Moreover, the preferential use of female shrubs offers a dual benefit: enhancing long-term rhizosphere SOC sequestration and controlling shrubs encroachment. This sex-informed strategy therefore provides a scalable framework for degraded alpine grasslands and serves as a transferable model for other drylands undergoing warming-wetting transitions, where alleviated water limitation increasingly enables vegetation-microbe-mediated carbon stabilization.},
}

@article {pmid42186944,
year = {2026},
author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F},
title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70160},
doi = {10.1111/1755-0998.70160},
pmid = {42186944},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; },
abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*DNA, Environmental/genetics
*Metagenomics/methods
*Computational Biology/methods
Bayes Theorem

@article {pmid42192676,
year = {2026},
author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW},
title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050456},
pmid = {42192676},
issn = {2079-6382},
support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; },
abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.},
}

@article {pmid42196140,
year = {2026},
author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL},
title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104155},
pmid = {42196140},
issn = {1422-0067},
support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; },
mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth & development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; },
abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.},
}

Animals
*Biofouling
*Microbiota
Larva/microbiology
Biofilms/growth & development
Quorum Sensing
Ecosystem
*Aquatic Organisms/microbiology

@article {pmid42196196,
year = {2026},
author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L},
title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104213},
pmid = {42196196},
issn = {1422-0067},
support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; },
abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/metabolism
*Metagenomics/methods
*Metabolomics/methods
Male
*Gastrointestinal Microbiome/genetics
Female
Aged
Middle Aged
Feces/microbiology
Multiomics
Metabolome
Biomarkers
RNA, Ribosomal, 16S/genetics
China
Case-Control Studies

@article {pmid42196214,
year = {2026},
author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT},
title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104232},
pmid = {42196214},
issn = {1422-0067},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; },
abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/genetics
*Protein Interaction Maps
*Deep Learning
Phenotype
*Gastrointestinal Microbiome
*Protein Interaction Mapping/methods
*Host Microbial Interactions

@article {pmid42196222,
year = {2026},
author = {Zhang, X and Cai, L and Bai, Y and Peng, F},
title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104238},
pmid = {42196222},
issn = {1422-0067},
support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; },
abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.},
}

*Metagenomics/methods
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
Nutrients

@article {pmid42197004,
year = {2026},
author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH},
title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101544},
pmid = {42197004},
issn = {2072-6643},
support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.

METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.

RESULTS: The results showed that the a-FMT group recovered α diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.

CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.},
}

Animals
*Dysbiosis/therapy/chemically induced/microbiology
*Fecal Microbiota Transplantation/methods
*Mannans/pharmacology
*Anti-Bacterial Agents/adverse effects
Mice
*Gastrointestinal Microbiome/drug effects
Male
*Physical Conditioning, Animal
Mice, Inbred C57BL

@article {pmid42197026,
year = {2026},
author = {Alsinani, Y and Rostamkhani, F and Shirvani, H},
title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101565},
pmid = {42197026},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Exercise/physiology
Fatty Acids, Volatile/metabolism

@article {pmid42197087,
year = {2026},
author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y},
title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.},
journal = {Nutrients},
volume = {18},
number = {10},
pages = {},
doi = {10.3390/nu18101627},
pmid = {42197087},
issn = {2072-6643},
support = {2020YFC2002902//Beijing Sport University/ ; },
mesh = {Humans ; Aged, 80 and over ; *Nutritional Status ; Female ; Male ; *Malnutrition/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Nursing Home Residents ; Feces/microbiology ; Nutrition Assessment ; Nursing Homes ; },
abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.

METHODS: A total of 129 nursing home residents (≥80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF ≥ 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.

RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.

CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.

CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).},
}

Humans
Aged, 80 and over
*Nutritional Status
Female
Male
*Malnutrition/microbiology/therapy
*Gastrointestinal Microbiome/physiology
*Exercise/physiology
Nursing Home Residents
Feces/microbiology
Nutrition Assessment
Nursing Homes

@article {pmid42197335,
year = {2026},
author = {Naranjo-Moran, J and Ratti, MF and Vera-Morales, M},
title = {Microorganisms from Antarctica: A Review of Their Potential in the Bioremediation of Hydrocarbon-Contaminated Soils.},
journal = {Microorganisms},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/microorganisms14050948},
pmid = {42197335},
issn = {2076-2607},
abstract = {Antarctica's extreme cryospheric conditions impose severe thermodynamic constraints on the natural attenuation of hydrocarbon pollutants. Despite the Antarctic Treaty System's protections, the footprint of human logistics has left persistent reservoirs of petroleum hydrocarbons that threaten endemic biodiversity. This review critically synthesizes the state-of-the-art in Antarctic bioremediation, moving beyond traditional culture-dependent studies to integrate recent multi-omics breakthroughs (2020-2025). We analyze the molecular mechanisms limiting bioavailability in frozen soils and highlight the adaptive strategies of psychrophilic consortia, including the modification of membrane fluidity and the expression of cold-active enzymes (e.g., RHDs, AlkB). Notably, we discuss emerging findings on novel long-chain alkane degradation genes (almA, ladA) identified in 2025, which challenge previous assumptions about recalcitrance. Furthermore, the review evaluates the engineering bottlenecks of in situ versus ex situ strategies, emphasizing the synergistic potential of bacterial-fungal co-cultures and the ecological necessity of "climate-smart" remediation to mitigate methane emissions from thawing permafrost. By bridging the gap between fundamental microbial genetics and applied field engineering, we propose a roadmap for the next generation of biotechnological solutions in the warming polar environment.},
}

@article {pmid42198703,
year = {2026},
author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S},
title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.},
journal = {Viruses},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/v18050500},
pmid = {42198703},
issn = {1999-4915},
support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; },
mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation & purification ; Tropical Climate ; Phylogeny ; *Virome ; },
abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.},
}

Seashore
*Geologic Sediments/virology
Seasons
Metagenomics
*Bays/virology
*Viruses/classification/genetics/isolation & purification
Tropical Climate
Phylogeny
*Virome

@article {pmid42199008,
year = {2026},
author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S},
title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2677951},
doi = {10.1080/19490976.2026.2677951},
pmid = {42199008},
issn = {1949-0984},
mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration & dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation & purification/genetics/metabolism ; },
abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.},
}

Humans
Male
*Tryptophan/metabolism
*Gastrointestinal Microbiome
Feces/microbiology
Cross-Over Studies
Middle Aged
*Plant Proteins/metabolism/administration & dosage
Adult
Diet
Cardiometabolic Risk Factors
Metabolome
Indoles/metabolism
Bacteria/classification/isolation & purification/genetics/metabolism

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {33},
number = {5-6},
pages = {643-659},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
mesh = {*RNA Editing/genetics ; Humans ; *Computational Biology/methods ; *Microbiota/genetics ; Escherichia coli/genetics ; Genome, Bacterial ; *RNA, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; },
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

*RNA Editing/genetics
Humans
*Computational Biology/methods
*Microbiota/genetics
Escherichia coli/genetics
Genome, Bacterial
*RNA, Bacterial/genetics
*Gastrointestinal Microbiome/genetics

@article {pmid41935109,
year = {2026},
author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J},
title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41935109},
issn = {2045-2322},
support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; },
mesh = {*Caves/microbiology ; China ; Humans ; Geologic Sediments/microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; *Human Activities ; Nitrogen/metabolism ; Phosphorus/metabolism ; Metagenomics ; },
abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.},
}

*Caves/microbiology
China
Humans
Geologic Sediments/microbiology
*Microbiota
*Bacteria/genetics/classification/metabolism
*Human Activities
Nitrogen/metabolism
Phosphorus/metabolism
Metagenomics

@article {pmid41972755,
year = {2026},
author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB},
title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.},
journal = {mSphere},
volume = {11},
number = {5},
pages = {e0011326},
doi = {10.1128/msphere.00113-26},
pmid = {41972755},
issn = {2379-5042},
support = {//Flu Lab/ ; },
mesh = {Humans ; *Machine Learning ; *Biomarkers/analysis ; *Metagenome ; *Mouth/virology/microbiology ; *Viruses/genetics/isolation & purification/classification ; *Environmental Monitoring/methods ; Microbiota ; *Nose/virology ; Saliva/virology ; Metagenomics ; },
abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.},
}

Humans
*Machine Learning
*Biomarkers/analysis
*Metagenome
*Mouth/virology/microbiology
*Viruses/genetics/isolation & purification/classification
*Environmental Monitoring/methods
Microbiota
*Nose/virology
Saliva/virology
Metagenomics

@article {pmid42018438,
year = {2026},
author = {Sun, X and Jiang, X and Zhang, L and Li, M},
title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117284},
doi = {10.1016/j.celrep.2026.117284},
pmid = {42018438},
issn = {2211-1247},
mesh = {Humans ; *Circadian Rhythm/physiology ; *Microbiota/genetics ; Female ; Adult ; Male ; *Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.},
}

Humans
*Circadian Rhythm/physiology
*Microbiota/genetics
Female
Adult
Male
*Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid42061404,
year = {2026},
author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC},
title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117301},
doi = {10.1016/j.celrep.2026.117301},
pmid = {42061404},
issn = {2211-1247},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; *Tissue Donors ; Female ; Metagenome ; Male ; },
abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Artificial Intelligence
*Gastrointestinal Microbiome/genetics
*Tissue Donors
Female
Metagenome
Male

@article {pmid42119140,
year = {2026},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.},
journal = {Environmental science & technology},
volume = {60},
number = {20},
pages = {14712-14725},
doi = {10.1021/acs.est.5c13903},
pmid = {42119140},
issn = {1520-5851},
mesh = {*Rivers/microbiology ; *Microbiota ; *Microplastics ; Seasons ; Temperature ; },
abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.},
}

*Rivers/microbiology
*Microbiota
*Microplastics
Seasons
Temperature

@article {pmid42140961,
year = {2026},
author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM},
title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42140961},
issn = {2041-1723},
support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
mesh = {*Introduced Species ; *Asteraceae/microbiology ; Species Specificity ; Microbiota ; Ecosystem ; Bacteria/genetics ; },
abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.},
}

*Introduced Species
*Asteraceae/microbiology
Species Specificity
Microbiota
Ecosystem
Bacteria/genetics

@article {pmid42141277,
year = {2026},
author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G},
title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.},
journal = {Nature food},
volume = {7},
number = {5},
pages = {428-440},
pmid = {42141277},
issn = {2662-1355},
mesh = {*Soil Microbiology ; *Microbiota ; *Ecosystem ; Agriculture ; Soil/chemistry ; Climate Change ; Global Warming ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.},
}

*Soil Microbiology
*Microbiota
*Ecosystem
Agriculture
Soil/chemistry
Climate Change
Global Warming
Bacteria/classification/genetics/isolation & purification

@article {pmid42176697,
year = {2026},
author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J},
title = {Artificial reefs alter viral communities and functional traits in coastal waters.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108131},
doi = {10.1016/j.marenvres.2026.108131},
pmid = {42176697},
issn = {1879-0291},
abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.},
}

@article {pmid41875615,
year = {2026},
author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J},
title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.},
journal = {Marine genomics},
volume = {86},
number = {},
pages = {101245},
doi = {10.1016/j.margen.2026.101245},
pmid = {41875615},
issn = {1876-7478},
mesh = {*Quorum Sensing/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Indian Ocean ; *Metagenome ; *Bacterial Proteins/genetics ; Databases, Protein ; Bacteria/genetics ; *Microbiota ; },
abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.},
}

*Quorum Sensing/genetics
*Geologic Sediments/microbiology
Metagenomics
Indian Ocean
*Metagenome
*Bacterial Proteins/genetics
Databases, Protein
Bacteria/genetics
*Microbiota

@article {pmid41887507,
year = {2026},
author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM},
title = {Microbiota changes in rumen and milk corresponding to dietary protein intake in transition dairy cows.},
journal = {Journal of dairy science},
volume = {109},
number = {6},
pages = {6287-6300},
doi = {10.3168/jds.2025-27576},
pmid = {41887507},
issn = {1525-3198},
mesh = {Animals ; Cattle ; *Milk/microbiology ; *Rumen/microbiology/metabolism ; Female ; Lactation ; Diet/veterinary ; *Dietary Proteins ; Animal Feed ; *Microbiota ; Postpartum Period ; },
abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively affected milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in MP supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (MP80) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (MP100) for an additional 14 d. Control cows (n = 6) were fed MP100 for the entire experiment. Samples of rumen content and milk were taken in the immediate postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental recovery phase on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated with the effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the MP100 compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.},
}

Animals
Cattle
*Milk/microbiology
*Rumen/microbiology/metabolism
Female
Lactation
Diet/veterinary
*Dietary Proteins
Animal Feed
*Microbiota
Postpartum Period

@article {pmid42070641,
year = {2026},
author = {Wu, M and Liao, H and Luo, Y and Yao, Y and Yang, D and Hu, Z and Gao, L and Xia, X},
title = {Moisture transfer-driven quality enhancement in solid-state fermented Daqu: Synergistic effects of microbial community adaptation and functional enzyme metabolism.},
journal = {Bioresource technology},
volume = {455},
number = {},
pages = {134771},
doi = {10.1016/j.biortech.2026.134771},
pmid = {42070641},
issn = {1873-2976},
mesh = {*Fermentation ; *Water/metabolism ; *Microbiota ; alpha-Amylases/metabolism ; },
abstract = {Solid-state fermented Daqu exhibits a typical heterogeneous structure, where moisture regulates the microbial activity by driving gas diffusion in the pores and nutrient enrichment, playing a crucial role in the quality of the final product. However, there is a lack of clarity regarding how moisture transfer affects Daqu microbial assembly and metabolic flux. This study pioneered a real-time controllable fermentation platform, employing stoichiometry, nuclear magnetic resonance, and metagenomics to investigate microbial saccharifying metabolic functions under moisture transfer regulation. Comparing representative low (LM: 34%, 36%) and high (HM: 38%, 40%) moisture groups, we found that porosity exhibited a strong positive correlation with water activity (coefficient > 0.9, p < 0.01), serving as the primary physicochemical contributor governing moisture transfer priority. Furthermore, steady-state mass transfer in the HM group (≥ 38%) enhanced the transfer rate from free water (T23) to capillary water (T22: 10-100 ms), shaping a saccharifying functional microbial community dominated by Rhizopus and Bacillus. Weighted network and functional gene predictions indicated that this process strengthened the substrate preference of core microorganisms toward starch, significantly reinforcing the metabolic synergy between glucoamylase and α-amylase. Conversely, transient mass transfer in the LM group (< 38%) triggered microbial functional differentiation, promoting the redistribution of non-starch polysaccharide hydrolases. Our research revealed the effects of moisture transfer on nutrient availability, microbial adaptation, and metabolic functions in stack-fermented Daqu. This work ensures Daqu stability and presents novel strategies to optimize solid-state fermentation efficiency through moisture-driven microbial metabolic trade-offs.},
}

*Fermentation
*Water/metabolism
*Microbiota
alpha-Amylases/metabolism

@article {pmid42102934,
year = {2026},
author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J},
title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.},
journal = {Bioresource technology},
volume = {455},
number = {},
pages = {134810},
doi = {10.1016/j.biortech.2026.134810},
pmid = {42102934},
issn = {1873-2976},
mesh = {Aerobiosis ; *Bacteria/metabolism ; *Fungi/metabolism ; *Food ; *Microbial Consortia ; *Waste Products/analysis ; Carboxylic Acids/metabolism ; Bioreactors/microbiology ; Food Loss and Waste ; },
abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.},
}

Aerobiosis
*Bacteria/metabolism
*Fungi/metabolism
*Food
*Microbial Consortia
*Waste Products/analysis
Carboxylic Acids/metabolism
Bioreactors/microbiology
Food Loss and Waste

@article {pmid42114574,
year = {2026},
author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J},
title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.},
journal = {Bioresource technology},
volume = {455},
number = {},
pages = {134795},
doi = {10.1016/j.biortech.2026.134795},
pmid = {42114574},
issn = {1873-2976},
mesh = {*Fatty Acids/biosynthesis ; *Microbiota/drug effects ; Animals ; *Egg Shell/chemistry ; *Fungi/metabolism ; *Bacteria/metabolism ; *Calcium ; Ethanol/metabolism ; *Waste Products/analysis ; Caproates ; },
abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.},
}

*Fatty Acids/biosynthesis
*Microbiota/drug effects
Animals
*Egg Shell/chemistry
*Fungi/metabolism
*Bacteria/metabolism
*Calcium
Ethanol/metabolism
*Waste Products/analysis
Caproates

@article {pmid42169351,
year = {2026},
author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S},
title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119400},
doi = {10.1016/j.foodres.2026.119400},
pmid = {42169351},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; *Metagenomics/methods ; Fermentation ; *Whey/microbiology ; *Food Microbiology ; Biogenic Amines/analysis ; China ; Milk/microbiology ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.},
}

*Cheese/microbiology/analysis
Animals
Goats
*Metagenomics/methods
Fermentation
*Whey/microbiology
*Food Microbiology
Biogenic Amines/analysis
China
Milk/microbiology
*Microbiota
Bacteria/genetics/classification

@article {pmid42170880,
year = {2026},
author = {Ershova-Menze, E and Westgaard, JI and Hjellnes, H and Falkenhaug, T},
title = {Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70149},
doi = {10.1111/1755-0998.70149},
pmid = {42170880},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Zooplankton/genetics/classification ; Animals ; Biodiversity ; DNA/genetics/isolation & purification ; *Metagenomics/methods ; Electron Transport Complex IV/genetics ; },
abstract = {DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.},
}

*DNA Barcoding, Taxonomic/methods
*Zooplankton/genetics/classification
Animals
Biodiversity
DNA/genetics/isolation & purification
*Metagenomics/methods
Electron Transport Complex IV/genetics

@article {pmid42171625,
year = {2026},
author = {Paietta, EN and Johnston, RA and Kraberger, S and Randrianarisoa, SF and Razanamahenina, TT and Ramboninarimalala, A and Velontsara, JB and Raherinirina, TG and Raveloson, L and Finley, NL and Baitchman, E and McAdoo, BG and Yoder, AD and Varsani, A},
title = {Mammal-infecting DNA viruses identified in lemurs and rodents in Madagascar mirror the evolutionary history of their hosts.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42171625},
issn = {2057-5858},
mesh = {Animals ; Madagascar ; *Lemur/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Rodentia/virology ; Rats/virology ; Metagenomics ; Genome, Viral ; },
abstract = {Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, Parvoviridae and Polyomaviridae and assessed their phylogenetic relationships to known viruses. Endemic lemurs and tufted-tailed rats displayed particularly novel DNA viral diversity mirroring the geographic isolation and subsequently rich evolutionary history of their hosts. Notably, we provide the first coding-complete sequences in lemurs of herpesviruses, polyomaviruses, adeno-associated viruses and circoviruses. In contrast, the DNA viral communities of black rats in Madagascar were similar to those found in globally distributed black and brown rat populations, given their broad geographic spread and relatively recent introduction to the island. Given the scarcity of viral research in natural populations of lemurs and rodents in Madagascar despite the island's exceptional biodiversity and escalating anthropogenic pressures, this study provides a genomic and phylogenetic foundation for DNA viruses infecting Malagasy lemurs and rodents.},
}

Animals
Madagascar
*Lemur/virology
*DNA Viruses/genetics/classification/isolation & purification
Phylogeny
*Rodentia/virology
Rats/virology
Metagenomics
Genome, Viral

@article {pmid42175735,
year = {2026},
author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X},
title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70408},
doi = {10.1111/mec.70408},
pmid = {42175735},
issn = {1365-294X},
support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; },
mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; },
abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.},
}

*Nitrogen/metabolism
*Soil Microbiology
*Phosphorus/metabolism
*Ecosystem
*Soil/chemistry
Microbiota/genetics
Tibet
Metagenomics
Bacteria/genetics

@article {pmid42175741,
year = {2026},
author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z},
title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70929},
doi = {10.1111/gcb.70929},
pmid = {42175741},
issn = {1365-2486},
support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; },
mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.},
}

*Climate Change
*Drug Resistance, Microbial/genetics
Oceans and Seas
*Microbiota
Virulence Factors/genetics
*Seawater/microbiology
Anti-Bacterial Agents/pharmacology

@article {pmid42119385,
year = {2026},
author = {Pan, L and Huang, Y and Chen, Y and Peng, T and Yang, J and Qiu, Y and Ji, M and Wu, X},
title = {Responses of soil microbes to antimony stress and coupled nutrient cycling in karst mining areas of Southwest China.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120248},
doi = {10.1016/j.ecoenv.2026.120248},
pmid = {42119385},
issn = {1090-2414},
mesh = {*Antimony/toxicity/analysis ; China ; *Soil Microbiology ; Mining ; *Soil Pollutants/toxicity/analysis ; *Microbiota/drug effects ; Environmental Monitoring ; Bacteria/drug effects ; Soil/chemistry ; },
abstract = {Persistent and poorly mobile heavy metals in soil present a widespread environmental challenge. Among these, antimony (Sb) is a contaminant of emerging concern whose transformation and migration in soil require further investigation to inform effective remediation strategies. Microbial processes are central to these dynamics, yet the mechanisms underlying Sb-microbe interactions remain poorly defined. In this study, we used integrated geochemical and metagenomic analyses to assess Sb contamination and microbial community responses systematically in an abandoned Sb mining area in Southwest China. The data reveal how microbial communities respond to low and moderate levels of Sb contamination. Contamination was highest in the mining area, followed by the smelting and tailings areas; the control area exhibited the lowest levels. Community structure analysis revealed significant enrichment of Thiobacillus, Geothrix, and Anaeromyxobacter in the mining area, while Nocardioides and Sphingomonas were more abundant in the smelting area. Bradyrhizobium dominated in the control area. These patterns reflect distinct microbial responses to the Sb contamination gradient. Critically, partial least squares path modeling revealed that Sb contamination did not directly affect microbial α-diversity. Instead, its influence was indirectly mediated through disruptions in sulfur cycling functions-a novel finding highlighting the indirect ecological impact of Sb. Sb, along with co-occurring copper, may drive adaptive microbial succession by interfering with sulfate respiration. This process enriches microbial groups with sulfur-cycling-related detoxification functions, resulting in simplified community structure and reduced diversity. Thus, the primary mechanism by which Sb alters microbial communities in karst soils is indirect, operating via perturbation of the sulfur cycle rather than direct toxicity. These findings offer a theoretical basis for developing targeted microbial remediation strategies and restoring ecological functions in Sb-contaminated environments by regulating key elemental cycles.},
}

*Antimony/toxicity/analysis
China
*Soil Microbiology
Mining
*Soil Pollutants/toxicity/analysis
*Microbiota/drug effects
Environmental Monitoring
Bacteria/drug effects
Soil/chemistry

@article {pmid42140024,
year = {2026},
author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L},
title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.},
journal = {International journal of food microbiology},
volume = {457},
number = {},
pages = {111847},
doi = {10.1016/j.ijfoodmicro.2026.111847},
pmid = {42140024},
issn = {1879-3460},
mesh = {*Microbiota ; Bacteria/classification/genetics/isolation & purification/metabolism ; Fungi/classification/isolation & purification/genetics/metabolism ; Hot Temperature ; China ; *Volatile Organic Compounds/analysis ; Taste ; Humans ; *Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; *Wine/microbiology/analysis ; },
abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.},
}

*Microbiota
Bacteria/classification/genetics/isolation & purification/metabolism
Fungi/classification/isolation & purification/genetics/metabolism
Hot Temperature
China
*Volatile Organic Compounds/analysis
Taste
Humans
*Alcoholic Beverages/microbiology/analysis
Food Microbiology
*Wine/microbiology/analysis

@article {pmid42169289,
year = {2026},
author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I},
title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {237},
number = {},
pages = {119324},
doi = {10.1016/j.foodres.2026.119324},
pmid = {42169289},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; },
abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.},
}

*Metabolomics/methods
*Meat Products/microbiology/analysis
*Odorants/analysis
Fermentation
*Metagenomics/methods
Volatile Organic Compounds/analysis
*Pea Proteins/metabolism
Animals
Gas Chromatography-Mass Spectrometry
Taste
Food Microbiology
Humans
Microbiota
Swine
Tandem Mass Spectrometry

@article {pmid41790075,
year = {2026},
author = {Kong, C and Jin, Y and Guo, F and Yang, Y and Liu, G and Chen, Z and Li, J and Wang, Q and Ma, Y},
title = {Revealing the Antagonistic Interactions of Faecalibacterium prausnitzii and Bacteroides fragilis in Colorectal Cancer.},
journal = {Gastroenterology},
volume = {170},
number = {7},
pages = {1501-1517},
doi = {10.1053/j.gastro.2025.12.030},
pmid = {41790075},
issn = {1528-0012},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/genetics ; *Bacteroides fragilis/metabolism ; Animals ; Male ; Female ; *Faecalibacterium prausnitzii/metabolism/genetics ; Mice ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; China ; Aged ; Exome Sequencing ; Case-Control Studies ; *Host Microbial Interactions ; },
abstract = {BACKGROUND & AIMS: Maladaptation of host-microbe metabolic interactions plays a crucial role in development of colorectal cancer (CRC). However, remains a lack of comprehensive studies using multi-omics analysis to illustrate host-microbe metabolic interactions in CRC.

METHODS: We collected and analyzed 440 stool samples from a discovery cohort in Shanghai China (255 patients with CRC and 185 healthy controls). Each sample was subjected to metagenomic sequencing and nontargeted liquid chromatography mass spectrometry. Fresh-frozen specimens of tumors and matched adjacent normal mucosae were extracted from 62 patients with CRC, and whole exome sequencing and RNA sequencing were performed to explore host genomic patterns and host-microbe metabolic interactions. Finally, relationships detected in the discovery cohort were validated against independent cohorts, organoid models, and mice experiments.

RESULTS: The relationship between disrupted microbial homeostasis and CRC progression is characterized by Bacteroides fragilis enrichment and reduction of Faecalibacterium prausnitzii. F prausnitzii metabolizes tryptophan into picolinic acid (PIA) via the enzyme 2-amino-3-carboxymuconate semialdehyde decarboxylase, with PIA exerting an antagonistic effect on enterotoxigenic B fragilis-mediated tumor progression. Mechanistically, enterotoxigenic B fragilis up-regulates the expression of genes associated with poor differentiation and recurrence, namely TCERG1 and CKAP2, and PIA induces tumor cell apoptosis by down-regulating these 2 genes. Independent validation cohorts and murine models corroborated that a tryptophan-rich diet effectively elevates circulating PIA levels, suggesting its potential as an anticancer dietary intervention.

CONCLUSIONS: Our research characterized a representative microbe-metabolite-host regulatory pathway occurring in CRC, namely the F prausnitzii-PIA-TCERG1/CKAP2 axis antagonizing enterotoxigenic B fragilis-induced CRC progression. As a treatment option, we highlight the therapeutic potential inherent in a tryptophan-rich diet and in manipulating microbial composition targeting the F prausnitzii-PIA axis to prevent CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/genetics
*Bacteroides fragilis/metabolism
Animals
Male
Female
*Faecalibacterium prausnitzii/metabolism/genetics
Mice
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology
China
Aged
Exome Sequencing
Case-Control Studies
*Host Microbial Interactions

@article {pmid42066541,
year = {2026},
author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X},
title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117442},
doi = {10.1016/j.diagmicrobio.2026.117442},
pmid = {42066541},
issn = {1879-0070},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Middle Aged ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification/classification ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; },
abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.

METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.

RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Male
Middle Aged
Female
*Tuberculosis, Pulmonary/diagnosis/microbiology
*Metagenomics/methods
*Microbiota/genetics
Aged
*Nontuberculous Mycobacteria/genetics/isolation & purification/classification
Adult
*Mycobacterium tuberculosis/genetics/isolation & purification/classification
*Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Aged, 80 and over

@article {pmid42081609,
year = {2026},
author = {Wang, Y and Zhang, B and Shen, C and Cao, M and Wang, N and Chen, T and He, G and Sun, G and Li, C and Li, Y and Yin, X and Sun, Y and Li, C and Zhou, X},
title = {N-Carbamoylglutamate enhances bull spermatogenesis via Paraprevotella-mediated vitamin B6 biosynthesis in rumen microbiota.},
journal = {Reproduction (Cambridge, England)},
volume = {171},
number = {5},
pages = {},
doi = {10.1093/reprod/xaag049},
pmid = {42081609},
issn = {1741-7899},
support = {CARS-36//The China Agriculture Research System of MOF and MARA/ ; 20240303081NC//The key Research and Development Program of Jilin Province/ ; XZ202401ZY0053//The key Research and Development Project of Tibet Autonomous Region/ ; },
mesh = {Animals ; Male ; *Spermatogenesis/drug effects ; Cattle ; *Rumen/microbiology/drug effects/metabolism ; *Glutamates/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Vitamin B 6/biosynthesis ; Mice ; },
abstract = {In brief: Emerging evidence suggests that gut microbial metabolites can influence male fertility, but how rumen microbiota regulate spermatogenesis in ruminants remains unclear. This study demonstrates that N-carbamoylglutamate promotes bull spermatogenesis through a rumen microbiota-vitamin B6 axis associated with Paraprevotella. Abstract: N-Carbamoylglutamate (NCG), a functional analog of the arginine precursor, shows strong potential in enhancing spermatogenesis in bulls. In this study, dietary NCG supplementation significantly increased sperm density and motility in XiangXi yellow bulls, the local beef cattle. Metagenomic and serum metabolomic analyses revealed that NCG altered the composition of rumen microbiota, notably increasing the abundance of Paraprevotella and elevating serum vitamin B6 levels (p < 0 .05), suggesting a possible microbiota-associated metabolic modulation underlying its reproductive benefits. To explore this mechanism, a busulfan-induced mouse model of impaired spermatogenesis was established. Mice received transplants of either rumen microbiota from NCG-treated bulls or the differential genus Paraprevotella. Both treatments alleviated reproductive damage and increased vitamin B6 levels in serum and testis. Mechanistic investigation indicated that Paraprevotella was associated with upregulated expression of 3-phosphoserine aminotransferase, a key enzyme involved in vitamin B6 biosynthesis. Subsequent vitamin B6 supplementation experiments showed increased testicular glutathione levels and reduced thiobarbituric acid-reactive substances level (expressed as MDA equivalents). These experiments supported a contributory role of vitamin B6 in promoting spermatogenesis, including increased sperm count and enhanced expression of spermatogenic cell markers. In summary, this study demonstrated that NCG enhanced spermatogenesis in bulls by reshaping the rumen microbiota, particularly through enrichment of Paraprevotella, which was associated with increased systemic vitamin B6 levels and contributed to reproductive improvement. These findings provide further insights into the application of NCG in improving fertility in ruminants.},
}

Animals
Male
*Spermatogenesis/drug effects
Cattle
*Rumen/microbiology/drug effects/metabolism
*Glutamates/pharmacology
*Gastrointestinal Microbiome/drug effects
*Vitamin B 6/biosynthesis
Mice

@article {pmid42166340,
year = {2026},
author = {Sato, M and Kanaly, RA and Mori, JF},
title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
pmid = {42166340},
issn = {1465-2080},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth & development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth & development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; },
abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Sphingomonadaceae/genetics/metabolism/growth & development
Biodegradation, Environmental
Genome, Bacterial
*Transcriptome
*Achromobacter/genetics/metabolism/growth & development
Soil Microbiology
*Achromobacter denitrificans/genetics/metabolism
Phylogeny
Genomics
Soil Pollutants/metabolism
Gene Expression Profiling
Microbial Consortia

@article {pmid42167281,
year = {2026},
author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC},
title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70327},
doi = {10.1111/1462-2920.70327},
pmid = {42167281},
issn = {1462-2920},
support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; },
mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; },
abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.},
}

*Wetlands
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Greenhouse Gases/analysis/metabolism
Congo
RNA, Ribosomal, 16S/genetics
*Plankton/genetics/classification
Ecosystem
Methane/metabolism
Phylogeny
Carbon Cycle
Biodiversity
Metagenome

@article {pmid41741009,
year = {2026},
author = {Li, S and Yan, Q and Tong, J and Li, Y and Bai, L and Peng, Q},
title = {Distinct Defence Mechanisms of Allelopathic Rice Against Quinclorac-Susceptible and -Resistant Barnyardgrass: Involvement of Specific Metabolites and Rhizosheath Microbiota.},
journal = {Plant biotechnology journal},
volume = {24},
number = {6},
pages = {3876-3896},
doi = {10.1111/pbi.70611},
pmid = {41741009},
issn = {1467-7652},
support = {U22A20461,32372564//National Natural Science Foundation of China/ ; },
mesh = {*Oryza/metabolism/microbiology/drug effects/genetics/physiology ; *Allelopathy ; *Herbicides/pharmacology ; *Quinolines/pharmacology ; Terpenes/metabolism ; *Microbiota ; *Echinochloa/drug effects ; Plant Roots/metabolism/microbiology ; *Herbicide Resistance ; Cyclopentanes/metabolism ; },
abstract = {Allelopathic rice is increasingly recognised as a promising strategy for sustainable weed management. Resistance to the herbicide quinclorac is widespread in barnyardgrass, but it remains unclear whether allelopathic rice exerts the same defence against herbicide-susceptible and -resistant barnyardgrass. We conducted integrated transcriptomic, metabolomic, and metagenomic analyses to investigate the responses of allelopathic rice to quinclorac-susceptible (S) and -resistant barnyardgrass (R) lines. Distinct chemical strategies were identified in allelopathic rice: Terpenoids (e.g., carnosic acid, phytocassane B, and ipomeatetrahydrofuran) mainly suppressed S, while amino acids (e.g., pipecolic acid, L-glutamate, and L-histidine) were key against R. Correspondingly, terpenoid biosynthesis and nitrogen metabolism were the most enriched pathways under S and R stress, respectively. Additionally, terpenoid accumulation correlated positively with salicylic acid (SA) and jasmonic acid (JA) concentrations in roots under S. Both terpenoids and amino acids formed the stable ecological networks with rhizosheath microbiota. Functional metagenomic analysis further showed that ABC transporter and quorum sensing pathways were upregulated under S, whereas nitrogen fixation predominated under R. Notably, amino acids formed a nitrogen-related ecological network with nitrogen-metabolising microbiota, contributing to improved plant-available soil nitrogen and total nitrogen content in rice plants. Bioassays showed that exogenous pipecolic acid (≥ 40 μM) and L-histidine (80 μM) inhibited barnyardgrass seedling growth without affecting allelopathic and non-allelopathic rice. These findings demonstrate that allelopathic rice employs divergent chemical-microbial defence strategies against S and R barnyardgrass, highlight the dual role of amino acids, and provide a basis for precision weed management, particularly for herbicide-resistant weeds in paddy fields.},
}

*Oryza/metabolism/microbiology/drug effects/genetics/physiology
*Allelopathy
*Herbicides/pharmacology
*Quinolines/pharmacology
Terpenes/metabolism
*Microbiota
*Echinochloa/drug effects
Plant Roots/metabolism/microbiology
*Herbicide Resistance
Cyclopentanes/metabolism

@article {pmid41816995,
year = {2026},
author = {Zhao, F and Zhang, R and Wei, R and Fan, H and Hu, Y and Shi, W and Wang, J},
title = {Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {29},
pages = {e16916},
doi = {10.1002/advs.202516916},
pmid = {41816995},
issn = {2198-3844},
support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; 32370053//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; },
mesh = {*Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/physiology/drug effects ; Animals ; Mice ; *Polysaccharides/metabolism/administration & dosage ; *Bacteriophages/genetics ; *Bacteria/virology/genetics ; Mice, Inbred C57BL ; Male ; },
abstract = {Phages dominate the human gut virome and are known for their ability to prey on bacteria and shape microbiota. However, their response to diet has only been elucidated using small-scale studies. By integrating a massive meta-analysis of 6932 diet-associated metagenomes with a time-resolved mouse model of a high-fat diet and polysaccharide intake, the impact of diet on the gut virome and phage-bacterial interactions was systematically characterized. Diet types, particularly high-fat and polysaccharide-rich diets, exert the strongest shaping force on the gut virome, enhancing the crosstalk between phages and bacteria. High-fat diets promote changes in phage abundance across a broad taxonomic range, from 34.21% to 50.00%, drive phages of diet-associated bacteria toward a lytic lifestyle, and remarkably enrich auxiliary metabolic genes related to amino acid metabolism. Conversely, fucoidan reversed HFD-induced dysbiosis and enhanced phage-mediated horizontal gene transfer by 8.5-fold relative to the baseline. crAssphages and Parabacteroides phages may be important contributors, broadly supporting horizontal gene transfer and auxiliary metabolism or strengthening phage-host interactions in polysaccharide interventions, including fucoidan supplementation. These findings provide a comprehensive landscape of diet-driven cross-kingdom interactions and phage-mediated gene exchange in the gut, offering new insights into potential strategies for precise nutritional interventions targeting the intestinal microbiota.},
}

*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/physiology/drug effects
Animals
Mice
*Polysaccharides/metabolism/administration & dosage
*Bacteriophages/genetics
*Bacteria/virology/genetics
Mice, Inbred C57BL
Male

@article {pmid41869887,
year = {2026},
author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J},
title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {29},
pages = {e20332},
doi = {10.1002/advs.202520332},
pmid = {41869887},
issn = {2198-3844},
support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Mice ; Animals ; *Bacterial Proteins/immunology/genetics/metabolism ; *Colorectal Neoplasms/immunology/microbiology ; *Cytokines/immunology/metabolism/genetics ; },
abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.},
}

Humans
*Gastrointestinal Microbiome/immunology/genetics
Mice
Animals
*Bacterial Proteins/immunology/genetics/metabolism
*Colorectal Neoplasms/immunology/microbiology
*Cytokines/immunology/metabolism/genetics

@article {pmid41935274,
year = {2026},
author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S},
title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {41935274},
issn = {1743-422X},
mesh = {Animals ; Swine ; England/epidemiology ; *Swine Diseases/virology ; *Diarrhea/veterinary/virology ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Feces/virology ; Weaning ; Metagenomics ; *Virus Diseases/veterinary/virology ; Gastrointestinal Microbiome ; Viral Load ; Gastrointestinal Tract/virology ; },
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.

METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.

RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.

CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.},
}

Animals
Swine
England/epidemiology
*Swine Diseases/virology
*Diarrhea/veterinary/virology
*Virome
*Viruses/classification/genetics/isolation & purification
Feces/virology
Weaning
Metagenomics
*Virus Diseases/veterinary/virology
Gastrointestinal Microbiome
Viral Load
Gastrointestinal Tract/virology

@article {pmid42162115,
year = {2026},
author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, ÅV and Walter, S and Simon, R},
title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42162115},
issn = {2045-2322},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; },
abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics
Female
*Metagenomics/methods
Adult
Middle Aged
Feces/microbiology
*Metagenome
Case-Control Studies

@article {pmid42162287,
year = {2026},
author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T},
title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.},
journal = {Archives of virology},
volume = {171},
number = {6},
pages = {},
pmid = {42162287},
issn = {1432-8798},
support = {ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; },
mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation & purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; },
abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.},
}

*Edible Grain/virology
Genome, Viral
Phylogeny
*Hordeum/virology
*Luteoviridae/genetics/classification/isolation & purification
*Plant Diseases/virology
France
*Virome/genetics
Metagenomics

@article {pmid42162574,
year = {2025},
author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E},
title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.},
journal = {Asian journal of anesthesiology},
volume = {63},
number = {1},
pages = {20-29},
doi = {10.6859/aja.202503_63(1).0003},
pmid = {42162574},
issn = {2468-824X},
mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; },
abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.

METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.

RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.},
}

Animals
*Sevoflurane/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Mice
Female
*Anesthetics, Inhalation/pharmacology
*Dysbiosis/chemically induced/microbiology
*Metagenomics/methods
Feces/microbiology
Longitudinal Studies
Sex Factors

@article {pmid42165805,
year = {2026},
author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM},
title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42165805},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; },
abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/physiology
*Colon/microbiology/virology
Escherichia coli/virology/genetics
Bacteria/genetics/virology/classification
Phage Therapy
Feces/microbiology

@article {pmid41628665,
year = {2026},
author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM},
title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: A proof-of-concept placebo-controlled randomized trial.},
journal = {Osteoarthritis and cartilage},
volume = {34},
number = {6},
pages = {869-881},
doi = {10.1016/j.joca.2026.01.630},
pmid = {41628665},
issn = {1522-9653},
mesh = {Humans ; Female ; Middle Aged ; Male ; *Gastrointestinal Microbiome/drug effects ; Aged ; Proof of Concept Study ; *Osteoarthritis/drug therapy/microbiology ; Delayed-Action Preparations ; *Butyric Acid/therapeutic use/administration & dosage ; Feces/microbiology ; Hand ; Double-Blind Method ; Treatment Outcome ; *Butyrates ; Streptococcus/drug effects ; },
abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600 mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.},
}

Humans
Female
Middle Aged
Male
*Gastrointestinal Microbiome/drug effects
Aged
Proof of Concept Study
*Osteoarthritis/drug therapy/microbiology
Delayed-Action Preparations
*Butyric Acid/therapeutic use/administration & dosage
Feces/microbiology
Hand
Double-Blind Method
Treatment Outcome
*Butyrates
Streptococcus/drug effects

@article {pmid41872600,
year = {2026},
author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E},
title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.},
journal = {Nature medicine},
volume = {32},
number = {5},
pages = {1884-1894},
pmid = {41872600},
issn = {1546-170X},
mesh = {Humans ; *Diet ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; Phenotype ; Male ; *Precision Medicine ; Metagenomics ; Adult ; Middle Aged ; },
abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.},
}

Humans
*Diet
*Gastrointestinal Microbiome/genetics/physiology
Female
Phenotype
Male
*Precision Medicine
Metagenomics
Adult
Middle Aged

@article {pmid41912529,
year = {2026},
author = {Achudhan, AB and Narayanan, R and Madhavan, T},
title = {Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41912529},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; India ; *Metagenome ; *Plastics ; *Genome, Microbial ; Microbiota ; },
abstract = {Plastic pollution is an escalating environmental concern, particularly in coastal regions where sediments serve as long-term sinks for plastic debris. Despite this, the microbial communities inhabiting plastic-contaminated sediments remain poorly characterized in highly polluted hotspots. In this study, we conducted a genome-resolved metagenomic investigation of sediment sample from plastic pollution hotspot in India. Using Illumina short-read sequencing and three high-performing binning tools we reconstructed 52 non-redundant metagenome-assembled genomes (MAGs) from 2,374 initial bins. All MAGs met the MIMAG criteria with 15% reaching near-complete genomes. Taxonomic classification revealed diverse representation of 18 different phyla. Interestingly, 90% of the MAGs could only be classified at intermediate taxonomic levels in the Genome Taxonomy Database (GTDB), suggesting the presence of novel microbial lineages. Taxonomic novelty was further confirmed using the Type Strain Genome Server (TYGS), which identified 3 novel orders, 16 families, and 28 genera. This study provides the first comprehensive genomic insight into microbial communities from plastic-polluted coastal sediments in India and lays the groundwork for exploring their ecological functions.},
}

*Geologic Sediments/microbiology
India
*Metagenome
*Plastics
*Genome, Microbial
Microbiota

@article {pmid41927746,
year = {2026},
author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA},
title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41927746},
issn = {2045-2322},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism/drug effects ; *Methane/metabolism ; *Plant Extracts/pharmacology ; Sheep/microbiology ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; Fermentation/drug effects ; Jatropha/chemistry ; Digestion/drug effects ; Metagenomics ; Aloe/chemistry ; },
abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.},
}

Animals
*Rumen/microbiology/metabolism/drug effects
*Methane/metabolism
*Plant Extracts/pharmacology
Sheep/microbiology
Animal Feed/analysis
*Gastrointestinal Microbiome/drug effects
Dietary Supplements
Fermentation/drug effects
Jatropha/chemistry
Digestion/drug effects
Metagenomics
Aloe/chemistry

@article {pmid41933095,
year = {2026},
author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W},
title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41933095},
issn = {2045-2322},
mesh = {Humans ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; *Lung/microbiology ; Aged ; *Pneumonia/diagnosis/microbiology/genetics ; Prospective Studies ; Gene Expression Profiling ; Transcriptome ; Metagenomics ; Sputum/microbiology ; Diagnosis, Differential ; Adult ; High-Throughput Nucleotide Sequencing ; },
abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.},
}

Humans
Male
*Microbiota/genetics
Female
Middle Aged
*Lung/microbiology
Aged
*Pneumonia/diagnosis/microbiology/genetics
Prospective Studies
Gene Expression Profiling
Transcriptome
Metagenomics
Sputum/microbiology
Diagnosis, Differential
Adult
High-Throughput Nucleotide Sequencing

@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
mesh = {Humans ; *Blastocystis/isolation & purification/physiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Diabetes Mellitus, Type 2/drug therapy/parasitology/metabolism ; Middle Aged ; Feces/microbiology/parasitology ; *Blastocystis Infections ; Metformin/therapeutic use ; Adult ; *Glucose/metabolism ; Cohort Studies ; *Blood Glucose/metabolism ; Aged ; Hypoglycemic Agents/therapeutic use ; },
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}

Humans
*Blastocystis/isolation & purification/physiology
*Gastrointestinal Microbiome/physiology
Male
Female
*Diabetes Mellitus, Type 2/drug therapy/parasitology/metabolism
Middle Aged
Feces/microbiology/parasitology
*Blastocystis Infections
Metformin/therapeutic use
Adult
*Glucose/metabolism
Cohort Studies
*Blood Glucose/metabolism
Aged
Hypoglycemic Agents/therapeutic use

@article {pmid42032888,
year = {2026},
author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z},
title = {Rhizosphere microbiome influences fruit quality in citrus.},
journal = {The New phytologist},
volume = {250},
number = {6},
pages = {3914-3931},
doi = {10.1111/nph.71159},
pmid = {42032888},
issn = {1469-8137},
support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; },
mesh = {*Rhizosphere ; *Citrus/microbiology ; *Microbiota ; *Fruit/microbiology ; Iron/metabolism ; Bacteria/genetics/metabolism ; Soil Microbiology ; Sugars/metabolism ; Siderophores/metabolism ; },
abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.},
}

*Rhizosphere
*Citrus/microbiology
*Microbiota
*Fruit/microbiology
Iron/metabolism
Bacteria/genetics/metabolism
Soil Microbiology
Sugars/metabolism
Siderophores/metabolism

@article {pmid42157352,
year = {2026},
author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H},
title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42157352},
issn = {1297-9716},
support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; },
abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.},
}

Animals
Swine
*Brachyspira hyodysenteriae/physiology
*Swine Diseases/microbiology/metabolism
*Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism
*Metabolome
Colon/metabolism/microbiology
Gastrointestinal Microbiome
*Dysentery/veterinary/microbiology/metabolism
Feces/microbiology
Metabolomics

@article {pmid42157462,
year = {2026},
author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR},
title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70320},
doi = {10.1111/1462-2920.70320},
pmid = {42157462},
issn = {1462-2920},
support = {R01GM085770/NH/NIH HHS/United States ; },
mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; },
abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.},
}

*Geologic Sediments/microbiology
*Polyketides/metabolism
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
Polyketide Synthases/genetics/metabolism
Metagenome
Seawater/microbiology
Biodiversity
Multiomics

@article {pmid42158968,
year = {2026},
author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W},
title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.},
journal = {Cancer medicine},
volume = {15},
number = {5},
pages = {e71946},
doi = {10.1002/cam4.71946},
pmid = {42158968},
issn = {2045-7634},
support = {82200151//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; },
abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.

METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).

RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.

CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Myelodysplastic Syndromes/drug therapy/immunology/microbiology
Male
Female
Aged
Middle Aged
*Dysbiosis/immunology
Case-Control Studies
DNA Methylation/drug effects
Feces/microbiology
Aged, 80 and over
High-Throughput Nucleotide Sequencing
Metabolic Networks and Pathways
Adult

@article {pmid42159601,
year = {2026},
author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y},
title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42159601},
issn = {2057-5858},
mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.},
}

Humans
*Mycoplasma pneumoniae/genetics/pathogenicity/metabolism
*Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis
Female
Male
Child, Preschool
Child
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Infant
Severity of Illness Index
Microbiota
Machine Learning
Anti-Bacterial Agents/pharmacology

@article {pmid42159838,
year = {2026},
author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA},
title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42159838},
issn = {1678-4405},
mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.},
}

Animals
*Feces/virology
*Porcupines/virology
Brazil
*Virome
Genome, Viral
Phylogeny
High-Throughput Nucleotide Sequencing
*Viruses/classification/genetics/isolation & purification

@article {pmid42159959,
year = {2026},
author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T},
title = {Animal gut microbes and microbiomes in the 21st century and beyond.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42159959},
issn = {1869-1889},
abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.},
}

@article {pmid41787122,
year = {2026},
author = {Panagiotou, K and Geesink, P and Köstlbacher, S and de Zwaan, GH and Ettema, TJG},
title = {Diversity, ecology, cell biology and evolution of the Asgard archaea.},
journal = {Nature reviews. Microbiology},
volume = {24},
number = {6},
pages = {377-391},
pmid = {41787122},
issn = {1740-1534},
mesh = {*Archaea/genetics/classification/physiology/cytology ; Phylogeny ; Genome, Archaeal ; *Biodiversity ; *Biological Evolution ; Evolution, Molecular ; Genetic Variation ; },
abstract = {The Asgard archaea are a clade of archaea that was first discovered through metagenomic surveys of marine sediments. The past decade has witnessed a substantial expansion of their genomic diversity, revealing diverse metabolic repertoires and providing insights into their ecological interactions and function. Notably, comprehensive phylogenomic analyses, together with the identification of numerous eukaryotic signature proteins in Asgard archaeal genomes, have provided compelling evidence that Asgard archaea had a central role in the emergence of eukaryotes. Studies have reported the characterization of cultured Asgard archaeal representatives, uncovering unique cell biological characteristics hinting at thus far undescribed lifestyles. Here, we review the current state of the research field focusing on these intriguing microorganisms and outline future research directions aiming to resolve their ecology, cell biology and evolution.},
}

*Archaea/genetics/classification/physiology/cytology
Phylogeny
Genome, Archaeal
*Biodiversity
*Biological Evolution
Evolution, Molecular
Genetic Variation

@article {pmid41940696,
year = {2026},
author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M},
title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0190325},
doi = {10.1128/aem.01903-25},
pmid = {41940696},
issn = {1098-5336},
support = {21TQ1400210//the Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 32071271//National Natural Science Foundation of China/ ; 32371332//National Natural Science Foundation of China/ ; 92478203//National Natural Science Foundation of China/ ; IPP30140//College Student Innovation and Practice Program of Shanghai Jiao Tong University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology ; *Metagenome ; *Bacteria/genetics/enzymology/classification/isolation & purification ; *Bacterial Proteins/genetics/metabolism ; Male ; Female ; Middle Aged ; Aged ; Phylogeny ; },
abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.},
}

Humans
*Gastrointestinal Microbiome
*Colorectal Neoplasms/microbiology
*Metagenome
*Bacteria/genetics/enzymology/classification/isolation & purification
*Bacterial Proteins/genetics/metabolism
Male
Female
Middle Aged
Aged
Phylogeny

@article {pmid41964077,
year = {2026},
author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ},
title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41964077},
issn = {2049-2618},
support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; },
mesh = {*Grassland ; *Soil Microbiology ; California ; *Soil/chemistry ; *Carbon/analysis/metabolism ; *Rain ; *Microbiota ; *Bacteria/genetics/classification/growth & development/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Seasons ; Carbon Cycle ; },
abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.

RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.

CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.},
}

*Grassland
*Soil Microbiology
California
*Soil/chemistry
*Carbon/analysis/metabolism
*Rain
*Microbiota
*Bacteria/genetics/classification/growth & development/metabolism/isolation & purification
RNA, Ribosomal, 16S/genetics
Seasons
Carbon Cycle

@article {pmid41973542,
year = {2026},
author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S},
title = {Functional gut microbiomes enhance performance in house fly larvae.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0001126},
doi = {10.1128/aem.00011-26},
pmid = {41973542},
issn = {1098-5336},
support = {NNF21OC0070910//Novo Nordisk Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Houseflies/microbiology/growth & development ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animal Feed/analysis ; },
abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.

IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.},
}

Animals
Larva/microbiology/growth & development
*Houseflies/microbiology/growth & development
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Animal Feed/analysis

@article {pmid42028995,
year = {2026},
author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y},
title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0026826},
doi = {10.1128/aem.00268-26},
pmid = {42028995},
issn = {1098-5336},
mesh = {*Medicago sativa/growth & development/microbiology ; *Soil Microbiology ; *Bacillus/physiology ; *Microbiota ; *Coal ; Soil/chemistry ; },
abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.

IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.},
}

*Medicago sativa/growth & development/microbiology
*Soil Microbiology
*Bacillus/physiology
*Microbiota
*Coal
Soil/chemistry

@article {pmid42029028,
year = {2026},
author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M},
title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0030826},
doi = {10.1128/aem.00308-26},
pmid = {42029028},
issn = {1098-5336},
support = {37/1027-1//Deutsche Forschungsgemeinschaft/ ; 503493769//Deutsche Forschungsgemeinschaft/ ; PE501078509-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; },
mesh = {Biodegradation, Environmental ; *Mining ; *Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Microbial Consortia ; *Peptococcaceae/metabolism/genetics ; Peru ; },
abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.},
}

Biodegradation, Environmental
*Mining
*Sulfates/metabolism
Hydrogen-Ion Concentration
*Microbial Consortia
*Peptococcaceae/metabolism/genetics
Peru

@article {pmid42037401,
year = {2026},
author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q},
title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {5},
pages = {e0248125},
doi = {10.1128/aem.02481-25},
pmid = {42037401},
issn = {1098-5336},
mesh = {*Polyphosphates/metabolism ; *Phosphates/metabolism ; China ; *Microbiota ; *Bacteria/metabolism/genetics/virology ; Geologic Sediments/microbiology/virology ; Phosphorus/metabolism ; *Bacteriophages/physiology/genetics ; Fresh Water/microbiology/virology ; Eutrophication ; },
abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.},
}

*Polyphosphates/metabolism
*Phosphates/metabolism
China
*Microbiota
*Bacteria/metabolism/genetics/virology
Geologic Sediments/microbiology/virology
Phosphorus/metabolism
*Bacteriophages/physiology/genetics
Fresh Water/microbiology/virology
Eutrophication

@article {pmid42082533,
year = {2026},
author = {Tamang, S and Sherpa, MT and Najar, IN and Kumar, S and Das, S and Sharma, P and Das, N and Chowdhury, R and Thaosen, R and Ranjan, RK and Pandey, P and Thakur, N},
title = {Metagenomic analysis of bacterial diversity, antibiotic resistance, and functional profiles in the ice core samples from two glaciers of Sikkim Himalaya.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42082533},
issn = {2045-2322},
support = {BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Ice Cover/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenomics/methods ; Sikkim ; Biodiversity ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Microbiota ; },
abstract = {Glaciers cover a substantial portion of the world and are home to various biological populations. The Himalayas constitute the largest glaciated region outside the poles; hence, they are regarded as "The Third Pole" of the World. There are around 84 glaciers in the Teesta basin (Sikkim Himalaya). There is substantially less data available on the microbial diversity embedded in the glacial ice core samples of the Sikkim Himalaya, as well as their physico-chemistry and potential geomorphological hazards related to their retreat or decrease in snow-line cover. The present study aims to evaluate the microbial diversity in the glacier ice core region and the study area; therefore, two glaciers in the Sikkim Himalaya were chosen: Frey-Peak and Rathong Glacier. The bacterial diversity analysis reveals the prevalence of various phyla, including Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota. The random forest model reveals the significant contributions of various elements, including Na, Mg, K, Ca, and Zn, to the alpha diversity of the studied glaciers. Among physicochemical parameters, pH was found to contribute the most in shaping bacterial diversity. Cluster of Orthologous Groups (COG) analysis underscored a predominance of genes associated with amino acids (23.5%), carbohydrates (18.93%), lipids (10.88%), energy (17.26%), coenzymes (9.38%), and ion transport/metabolism (14.71%). KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology (KO) analysis revealed the presence of 4,915 to 96,954 genes. Interestingly, the metagenomic analysis revealed the presence of specific species of Bradyrhizobium, Beijerinckia, Burkholderia, and Corynebacterium, which are associated with nitrogen metabolism, suggesting their potential involvement in biogeochemical processes. Additionally, a total of 59 to 419 bacterial genes related to sulphur metabolism were deduced through the KEGG functional analysis. The study detected the presence of various antibiotic resistance genes corresponding to different classes of antibiotics, including aminoglycoside, tetracycline, fluoroquinolone, macrolide, and erythromycin. Network analysis reveals that antibiotic resistance genes primarily interact with the phyla Pseudomonadota, Bacillota, and Actinomycetota. The melting of glaciers, a significant effect of climate change, may release contaminants, antibiotic resistance genes, and pathogenic bacteria into free-flowing rivers, potentially impacting human health.},
}

*Ice Cover/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Metagenomics/methods
Sikkim
Biodiversity
*Drug Resistance, Microbial/genetics
*Metagenome
Microbiota

@article {pmid42150526,
year = {2026},
author = {Thompson, LR},
title = {Microbial ecology: Rise of the planet of the microbes.},
journal = {Current biology : CB},
volume = {36},
number = {10},
pages = {R432-R434},
doi = {10.1016/j.cub.2026.03.072},
pmid = {42150526},
issn = {1879-0445},
mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; },
abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.},
}

*Microbiota/genetics
Metagenomics
Ecosystem
*Bacteria/genetics
*Metagenome

@article {pmid42151303,
year = {2026},
author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E},
title = {The soil microbiome of the Caatinga drylands in Brazil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50433-1},
pmid = {42151303},
issn = {2045-2322},
support = {20-122//Conrad Prebys Foundation/ ; },
abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.},
}

@article {pmid42151682,
year = {2026},
author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS},
title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3000},
number = {},
pages = {251-275},
pmid = {42151682},
issn = {1940-6029},
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; },
abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology
*Space Flight
*Microbiota
Weightlessness
*Host Microbial Interactions

@article {pmid42154337,
year = {2026},
author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP},
title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42154337},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/metabolism/pathology/microbiology
*alpha-Synuclein/metabolism
Animals
Dysbiosis
*Protein Aggregates

@article {pmid42156647,
year = {2026},
author = {Ravikrishnan, A},
title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {1-23},
pmid = {42156647},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; },
abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.},
}

*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Software
Workflow
Sequence Analysis, DNA/methods
Humans
Data Analysis

@article {pmid42156648,
year = {2026},
author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A},
title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {25-32},
pmid = {42156648},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.},
}

*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Microbiota/genetics
Metagenome
Humans
Sequence Analysis, DNA/methods