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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42062603,
year = {2026},
author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N},
title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
pmid = {42062603},
issn = {2662-8457},
support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.},
}

@article {pmid42063256,
year = {2026},
author = {Liu, Y and Wu, J and Yang, Y and He, Y and Zhou, R and Li, Y and Sun, J and Gong, M and Mei, X and Li, Y and Huang, H and Du, F and Deng, W and Ye, C and He, X and Li, L and Hao, J and Yang, M and Zhu, Y and Zhu, S},
title = {Decoupling the 'Attract-and-Kill' Strategy: Independent Functions for Zoospore Attraction and ROS-Executed Killing Synergize in Disease-Suppressive Intercropping.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101876},
doi = {10.1016/j.xplc.2026.101876},
pmid = {42063256},
issn = {2590-3462},
abstract = {Soilborne Phytophthora diseases pose a major threat to agricultural sustainability. How non-host roots disrupt the transmission of soilborne Phytophthora pathogens without relying on classical antimicrobial exudates remains unknown. Through a decade-long field study, we demonstrate that strip intercropping achieves sustainable disease suppression (up to 46.85%) by leveraging non-host roots as ecological barriers that intercept zoospore transmission. Moving beyond the conventional focus on antimicrobial exudates, we decouple the 'attract-and-kill' strategy into two discrete functions: a broad-spectrum attraction function widespread among non-host plants (13 of 15 genera), which alone reduces disease by 9.2-24.4%; and a specialized killing function restricted to few species (e.g., garlic), where elevated root-interface concentrations of sulfur compounds induce cystospore rupture and germination inhibition, delivering 42.9-49.3% field suppression. The synergy of universal attraction and targeted killing intensifies efficacy at the rhizosphere interface. Mechanistically, killing is executed through a conserved ROS-PCD pathway, with pathogen sensitivity determined by intrinsic redox-buffering capacity. Metagenomic profiling further revealed that garlic roots and sulfur compounds enrich microbial motility genes and apoptosis pathways, adding a complementary mechanistic layer to the 'attract and kill'framework. We thus propose this two-component, ecology-based strategy for sustainable Phytophthora management in diversified cropping systems.},
}

@article {pmid42063908,
year = {2026},
author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D},
title = {Gut microbial profiles of COVID-19 patients in Uganda.},
journal = {African health sciences},
volume = {26},
number = {1},
pages = {1-15},
pmid = {42063908},
issn = {1729-0503},
mesh = {Humans ; *COVID-19/microbiology/epidemiology ; Uganda/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Bacteria/isolation & purification/genetics ; },
abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.

METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.

RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.

CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
*COVID-19/microbiology/epidemiology
Uganda/epidemiology
*Gastrointestinal Microbiome
Female
Male
Adult
Middle Aged
SARS-CoV-2
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Severity of Illness Index
Bacteria/isolation & purification/genetics

@article {pmid41854352,
year = {2026},
author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J},
title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.},
journal = {Lupus},
volume = {35},
number = {7},
pages = {667-677},
doi = {10.1177/09612033261432163},
pmid = {41854352},
issn = {1477-0962},
mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Pilot Projects ; Female ; India ; Adult ; *Gastrointestinal Microbiome/immunology ; Male ; Middle Aged ; *Dysbiosis/microbiology/immunology ; Case-Control Studies ; *Saliva/microbiology ; *Mouth/microbiology ; Feces/microbiology ; CD8-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/immunology ; Young Adult ; Killer Cells, Natural/immunology ; },
abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.},
}

Humans
*Lupus Erythematosus, Systemic/microbiology/immunology
Pilot Projects
Female
India
Adult
*Gastrointestinal Microbiome/immunology
Male
Middle Aged
*Dysbiosis/microbiology/immunology
Case-Control Studies
*Saliva/microbiology
*Mouth/microbiology
Feces/microbiology
CD8-Positive T-Lymphocytes/immunology
CD4-Positive T-Lymphocytes/immunology
Young Adult
Killer Cells, Natural/immunology

@article {pmid42062403,
year = {2026},
author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR},
title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42062403},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.},
}

*Wastewater/microbiology
Egypt
*Metagenomics/methods
Hospitals
*Drinking Water/microbiology
Humans
*Microbiota/genetics
Water Microbiology
*Metagenome
*Bacteria/genetics/classification/drug effects
*Drug Resistance, Bacterial/genetics

@article {pmid42054100,
year = {2026},
author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE},
title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001705},
pmid = {42054100},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; },
abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.},
}

Animals
*Metagenomics/methods
*Food Microbiology
Chickens/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
*Meat/microbiology
Cattle
Sheep
Salmon/microbiology
United Kingdom
Microbiota/genetics
Anti-Bacterial Agents/pharmacology
Swine

@article {pmid42054365,
year = {2026},
author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H},
title = {Resource availability structures microbial competition through genomic niche partitioning.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2526391123},
doi = {10.1073/pnas.2526391123},
pmid = {42054365},
issn = {1091-6490},
support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/15842-6//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 23/02850-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 20/11953-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; },
mesh = {Humans ; Ecosystem ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Biodiversity ; Bacteria/genetics/classification ; Metagenomics/methods ; Soil Microbiology ; Genomics ; Microbiota/genetics ; *Microbial Interactions ; },
abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.},
}

Humans
Ecosystem
Metagenome
Phylogeny
*Gastrointestinal Microbiome/genetics
Biodiversity
Bacteria/genetics/classification
Metagenomics/methods
Soil Microbiology
Genomics
Microbiota/genetics
*Microbial Interactions

@article {pmid42059663,
year = {2026},
author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y},
title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {42059663},
issn = {1477-4054},
support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *COVID-19/complications/virology/microbiology ; Male ; *SARS-CoV-2 ; Female ; Middle Aged ; Disease Progression ; *Pulmonary Fibrosis/microbiology/etiology/virology/pathology ; *Microbiota ; Aged ; Gastrointestinal Microbiome ; Bronchoalveolar Lavage Fluid/microbiology ; Transcriptome ; Metagenomics ; Multiomics ; },
abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.},
}

Humans
*COVID-19/complications/virology/microbiology
Male
*SARS-CoV-2
Female
Middle Aged
Disease Progression
*Pulmonary Fibrosis/microbiology/etiology/virology/pathology
*Microbiota
Aged
Gastrointestinal Microbiome
Bronchoalveolar Lavage Fluid/microbiology
Transcriptome
Metagenomics
Multiomics

@article {pmid41990134,
year = {2026},
author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J},
title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {5},
pages = {},
pmid = {41990134},
issn = {1574-6941},
support = {32471603//National Natural Science Foundation of China/ ; XZ202601ZY0248//Key Research and Development Program of Xizang Autonomous Region/ ; 2024-TG16//Central Financial Funds for Forestry and Grassland Reform and Development in 2024/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Rats ; *Hypoxia/microbiology ; Male ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Altitude ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Metabolic Reprogramming ; },
abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.},
}

Animals
*Gastrointestinal Microbiome/physiology
Rats
*Hypoxia/microbiology
Male
*Bacteria/classification/genetics/metabolism/isolation & purification
Altitude
RNA, Ribosomal, 16S/genetics
Rats, Sprague-Dawley
Metagenomics
High-Throughput Nucleotide Sequencing
Metabolic Reprogramming

@article {pmid42048337,
year = {2026},
author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM},
title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347959},
pmid = {42048337},
issn = {1932-6203},
mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; },
abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.},
}

Colombia
*Mangifera/microbiology
*Bacteria/genetics/classification/drug effects
Metagenomics
RNA, Ribosomal, 16S/genetics
*Air Pollutants/metabolism
Microbiota/genetics
*Metagenome
Phylogeny
Cities

@article {pmid42049248,
year = {2026},
author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM},
title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70161},
pmid = {42049248},
issn = {2040-4603},
support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; },
abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.

METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.

RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.

CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.},
}

Humans
Male
Female
*Gastrointestinal Microbiome/physiology
*Lactobacillus/physiology
Prospective Studies
Middle Aged
*Pulmonary Arterial Hypertension/microbiology/physiopathology
Adult
Aged
*Hypertension, Pulmonary/microbiology
Ventricular Dysfunction, Right

@article {pmid42052831,
year = {2026},
author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S},
title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48982},
doi = {10.31083/FBL48982},
pmid = {42052831},
issn = {2768-6698},
support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.

METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.

RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation.

CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Glomerulonephritis, Membranous/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Feces/microbiology
Adult
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid42000556,
year = {2026},
author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K},
title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.},
journal = {Marine environmental research},
volume = {218},
number = {},
pages = {108055},
doi = {10.1016/j.marenvres.2026.108055},
pmid = {42000556},
issn = {1879-0291},
mesh = {*Geologic Sediments/microbiology ; *Environmental Monitoring/methods ; Iceland ; *Metagenome ; Norway ; *Microbiota ; Animals ; Aquaculture ; },
abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.},
}

*Geologic Sediments/microbiology
*Environmental Monitoring/methods
Iceland
*Metagenome
Norway
*Microbiota
Animals
Aquaculture

@article {pmid42039195,
year = {2026},
author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H},
title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1749584},
pmid = {42039195},
issn = {1664-3224},
mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; },
abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.

METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.

RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.

CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.},
}

Female
Humans
*Virome
*Mycobiome
*Vaginosis, Bacterial/microbiology/virology
*Microbiota
Papillomavirus Infections/microbiology/virology
Vagina/microbiology/virology
*Reproductive Health
*Genitalia, Female/microbiology/virology
Bacteriophages

@article {pmid42043232,
year = {2026},
author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S},
title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
pmid = {42043232},
issn = {1999-4915},
support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; },
mesh = {Animals ; China ; Phylogeny ; *Virome/genetics ; *Ticks/virology ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.},
}

Animals
China
Phylogeny
*Virome/genetics
*Ticks/virology
Genome, Viral
*RNA Viruses/genetics/classification/isolation & purification
Metagenomics

@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Mice
Germ-Free Life
*Fecal Microbiota Transplantation/methods
Feces/microbiology
*Metagenomics
Reproducibility of Results
High-Throughput Nucleotide Sequencing
Male
*Metagenome
Mice, Inbred C57BL
Female

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

Humans
Animals
*Periodontal Diseases/microbiology/immunology
*Eubacteriales/pathogenicity
*Periodontitis/microbiology
Microbiota
Disease Models, Animal

@article {pmid41800589,
year = {2026},
author = {Juan, DR and Dilanaz, A and Camila, RV and Fernando, DG and Pedro, SR and Ana, MB and Ricardo, U and Barrie, JD and Mario, V and Díez, B and Matías, C and Pedro, T and Alejandra, G and Francisco, I and Raquel, Q},
title = {Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag048},
pmid = {41800589},
issn = {1751-7370},
mesh = {*Sulfur/metabolism/analysis ; *Rivers/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Argentina ; *Bacteria/classification/genetics/metabolism ; Metagenomics ; Volcanic Eruptions ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics/chemistry ; Water Movements ; },
abstract = {Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.},
}

*Sulfur/metabolism/analysis
*Rivers/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Argentina
*Bacteria/classification/genetics/metabolism
Metagenomics
Volcanic Eruptions
*Microbiota
Biodiversity
DNA, Bacterial/genetics/chemistry
Water Movements

@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {11},
number = {4},
pages = {e0085625},
doi = {10.1128/msphere.00856-25},
pmid = {41910342},
issn = {2379-5042},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics ; Irritable Bowel Syndrome/microbiology/metabolism ; Metabolomics ; Female ; *Glutens/metabolism ; Male ; Adult ; Archaea/genetics/classification ; Metabolome ; Middle Aged ; Bacteria/classification/genetics ; },
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Metagenomics
Irritable Bowel Syndrome/microbiology/metabolism
Metabolomics
Female
*Glutens/metabolism
Male
Adult
Archaea/genetics/classification
Metabolome
Middle Aged
Bacteria/classification/genetics

@article {pmid41946403,
year = {2026},
author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y},
title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.},
journal = {Bioresource technology},
volume = {452},
number = {},
pages = {134561},
doi = {10.1016/j.biortech.2026.134561},
pmid = {41946403},
issn = {1873-2976},
mesh = {Ammonium Compounds ; Oxidation-Reduction ; *Cephalexin/toxicity ; *Bioreactors ; *Microbial Consortia/drug effects ; Molecular Docking Simulation ; Stress, Physiological ; *Water Purification ; *Water Pollutants, Chemical/toxicity ; },
abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.},
}

Ammonium Compounds
Oxidation-Reduction
*Cephalexin/toxicity
*Bioreactors
*Microbial Consortia/drug effects
Molecular Docking Simulation
Stress, Physiological
*Water Purification
*Water Pollutants, Chemical/toxicity

@article {pmid42036837,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70359},
pmid = {42036837},
issn = {1751-7915},
support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; },
mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; },
abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.},
}

*Microbiota
*Chitin/metabolism
Soil Microbiology
*Bacteria/enzymology/genetics/classification
Phenotype
Chitinases/genetics/metabolism
Genetic Association Studies

@article {pmid42037322,
year = {2026},
author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP},
title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {9},
pages = {e71828},
pmid = {42037322},
issn = {1530-6860},
support = {APIDOM-BACTERIOB//CHU de La Réunion/ ; //Institut National de la Santé et de la Recherche Médicale (Inserm)/ ; //University of La Réunion/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Periodontitis/microbiology/metabolism/complications/pathology ; Male ; Female ; *Intra-Abdominal Fat/metabolism/pathology ; Middle Aged ; Adult ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/metabolism/microbiology/pathology ; *Metabolic Diseases/microbiology/metabolism ; Dysbiosis/microbiology ; Porphyromonas gingivalis ; *Mouth/microbiology ; },
abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Periodontitis/microbiology/metabolism/complications/pathology
Male
Female
*Intra-Abdominal Fat/metabolism/pathology
Middle Aged
Adult
*Obesity, Morbid/microbiology/complications/metabolism
*Inflammation/metabolism/microbiology/pathology
*Metabolic Diseases/microbiology/metabolism
Dysbiosis/microbiology
Porphyromonas gingivalis
*Mouth/microbiology

@article {pmid42038409,
year = {2026},
author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ},
title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {2},
pages = {lqag040},
pmid = {42038409},
issn = {2631-9268},
mesh = {Animals ; *Rivers/microbiology ; *Biodiversity ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; *Nanopore Sequencing/methods ; DNA, Environmental/genetics ; Environmental Health ; Animals, Wild/genetics ; Metagenome ; },
abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.},
}

Animals
*Rivers/microbiology
*Biodiversity
*Metagenomics/methods
*Environmental Monitoring/methods
Humans
*Nanopore Sequencing/methods
DNA, Environmental/genetics
Environmental Health
Animals, Wild/genetics
Metagenome

@article {pmid41655211,
year = {2026},
author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X},
title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {24},
pages = {e04247},
doi = {10.1002/advs.202504247},
pmid = {41655211},
issn = {2198-3844},
support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; },
mesh = {Animals ; *Receptors, Dopamine D2/deficiency/genetics/metabolism ; Mice ; *Pituitary Neoplasms/metabolism/microbiology/genetics/pathology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Escherichia coli/pathogenicity ; *Adenoma/metabolism/microbiology/genetics ; Female ; Disease Models, Animal ; *Bacterial Translocation ; Male ; Prolactinoma/metabolism ; Mice, Inbred C57BL ; },
abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.},
}

Animals
*Receptors, Dopamine D2/deficiency/genetics/metabolism
Mice
*Pituitary Neoplasms/metabolism/microbiology/genetics/pathology
Humans
*Gastrointestinal Microbiome/physiology
*Escherichia coli/pathogenicity
*Adenoma/metabolism/microbiology/genetics
Female
Disease Models, Animal
*Bacterial Translocation
Male
Prolactinoma/metabolism
Mice, Inbred C57BL

@article {pmid41851530,
year = {2026},
author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E},
title = {Advances and opportunities in measuring dietary intake: from omics to AI.},
journal = {Nature metabolism},
volume = {8},
number = {4},
pages = {795-809},
pmid = {41851530},
issn = {2522-5812},
mesh = {Humans ; *Artificial Intelligence ; *Eating/physiology ; *Diet ; Gastrointestinal Microbiome ; Nutrition Assessment ; Proteomics ; },
abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.},
}

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

@article {pmid42026803,
year = {2026},
author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R},
title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662690},
doi = {10.1080/19490976.2026.2662690},
pmid = {42026803},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics/drug effects ; *Neoplasms/drug therapy/microbiology ; Deep Learning ; Biomarkers, Tumor/genetics ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Metagenomics ; },
abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Microbiome/genetics/drug effects
*Neoplasms/drug therapy/microbiology
Deep Learning
Biomarkers, Tumor/genetics
*Bacteria/classification/genetics/isolation & purification
Female
Male
Metagenomics

@article {pmid42031746,
year = {2026},
author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q},
title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031746},
issn = {2041-1723},
support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrous Oxide/metabolism/analysis ; *Methane/metabolism/analysis ; *Lakes/chemistry/microbiology ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism/analysis ; Metagenomics ; },
abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.},
}

*Nitrous Oxide/metabolism/analysis
*Methane/metabolism/analysis
*Lakes/chemistry/microbiology
*Geologic Sediments/chemistry/microbiology
Denitrification
Nitrification
Eutrophication
Greenhouse Gases/metabolism/analysis
Metagenomics

@article {pmid42031750,
year = {2026},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031750},
issn = {2041-1723},
}

@article {pmid42032992,
year = {2025},
author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M},
title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {50},
number = {12},
pages = {2312-2324},
pmid = {42032992},
issn = {1672-7347},
support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Child ; Feces/microbiology ; Male ; Female ; *Pediatric Obesity/microbiology ; *Obesity/microbiology/complications ; Adolescent ; },
abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.

METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. α-diversity, β-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.

RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). α-diversity analysis showed that in the overall population, the Shannon index (5.49±1.11) and Chao1 index (1 843.04±580.78) in the V3 to V4 region were higher than the Shannon index (4.98±0.65) and Chao1 index (379.59±47.27) in the V4 region (all P<0.001). β-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41±1.62) was not significantly different from that of metagenomic sequencing (6.39±0.42) (P=0.169), while the Chao1 index (1 889.92±781.73) was lower than that of metagenomic sequencing (3 092.71±505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89±0.94 vs 6.39±0.42, 362.41±35.22 vs 3 092.71±505.89, respectively, both P<0.01).

CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of α-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
Child
Feces/microbiology
Male
Female
*Pediatric Obesity/microbiology
*Obesity/microbiology/complications
Adolescent

@article {pmid42034426,
year = {2026},
author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H},
title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107059},
doi = {10.1016/j.pestbp.2026.107059},
pmid = {42034426},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; },
abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Metagenome
China

@article {pmid42026082,
year = {2026},
author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P},
title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07163-w},
pmid = {42026082},
issn = {2052-4463},
support = {240859//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.},
}

@article {pmid42024170,
year = {2026},
author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y},
title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.},
journal = {Clinical oral investigations},
volume = {30},
number = {5},
pages = {},
pmid = {42024170},
issn = {1436-3771},
support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; },
mesh = {*Biofilms/growth & development ; Humans ; *Dental Caries/microbiology ; Candida albicans ; Adult ; Saliva/microbiology ; *Microbiota ; Streptococcus mutans ; Male ; Veillonella ; Female ; Microscopy, Electron, Scanning ; Microscopy, Atomic Force ; Microscopy, Confocal ; Metagenomics ; Middle Aged ; },
abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.

MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.

RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.

CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.

CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.},
}

*Biofilms/growth & development
Humans
*Dental Caries/microbiology
Candida albicans
Adult
Saliva/microbiology
*Microbiota
Streptococcus mutans
Male
Veillonella
Female
Microscopy, Electron, Scanning
Microscopy, Atomic Force
Microscopy, Confocal
Metagenomics
Middle Aged

@article {pmid40812586,
year = {2026},
author = {Zhu, C and Zhang, D and Wang, Y and Zhang, C and Wang, S and Xue, J and Lan, Z and Xun, Z and Zhang, L and Chao, J and Liang, Y and Xue, W and Pu, Z and Zhu, T and Ning, C and Sang, X and Wang, H and Jiang, X and Yang, X and Zhao, H},
title = {Gut microbiota and metabolite signatures predict severe immune-related adverse events in advanced hepatobiliary cancers.},
journal = {Journal of advanced research},
volume = {83},
number = {},
pages = {775-787},
doi = {10.1016/j.jare.2025.08.016},
pmid = {40812586},
issn = {2090-1224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Aged ; *Liver Neoplasms/immunology/drug therapy/metabolism/mortality/pathology ; *Immune Checkpoint Inhibitors/adverse effects ; *Biliary Tract Neoplasms/immunology/drug therapy/metabolism/microbiology ; *Metabolome ; *Drug-Related Side Effects and Adverse Reactions ; },
abstract = {INTRODUCTION: Immune checkpoint inhibition (ICI) has proven to be a major breakthrough in hepatobiliary cancers treatment. However, immune-related adverse events (irAEs) remain a major concern. The gut microbiome has been implicated in ICI efficacy; however, specific alterations in the multi-kingdom gut microbiota associated with severe irAEs are not well understood.

OBJECTIVES: We aimed to identify the signatures of gut microbiota, fungi, and metabolites in patients with advanced hepatobiliary cancers with severe irAEs compared to those in patients experiencing mild or no irAEs.

METHODS: We enrolled 168 patients with advanced hepatobiliary cancers between June 2018 and June 2022 (72 in the train set, 31 in test set 1, and 65 in test set 2). Multi-kingdom microbiota profiles were investigated using metagenomic, ITS2, and metabolomic datasets.

RESULTS: The presence of severe irAEs was associated with significantly longer overall survival compared with the irAE-Mild and irAE-No groups. Patients with severe irAEs showed significant differences in the composition of bacteria and metabolites, but relatively few differences in fungi, and had more complex network associations of multi-kingdom gut microbiota compared with the irAE-Mild and irAE-No groups. A predictive model based on four bacteria and six metabolites simultaneously discriminated irAE-Severe from irAE-Mild and irAE-No with high accuracy.

CONCLUSION: Patients with severe irAEs exhibited unique changes in microbiota-fungi-metabolite interactions. Gut microbiota- and/or metabolite-based algorithms could be used as additional tools for predicting severe irAEs and as potential prognostic markers in advanced hepatobiliary cancers.},
}

Humans
*Gastrointestinal Microbiome/immunology
Male
Female
Middle Aged
Aged
*Liver Neoplasms/immunology/drug therapy/metabolism/mortality/pathology
*Immune Checkpoint Inhibitors/adverse effects
*Biliary Tract Neoplasms/immunology/drug therapy/metabolism/microbiology
*Metabolome
*Drug-Related Side Effects and Adverse Reactions

@article {pmid40850684,
year = {2026},
author = {Lei, G and Han, Z and Wang, X and Malacrinò, A and Kang, T and Zhang, D and Zhang, J and Zhang, Z and Wu, H},
title = {Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.},
journal = {Journal of advanced research},
volume = {83},
number = {},
pages = {113-128},
doi = {10.1016/j.jare.2025.08.040},
pmid = {40850684},
issn = {2090-1224},
mesh = {*Fragaria/microbiology/growth & development ; *Soil Microbiology ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; Rhizosphere ; Fusarium ; Soil/chemistry ; Metagenomics/methods ; Biomass ; Bacteria ; },
abstract = {INTRODUCTION: Synthetic microbial communities (SynCom) contribute to mitigating soil-borne crop diseases while enhancing both crop quality and yield. However, relatively little research has been done on the intricate regulatory mechanisms of SynCom on the suppression of soil-borne diseases.

OBJECTIVES: We aimed to elucidate the dynamic regulatory mechanisms and legacy effects of a SynCom on the composition of soil functional microorganisms, soil multifunctionality and crucial functions, and the suppression of soil-borne diseases.

METHODS: We conducted an extensive series of experiments to assess the effect of a SynCom on the changes in the rhizosphere functional microorganisms and soil functions (e.g., multifunctionality, functionality of C, N, and P cycling) across six successive generations of strawberry in consecutive monoculture soils by employing amplicon metagenomics and transcriptome sequencing.

RESULTS: Our results showed that the SynCom increased the aboveground fresh biomass of strawberry by 31-70.3% and the fruit biomass by 171.39-280.71%, and decreased the Fusarium oxysporum abundance by 17.91-49.51% compared to the consecutive monoculture. The SynCom significantly enhanced the soil C cycling and P cycling function, and soil multifunctionality (SMF). SynCom treatment significantly increased the Shannon diversity index and relative abundances of potentially beneficial bacteria and consumer protistan communities, while exerted a significant inhibitory effect on the Shannon diversity index and relative abundances of fungal pathogen. SEM result showed that SynCom significantly affected SMF by influencing soil nutrients, the abundance and diversity of functional microbial community. Our result also showed that the SynCom established the positive legacy effects on the abundance of rhizosphere soil beneficial bacteria, strawberry biomass and plant disease resistance-associated pathways (phenylpropanoid biosynthesis pathway, alpha-linolenic acid metabolism pathway), and negative effect on the abundance of pathogenic F. oxysporum under the 7th generation of strawberry cropping.

CONCLUSION: Collectively, our study demonstrated the effectiveness of employing SynCom in mitigating soil-borne Fusarium oxysporum diseases by enhancing soil functional microbial abundance and soil multifunctionality.},
}

*Fragaria/microbiology/growth & development
*Soil Microbiology
*Plant Diseases/microbiology/prevention & control
*Microbiota
Rhizosphere
Fusarium
Soil/chemistry
Metagenomics/methods
Biomass
Bacteria

@article {pmid41738843,
year = {2026},
author = {Feng, T and Wu, Y and Xu, Y and Chen, WH},
title = {A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
doi = {10.1093/gigascience/giag016},
pmid = {41738843},
issn = {2047-217X},
support = {5001170159//Provincial Departments Affiliated Universities in Hubei Province/ ; },
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Vitamins/biosynthesis ; Metagenomics/methods ; *Biosynthetic Pathways/genetics ; Metagenome ; *Bacteria/genetics/metabolism/classification ; },
abstract = {BACKGROUND: The ruminant gastrointestinal tract (GIT) serves as a natural microbial reservoir in which vitamin-synthesizing microbes play key integrated roles in digestion, nutrient absorption, and metabolic balance; however, studies systematically elucidating their functional characteristics and ecological roles remain limited due to the lack of a large-scale reference genome catalog for ruminant gastrointestinal vitamin-synthesizing microbes. Here, based on 2,325 metagenomic samples from 8 ruminant hosts, we comprehensively reconstructed and analyzed the ruminant GIT microbiome and the distribution patterns of vitamin-synthesizing microbes.

RESULTS: We reconstructed a unified ruminant gastrointestinal microbiome catalog (CRMC) with 39,696 MAGs, achieving the highest mapping rate (~83.45%) among 2,325 metagenomic datasets, surpassing GTDB, RGMGC, and other catalogs. Across the 8 ruminant hosts, we identified a total of 17,349 vitamin-synthesizing microbes spanning 9 biosynthetic pathways (thiamine, riboflavin, niacin, pantothenate, pyridoxine, biotin, folate, cobalamin, and menaquinone). These microbes exhibited unified pathway selection patterns consistent with those in the human gut microbiome. Furthermore, within the major vitamin-synthesizing pathways commonly selected across ruminants, vitamin-synthesizing microbes displayed concentrated co-selection of specific functional gene nodes, revealing that despite taxonomic differences among gastrointestinal vitamin-synthesizing communities, they share highly convergent pathway preferences and common node-level selection patterns.

CONCLUSIONS: Together, by reconstructing the ruminant GIT microbiome reference genome catalog (CRMC), we elucidated the core microbial taxa and their functional features across ruminants, as well as the pathway preferences and distribution patterns of vitamin-synthesizing microbes. These findings provide an effective reference for advancing ruminant GIT microbiome research, offering gene co-selection insights for microbial synthetic biology design, and guiding microbiome-based interventions in ruminant systems.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Vitamins/biosynthesis
Metagenomics/methods
*Biosynthetic Pathways/genetics
Metagenome
*Bacteria/genetics/metabolism/classification

@article {pmid41845390,
year = {2026},
author = {Sung, H and Hyun, DW and Whon, TW and Kim, PS and Kim, HS and Lee, JY and Lee, SY and Choi, JW and Yoo, JH and Jung, MJ and Yun, JH and Lee, JY and Tak, EJ and Jeong, YS and Kim, SW and Baeg, M and Eun, YG and Lee, YC and Bae, JW},
title = {Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
pmid = {41845390},
issn = {1741-7007},
support = {RS-2020-NR049315//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; },
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/diagnosis ; *Microbiota ; Prognosis ; Male ; *Mouth/microbiology ; Female ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Head and neck cancer, predominantly squamous cell carcinoma, has emerged as a significant global health concern. Growing evidence has established a strong association between dysbiosis of the oral microbiota and both oral and systemic diseases. However, the association between the oral microbiota and head and neck cancer has not yet been fully described. This study aimed to investigate the distinct profiles of the oral microbiota in patients with head and neck cancer and their potential as diagnostic and prognostic biomarkers for head and neck cancer.

RESULTS: Comparative analyses revealed that compared to controls, the oral microbiota of patients with head and neck squamous cell carcinoma (HNSCC) exhibited an increased abundance of anaerobic, biofilm-forming bacteria, and potential pathogens. A machine learning model successfully differentiated HNSCC patients from controls with an area under the curve of 0.902. Key features of this model, such as Peptostreptococcus and Capnocytophaga, were found to be candidate biomarkers for HNSCC, with certain taxa, such as Abiotrophia, serving as prognostic indicators. Although pronounced differences in oral microbiota among HNSCC patients primarily resulted from inter-individual variations, distinct community types were identified, with the type dominated by Proteobacteria being associated with the lowest probability of survival.

CONCLUSIONS: Our findings indicate that the oral microbiota may predict HNSCC and may act as a therapeutic target to improve the prognosis of HNSCC. This investigation underscores the crucial role of oral microbial dysbiosis in the etiopathogenesis and clinical prognosis of HNSCC, making a case for further integrative metagenomic and clinical research.},
}

Humans
*Head and Neck Neoplasms/microbiology/diagnosis
*Microbiota
Prognosis
Male
*Mouth/microbiology
Female
*Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology
Middle Aged
Aged

@article {pmid41845494,
year = {2026},
author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P},
title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41845494},
issn = {2049-2618},
support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Animals ; Cattle ; *MicroRNAs/genetics/metabolism ; *Extracellular Vesicles/metabolism ; Female ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; *Metabolome ; Milk/metabolism/chemistry ; *Heat-Shock Response ; *Mammary Glands, Animal/microbiology/metabolism/physiology ; *Microbiota ; *Gastrointestinal Microbiome ; Fermentation ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.

RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.

CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.},
}

Animals
Cattle
*MicroRNAs/genetics/metabolism
*Extracellular Vesicles/metabolism
Female
*Rumen/microbiology/metabolism
*Lactation/physiology
*Metabolome
Milk/metabolism/chemistry
*Heat-Shock Response
*Mammary Glands, Animal/microbiology/metabolism/physiology
*Microbiota
*Gastrointestinal Microbiome
Fermentation
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid42022809,
year = {2026},
author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH},
title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799859},
pmid = {42022809},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Prospective Studies ; *Metabolome ; Longitudinal Studies ; Female ; Male ; Infant, Newborn ; Feces/microbiology ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Infant ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; Biomarkers ; Dysbiosis/microbiology ; Multiomics ; },
abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.},
}

Humans
*Gastrointestinal Microbiome
*Infant, Premature
Prospective Studies
*Metabolome
Longitudinal Studies
Female
Male
Infant, Newborn
Feces/microbiology
*Neurodevelopmental Disorders/microbiology
Metagenomics
Infant
Metabolomics
Bacteria/classification/genetics/isolation & purification
Biomarkers
Dysbiosis/microbiology
Multiomics

@article {pmid42023591,
year = {2026},
author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y},
title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662556},
doi = {10.1080/19490976.2026.2662556},
pmid = {42023591},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Energy Metabolism ; Male ; Animals ; *Major Depressive Disorder/microbiology/metabolism/therapy ; Mice ; Female ; Fecal Microbiota Transplantation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Adult ; Mice, Inbred C57BL ; Disease Models, Animal ; Metabolomics ; Mitochondria/metabolism ; },
abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Energy Metabolism
Male
Animals
*Major Depressive Disorder/microbiology/metabolism/therapy
Mice
Female
Fecal Microbiota Transplantation
*Bacteria/classification/genetics/metabolism/isolation & purification
Middle Aged
Adult
Mice, Inbred C57BL
Disease Models, Animal
Metabolomics
Mitochondria/metabolism

@article {pmid42023670,
year = {2026},
author = {Santillan, E and Neshat, SA and Wuertz, S},
title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag099},
pmid = {42023670},
issn = {1751-7370},
abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.},
}

@article {pmid41691450,
year = {2026},
author = {Chen, S and Gu, Y and Bahadur, A and Liu, E and Wu, T and Zhu, X and Zou, Y and Liang, H and Wei, P and Wu, L and Wu, Q and Yang, P and Yu, H and Yang, Y},
title = {Divergent Responses of Bacterial Communities to Permafrost Degradation and Their Associations With Carbon Across Vertical Profiles.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {23},
pages = {e10516},
pmid = {41691450},
issn = {2198-3844},
support = {2022YFF0801903//National Key R&D Program of China/ ; xbzg-zdsys-202214//"Light of the West" Cross-team Project of the Chinese Academy of Sciences/ ; U23A2062//National Natural Science Foundation of China/ ; U24A20586//National Natural Science Foundation of China/ ; 23ZDFA017//Science and Technology Program of Gansu Province/ ; CSFSE-FX-2505//Freedom Project of the State Key Laboratory of Cryospheric Science and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, CAS/ ; },
mesh = {*Permafrost/microbiology ; *Carbon/metabolism ; *Bacteria/genetics/metabolism ; Soil Microbiology ; *Microbiota/physiology ; },
abstract = {Permafrost degradation poses a significant threat to the organic carbon (C) pool primarily through regulating microorganisms. However, microbial responses and their associations with C loss across vertical profiles remain unclear. Here, we use metagenomic sequencing to investigate bacterial communities in 125 samples from five 15 m-depth permafrost cores, spanning from the active layer to the permafrost layer along a degradation gradient on the Qinghai-Tibet Plateau. We find that α-diversity decreases, while stochastic processes and community stability increase from the active layer to the permafrost layer. Along permafrost degradation, these community attributes follow similar variations within the active layer but remain constant within the permafrost layer. The relative abundance and interaction of core taxa play important roles in maintaining community stability in the active and permafrost layers, respectively. As permafrost degrades, the negative relationships between community stability and C storage become more intense, especially in the active layer. These findings demonstrate that degradation induces microbial responses that potentially amplify C release, supporting a positive feedback loop to climate warming. Our work provides novel insights into the vertical heterogeneity of this mechanism and is crucial for modeling future permafrost C dynamics.},
}

*Permafrost/microbiology
*Carbon/metabolism
*Bacteria/genetics/metabolism
Soil Microbiology
*Microbiota/physiology

@article {pmid41840712,
year = {2026},
author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z},
title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41840712},
issn = {2049-2618},
support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Dogs ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics/methods ; *Police ; Male ; Age Factors ; Female ; Metagenome ; Feces/microbiology ; },
abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.

RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.

CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.},
}

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

@article {pmid41840729,
year = {2026},
author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T},
title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41840729},
issn = {2049-2618},
support = {JPMJND2206//Japan Science and Technology Agency/ ; },
mesh = {*Metagenome ; *Metadata ; *Microbiota/genetics ; *Metagenomics/methods ; Molecular Sequence Annotation ; Databases, Genetic ; *Bacteria/classification/genetics ; Software ; Phylogeny ; Computational Biology/methods ; },
abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.

RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.},
}

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

@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
mesh = {*Wastewater/microbiology ; *Chromium/toxicity ; *Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Reactive Oxygen Species/metabolism ; Antioxidants/pharmacology ; Extracellular Polymeric Substance Matrix/metabolism ; Plasmids/genetics ; *Drug Resistance, Microbial/genetics ; Deinococcus/genetics ; },
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}

*Wastewater/microbiology
*Chromium/toxicity
*Microbiota/drug effects
*Water Pollutants, Chemical/toxicity
Reactive Oxygen Species/metabolism
Antioxidants/pharmacology
Extracellular Polymeric Substance Matrix/metabolism
Plasmids/genetics
*Drug Resistance, Microbial/genetics
Deinococcus/genetics

@article {pmid41955799,
year = {2026},
author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G},
title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141956},
doi = {10.1016/j.jhazmat.2026.141956},
pmid = {41955799},
issn = {1873-3336},
mesh = {*Cadmium/metabolism ; Mining ; Sulfates/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Water Pollutants, Chemical/metabolism ; Bioreactors/microbiology ; *Extracellular Polymeric Substance Matrix/metabolism/chemistry ; Microbial Consortia ; Sewage/microbiology ; Bacteria/metabolism ; },
abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.},
}

*Cadmium/metabolism
Mining
Sulfates/metabolism
Biodegradation, Environmental
Metagenomics
*Water Pollutants, Chemical/metabolism
Bioreactors/microbiology
*Extracellular Polymeric Substance Matrix/metabolism/chemistry
Microbial Consortia
Sewage/microbiology
Bacteria/metabolism

@article {pmid41955854,
year = {2026},
author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H},
title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {398},
number = {},
pages = {128089},
doi = {10.1016/j.envpol.2026.128089},
pmid = {41955854},
issn = {1873-6424},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Sulfur/metabolism ; *Microplastics ; *Water Pollutants, Chemical ; Bacteria/metabolism ; Microbiota ; },
abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.},
}

*Geologic Sediments/microbiology/chemistry
*Sulfur/metabolism
*Microplastics
*Water Pollutants, Chemical
Bacteria/metabolism
Microbiota

@article {pmid42016964,
year = {2026},
author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X},
title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73260},
pmid = {42016964},
issn = {2045-7758},
abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.},
}

@article {pmid42018637,
year = {2026},
author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM},
title = {Defining metabolic niches for marine microbial heterotrophs.},
journal = {Science advances},
volume = {12},
number = {17},
pages = {eadz0537},
pmid = {42018637},
issn = {2375-2548},
mesh = {Phytoplankton/metabolism ; *Heterotrophic Processes ; Ecosystem ; Carbon Cycle ; *Microbiota ; *Aquatic Organisms/metabolism ; Biomass ; *Seawater/microbiology ; Metagenomics ; },
abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.},
}

Phytoplankton/metabolism
*Heterotrophic Processes
Ecosystem
Carbon Cycle
*Microbiota
*Aquatic Organisms/metabolism
Biomass
*Seawater/microbiology
Metagenomics

@article {pmid42019335,
year = {2026},
author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A},
title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129718},
doi = {10.1016/j.jenvman.2026.129718},
pmid = {42019335},
issn = {1095-8630},
abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.},
}

@article {pmid42020064,
year = {2026},
author = {Peters, BA},
title = {Evidence grows for the gut-kidney axis, but questions still remain.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {832-834},
doi = {10.1016/j.kint.2026.02.015},
pmid = {42020064},
issn = {1523-1755},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; },
abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.},
}

Humans
*Gastrointestinal Microbiome
*Kidney/microbiology/metabolism
Metabolomics
Cross-Sectional Studies
Metagenomics

@article {pmid42020426,
year = {2026},
author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ},
title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42020426},
issn = {2041-1723},
support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; },
mesh = {*Milk, Human/chemistry/metabolism ; Humans ; *Oligosaccharides/metabolism ; *Escherichia coli/physiology/growth & development/genetics/metabolism ; *Symbiosis/physiology ; Female ; *Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development ; Gastrointestinal Microbiome ; Feces/microbiology ; Infant, Newborn ; Infant ; Breast Feeding ; Trisaccharides/metabolism ; Male ; Metagenomics ; Adult ; },
abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.},
}

*Milk, Human/chemistry/metabolism
Humans
*Oligosaccharides/metabolism
*Escherichia coli/physiology/growth & development/genetics/metabolism
*Symbiosis/physiology
Female
*Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development
Gastrointestinal Microbiome
Feces/microbiology
Infant, Newborn
Infant
Breast Feeding
Trisaccharides/metabolism
Male
Metagenomics
Adult

@article {pmid42021075,
year = {2026},
author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K},
title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.},
journal = {The journal of medical investigation : JMI},
volume = {73},
number = {1.2},
pages = {186-207},
doi = {10.2152/jmi.73.186},
pmid = {42021075},
issn = {1349-6867},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ampicillin/adverse effects/pharmacology ; Mice, Inbred C57BL ; Mice ; *Fatty Liver/etiology/microbiology ; *Diet, Western/adverse effects ; Female ; *Anti-Bacterial Agents/adverse effects ; Male ; Dysbiosis/chemically induced ; },
abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Ampicillin/adverse effects/pharmacology
Mice, Inbred C57BL
Mice
*Fatty Liver/etiology/microbiology
*Diet, Western/adverse effects
Female
*Anti-Bacterial Agents/adverse effects
Male
Dysbiosis/chemically induced

@article {pmid40966011,
year = {2026},
author = {Pan, Y and Lv, Y},
title = {Challenges and prospects for the application of skin microbiome to forensic individual identification: A narrative review.},
journal = {Medicine, science, and the law},
volume = {66},
number = {2},
pages = {142-154},
doi = {10.1177/00258024251378811},
pmid = {40966011},
issn = {2042-1818},
mesh = {Humans ; *Skin/microbiology ; *Microbiota ; *Forensic Sciences/methods ; Metagenomics ; Metabolomics ; Machine Learning ; Skin Microbiome ; },
abstract = {The microbiome has been at the center of a cross-section of disciplines with a wide range of applications and research methodologies, the impact of which is also reflected in forensic science. The skin microbiome is considered a "microbial fingerprint" due to its highly personalized characteristics and can be used for forensic individual identification. This narrative review systematically combs through the literature on skin microbiome and forensic applications, focusing on the characteristics, current applications, challenges, and future prospects of the skin microbiome in the field of forensic individual identification. It first explores host specificity, temporal stability, and marker characteristics. Then, by linking individuals with objects, individuals, and the environment, it analyzes the applications in forensic scenarios. It also introduces two commonly used main analytical techniques and their respective advantages and disadvantages. With the development of technology, machine learning has gradually been applied to forensic work. However, there are still four major challenges in practical application, namely ethical, technical, database and biological challenges. In this context, we provide a standardized process through a hypothetical case and propose a multi-omics collaborative analysis framework for the first time, combining metagenomics, metabolomics, and non-omics data (such as geographical information, image records) to illustrate its enhanced effects in scenarios such as sexual assault and disaster victim identification. Overall, despite the challenges, the application of skin microbiome in forensic science is promising and is expected to play an important role in the future of forensic practice.},
}

Humans
*Skin/microbiology
*Microbiota
*Forensic Sciences/methods
Metagenomics
Metabolomics
Machine Learning
Skin Microbiome

@article {pmid41724378,
year = {2026},
author = {Lin, YT and Graells, T and Sayols-Baixeras, S and Dekkers, KF and Schillemans, T and Baldanzi, G and Wuopio, J and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Association between the gut microbiota and estimated glomerular filtration rate in two Swedish population-based cohorts.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {1004-1013},
doi = {10.1016/j.kint.2026.01.021},
pmid = {41724378},
issn = {1523-1755},
mesh = {Humans ; *Glomerular Filtration Rate ; *Gastrointestinal Microbiome ; Female ; Sweden/epidemiology ; Male ; Middle Aged ; Adult ; Feces/microbiology ; Aged ; Metagenomics ; *Kidney/physiopathology ; *Bacteria/metabolism/classification/genetics ; *Renal Insufficiency, Chronic/physiopathology/microbiology ; Cohort Studies ; Methylamines/metabolism/blood ; Carnitine/metabolism ; Metagenome ; },
abstract = {INTRODUCTION: Evidence for gut-kidney interactions in early kidney disease is limited, particularly in community-dwelling adults with largely preserved kidney function. Here, we quantified links between gut microbiota and estimated glomerular filtration rate (eGFR) in two population-based Swedish cohorts.

METHODS: Deep shotgun metagenomics profiled fecal samples from 9788 adults in the Swedish CArdioPulmonary BioImage Study (SCAPIS) discovery cohort (mean age 58 ± 4 years; 52% women) and 2080 adults in the Malmö Offspring Study (MOS) replication cohort (mean age 40 ± 14 years; 52% women). Linear regression related the relative abundance of 494 metagenome-assembled species to the creatinine-based eGFR (by CKD-EPI equation), adjusting for demographics, albuminuria, cardiovascular risk factors and technical variables. Species passing false discovery rate under 0.05 in SCAPIS were tested in MOS for significant concordant direction. Functional enrichment linked eGFR-associated species to gut metabolic modules and plasma metabolites; partial Spearman correlations were used to assessed metabolite/species/eGFR relationships.

RESULTS: The alpha diversity showed a modest inverse association with eGFR across both cohorts. We identified 44 bacterial species consistently associated with eGFR in both cohorts, collectively explaining 7% of its variance. Enrichment analysis highlighted histidine and carnitine metabolism among the top three pathways involved. Their key products, trimethylamine N-oxide and imidazole propionate, were inversely related to eGFR, and a metabolite panel accounted for 51% of eGFR variation, underscoring metabolite-mediated microbial effects. Sensitivity analyses upheld these findings.

CONCLUSIONS: Gut microbial diversity and 44 reproducible species are independently linked to kidney function in community-dwelling adults. Enrichment of histidine and carnitine pathways and their circulating metabolites implicates microbial metabolism as a contributor to eGFR variability, suggesting tractable targets for early kidney protection.},
}

Humans
*Glomerular Filtration Rate
*Gastrointestinal Microbiome
Female
Sweden/epidemiology
Male
Middle Aged
Adult
Feces/microbiology
Aged
Metagenomics
*Kidney/physiopathology
*Bacteria/metabolism/classification/genetics
*Renal Insufficiency, Chronic/physiopathology/microbiology
Cohort Studies
Methylamines/metabolism/blood
Carnitine/metabolism
Metagenome

@article {pmid41841737,
year = {2026},
author = {Cruz, MC and Ruhal, R and Lavin, J and Bridwell, S and Maghboli Balasjin, N and Raasch, B and Melton, R and Mayer, BK and Marshall, CW and Hristova, K},
title = {Acinetobacter spp. with lower susceptibility to quaternary ammonium compounds enriched in microbial communities of frequently used sinks.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {4},
pages = {e0196825},
doi = {10.1128/aem.01968-25},
pmid = {41841737},
issn = {1098-5336},
support = {W9132T-22-2-0001//U.S. Department of Defense/ ; },
mesh = {*Quaternary Ammonium Compounds/pharmacology ; *Microbiota/drug effects ; *Disinfectants/pharmacology ; *Acinetobacter/drug effects/genetics/physiology/isolation & purification ; Biofilms/drug effects ; },
abstract = {Sanitary environments that undergo frequent cleaning and disinfection may harbor microbial communities with potential health risks. While biofilms in healthcare settings are well studied, comparatively less is known about sink-drain microbiomes in public and educational buildings, where hundreds of people may interact with shared sink fixtures. This study characterized the spatial and temporal heterogeneity of sink-drain biofilm microbiomes in academic buildings. We sampled 16 sinks from two buildings (four floors each, with sinks closest and furthest to the bathroom entrance), which are cleaned daily with quaternary ammonium compound (QAC) disinfectants, during periods of low and high student traffic (during and after academic breaks, respectively) across winter, spring, and summer. We observed significant spatial and temporal variations in microbial assemblages. Individual sinks accounted for 43% (PERMANOVA, P < 0.0001) of the variation in microbial communities. Microbiomes in each building were dominated by two genera, which together accounted for 30% of the community composition: Acinetobacter and Enhydrobacter (also classified as Moraxella) in the newer building, and Sphingomonas and Mycobacterium in the older building. Acinetobacter abundance varied seasonally and showed higher relative abundance during periods of high traffic. Metagenomic analysis of selected sinks revealed a high prevalence of qac genes and metagenome-assembled genomes (MAGs) harboring antimicrobial resistance genes (ARGs), including A. parvus. Notably, 34%-53% of qac genes were co-localized on contigs associated with mobile genetic elements. These findings suggest that disinfected sink drains serve as persistent reservoirs of diverse microorganisms and potentially mobile resistance elements.IMPORTANCESink drains are recognized as environmental reservoirs for multidrug-resistant bacteria and have been linked to healthcare-associated outbreaks. In public and educational buildings, these microbiomes are shaped by frequent human activity, making them potential sources of exposure and contributors to the environmental dissemination of antibiotic resistance genes. Quaternary ammonium compound (QAC) disinfectants are widely used on surfaces; however, they can select for resistant taxa and co-select for antibiotic resistance. In this study, despite routine cleaning of sink surfaces with QACs, public restroom sink drains remain colonized by resilient biofilms, posing a potential risk to multiple users. Additionally, factors such as human traffic and seasonal variation may influence drain usage and microbial community composition. Elucidating how seasonal dynamics and human activity shape sink-drain biofilms is essential for understanding their role in the environmental transmission of antimicrobial resistance and informing mitigation strategies in nonclinical settings.},
}

*Quaternary Ammonium Compounds/pharmacology
*Microbiota/drug effects
*Disinfectants/pharmacology
*Acinetobacter/drug effects/genetics/physiology/isolation & purification
Biofilms/drug effects

@article {pmid41910252,
year = {2026},
author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y},
title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {4},
pages = {e0252325},
doi = {10.1128/aem.02523-25},
pmid = {41910252},
issn = {1098-5336},
support = {2024CXPT056//Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; 32170093//National Natural Science Foundation of China/ ; },
mesh = {*Volatile Organic Compounds/metabolism ; Rhizosphere ; *Solanum lycopersicum/microbiology/growth & development/metabolism ; Metagenomics ; *Brassica rapa/microbiology/growth & development ; *Bacillus subtilis/metabolism/genetics ; Butylene Glycols/metabolism ; Acetoin/metabolism ; Metabolomics ; Microbiota ; *Bacillus/metabolism ; Soil Microbiology ; },
abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.},
}

*Volatile Organic Compounds/metabolism
Rhizosphere
*Solanum lycopersicum/microbiology/growth & development/metabolism
Metagenomics
*Brassica rapa/microbiology/growth & development
*Bacillus subtilis/metabolism/genetics
Butylene Glycols/metabolism
Acetoin/metabolism
Metabolomics
Microbiota
*Bacillus/metabolism
Soil Microbiology

@article {pmid41914733,
year = {2026},
author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D},
title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {4},
pages = {e0235725},
doi = {10.1128/aem.02357-25},
pmid = {41914733},
issn = {1098-5336},
support = {NJ01180//USDA | USDA Rural Development (RD)/ ; 2128073//National Science Foundation/ ; //Schmidt Sciences and FFAR/ ; },
mesh = {*Sargassum/metabolism/microbiology ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; },
abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.},
}

*Sargassum/metabolism/microbiology
*Microbiota
*Bacteria/metabolism/genetics/classification

@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {4},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
support = {2024J010010//Natural Science Foundation of Fujian Province/ ; 20720240092//Headmaster' Faculty Fund/The Fundamental Research Funds for the Central Universities/ ; 423B2603//National Natural Science Foundation of China/ ; 42522607//National Natural Science Foundation of China/ ; 2023YFC3108600//National Key Research and Development Program of China/ ; },
mesh = {*Symbiosis ; *Microbiota ; *Diatoms/physiology/classification ; Stochastic Processes ; Seawater/microbiology ; },
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}

*Symbiosis
*Microbiota
*Diatoms/physiology/classification
Stochastic Processes
Seawater/microbiology

@article {pmid41919968,
year = {2026},
author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C},
title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {4},
pages = {e0039226},
doi = {10.1128/aem.00392-26},
pmid = {41919968},
issn = {1098-5336},
support = {52374051//National Natural Science Foundation of China/ ; U24B2037//National Natural Science Foundation of China/ ; },
mesh = {Biodegradation, Environmental ; China ; *Microbiota ; *Oil and Gas Fields/microbiology ; Metagenomics ; *Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Petroleum ; Phylogeny ; },
abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.},
}

Biodegradation, Environmental
China
*Microbiota
*Oil and Gas Fields/microbiology
Metagenomics
*Metagenome
*Bacteria/genetics/metabolism/classification/isolation & purification
Petroleum
Phylogeny

@article {pmid42002357,
year = {2026},
author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z},
title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.},
journal = {Carbohydrate polymers},
volume = {382},
number = {},
pages = {125292},
doi = {10.1016/j.carbpol.2026.125292},
pmid = {42002357},
issn = {1879-1344},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Curcuma/chemistry ; Dextran Sulfate/toxicity ; *Fructans/pharmacology/chemistry/isolation & purification/therapeutic use ; Mice, Inbred C57BL ; Male ; Metabolic Networks and Pathways/drug effects ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; *Colitis/chemically induced/drug therapy ; Disease Models, Animal ; },
abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Curcuma/chemistry
Dextran Sulfate/toxicity
*Fructans/pharmacology/chemistry/isolation & purification/therapeutic use
Mice, Inbred C57BL
Male
Metabolic Networks and Pathways/drug effects
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism
*Colitis/chemically induced/drug therapy
Disease Models, Animal

@article {pmid42002835,
year = {2026},
author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E},
title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659397},
pmid = {42002835},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs & derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Piperidines/adverse effects/therapeutic use
*Adenine/analogs & derivatives/adverse effects/therapeutic use
Male
Female
Middle Aged
Aged
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Feces/microbiology
Treatment Outcome
*Antineoplastic Agents/adverse effects/therapeutic use
Adult

@article {pmid42004633,
year = {2026},
author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D},
title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e174893},
pmid = {42004633},
issn = {1314-2828},
abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).},
}

@article {pmid42010766,
year = {2026},
author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K},
title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2661415},
doi = {10.1080/19490976.2026.2661415},
pmid = {42010766},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Animals ; *Exercise/physiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Animals
*Exercise/physiology
Bacteria/classification/genetics/metabolism/isolation & purification
Physical Conditioning, Animal
Fatty Acids, Volatile/metabolism

@article {pmid42011762,
year = {2026},
author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL},
title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.},
journal = {Zoological research},
volume = {47},
number = {2},
pages = {606-620},
doi = {10.24272/j.issn.2095-8137.2025.134},
pmid = {42011762},
issn = {2095-8137},
mesh = {Animals ; *Mammals/virology ; *Animals, Zoo/virology ; *Bacteriophages/genetics ; *Genetic Variation ; *Virome/genetics ; Phylogeny ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome ; },
abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.},
}

Animals
*Mammals/virology
*Animals, Zoo/virology
*Bacteriophages/genetics
*Genetic Variation
*Virome/genetics
Phylogeny
*Viruses/genetics/classification
*Gastrointestinal Microbiome

@article {pmid41108124,
year = {2026},
author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ},
title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.},
journal = {Journal of dental research},
volume = {105},
number = {5},
pages = {578-586},
pmid = {41108124},
issn = {1544-0591},
mesh = {Humans ; *Saliva/microbiology/chemistry ; *Lipopolysaccharides/blood/analysis/metabolism ; Male ; Female ; *Microbiota ; Middle Aged ; Case-Control Studies ; Adult ; *Mouth/microbiology ; },
abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.},
}

Humans
*Saliva/microbiology/chemistry
*Lipopolysaccharides/blood/analysis/metabolism
Male
Female
*Microbiota
Middle Aged
Case-Control Studies
Adult
*Mouth/microbiology