@article {pmid41790792,
year = {2026},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344114},
pmid = {41790792},
issn = {1932-6203},
mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; },
abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.},
}

*Soil Microbiology
Bangladesh
*Bacillus/genetics/classification/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
Gardens
Soil/chemistry
Biodiversity

@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0191025},
pmid = {41609371},
issn = {2165-0497},
support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; *Swine Diseases/microbiology/virology ; *Coinfection/microbiology/veterinary/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Porcine respiratory and reproductive syndrome virus/isolation & purification/genetics ; Influenza A virus/isolation & purification/genetics ; *Bacterial Infections/veterinary/microbiology ; Respiratory System/microbiology/virology ; Metagenomics ; },
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}

Animals
Swine
*Virulence Factors/genetics
*Bacteria/genetics/classification/isolation & purification/pathogenicity
*Swine Diseases/microbiology/virology
*Coinfection/microbiology/veterinary/virology
*Respiratory Tract Infections/veterinary/microbiology/virology
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Porcine respiratory and reproductive syndrome virus/isolation & purification/genetics
Influenza A virus/isolation & purification/genetics
*Bacterial Infections/veterinary/microbiology
Respiratory System/microbiology/virology
Metagenomics

@article {pmid41570402,
year = {2026},
author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL},
title = {Gut microbiota is different before the development of preeclampsia.},
journal = {Pregnancy hypertension},
volume = {43},
number = {},
pages = {101415},
doi = {10.1016/j.preghy.2026.101415},
pmid = {41570402},
issn = {2210-7797},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology/diagnosis ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; },
abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.

STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.

MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.

RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.

CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.},
}

Humans
Female
Pregnancy
*Pre-Eclampsia/microbiology/physiopathology/diagnosis
*Gastrointestinal Microbiome
Adult
Feces/microbiology
Blood Pressure
Case-Control Studies

@article {pmid41312680,
year = {2026},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {53},
number = {3},
pages = {430-436},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/immunology ; *Cyclosporine/therapeutic use/pharmacology ; Male ; Female ; Adult ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Skin/microbiology/drug effects/immunology ; Middle Aged ; *Mycobiome/drug effects ; Malassezia/isolation & purification ; Young Adult ; Calcineurin Inhibitors/therapeutic use/pharmacology ; DNA, Fungal/isolation & purification ; Treatment Outcome ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}

Humans
*Dermatitis, Atopic/drug therapy/microbiology/immunology
*Cyclosporine/therapeutic use/pharmacology
Male
Female
Adult
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Skin/microbiology/drug effects/immunology
Middle Aged
*Mycobiome/drug effects
Malassezia/isolation & purification
Young Adult
Calcineurin Inhibitors/therapeutic use/pharmacology
DNA, Fungal/isolation & purification
Treatment Outcome

@article {pmid41025937,
year = {2026},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {45},
number = {3},
pages = {250-265},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; *Bacillus ; Middle Aged ; Adult ; *Dietary Supplements ; Feces/microbiology ; Flatulence ; },
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).

METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.

RESULTS: Eighty participants (54% female; age: 50.3 ± 10.1 years) were randomized to BV379 (n = 39) or placebo (n = 41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p = 0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p = 0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.

CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
Double-Blind Method
Female
*Gastrointestinal Microbiome/drug effects
Male
*Bacillus
Middle Aged
Adult
*Dietary Supplements
Feces/microbiology
Flatulence

@article {pmid40175821,
year = {2026},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {71},
number = {1},
pages = {143-154},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA　2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
mesh = {Humans ; *Dyslipidemias/microbiology/epidemiology ; Japan/epidemiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}

Humans
*Dyslipidemias/microbiology/epidemiology
Japan/epidemiology
Male
Female
Middle Aged
*Mouth/microbiology
*Microbiota
Aged
RNA, Ribosomal, 16S/genetics
Adult
Bacteria/classification/genetics/isolation & purification
Metagenomics

@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth & development ; Metagenomics/methods ; *Microbial Interactions ; Microbial Consortia/genetics ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}

*Vitamin B 12/metabolism/biosynthesis/genetics
*Mesorhizobium/genetics/metabolism
*Synechococcus/genetics/metabolism/growth & development
Metagenomics/methods
*Microbial Interactions
Microbial Consortia/genetics
Transcriptome
Gene Expression Profiling
Multiomics

@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {41785052},
issn = {1477-4054},
mesh = {Humans ; *Lung Diseases/microbiology ; *Microbiota ; *Databases, Factual ; Bacteria/classification/genetics ; Machine Learning ; },
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}

Humans
*Lung Diseases/microbiology
*Microbiota
*Databases, Factual
Bacteria/classification/genetics
Machine Learning

@article {pmid41783570,
year = {2026},
author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW},
title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.},
journal = {Marine life science & technology},
volume = {8},
number = {1},
pages = {206-220},
pmid = {41783570},
issn = {2662-1746},
abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.},
}

@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
pmid = {41778780},
issn = {1949-0984},
mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; },
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}

Humans
*Tuberculosis/microbiology/diagnosis/therapy
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Animals
Antitubercular Agents/therapeutic use
Metabolomics
Lung/microbiology

@article {pmid41761979,
year = {2026},
author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X},
title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {48584},
doi = {10.31083/FBL48584},
pmid = {41761979},
issn = {2768-6698},
support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; },
mesh = {*Arsenic Trioxide/pharmacology/therapeutic use ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy ; Homeostasis/drug effects ; Humans ; *Bifidobacterium ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; *Tumor Microenvironment/drug effects/immunology ; *Antineoplastic Agents/therapeutic use/pharmacology ; Dysbiosis ; *Intestines/drug effects/microbiology/immunology ; *Probiotics/administration & dosage ; Disease Models, Animal ; },
abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.

METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.

RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.

CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.},
}

*Arsenic Trioxide/pharmacology/therapeutic use
Animals
Gastrointestinal Microbiome/drug effects
Mice
*Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy
Homeostasis/drug effects
Humans
*Bifidobacterium
RNA, Ribosomal, 16S/genetics
Male
Female
*Tumor Microenvironment/drug effects/immunology
*Antineoplastic Agents/therapeutic use/pharmacology
Dysbiosis
*Intestines/drug effects/microbiology/immunology
*Probiotics/administration & dosage
Disease Models, Animal

@article {pmid41747903,
year = {2026},
author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X},
title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134276},
doi = {10.1016/j.biortech.2026.134276},
pmid = {41747903},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Microbial Consortia/physiology ; Anaerobiosis ; Acetates/metabolism ; *Autotrophic Processes ; *Carbon Cycle ; *Bioelectric Energy Sources/microbiology ; Pressure ; Electrodes ; Carbon/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study presents a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.},
}

*Sewage/microbiology
*Microbial Consortia/physiology
Anaerobiosis
Acetates/metabolism
*Autotrophic Processes
*Carbon Cycle
*Bioelectric Energy Sources/microbiology
Pressure
Electrodes
Carbon/metabolism
Carbon Dioxide/metabolism

@article {pmid41707528,
year = {2026},
author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y},
title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119865},
doi = {10.1016/j.ecoenv.2026.119865},
pmid = {41707528},
issn = {1090-2414},
mesh = {China ; *Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Mining ; *Environmental Monitoring ; Manganese/analysis ; Agriculture ; Soil/chemistry ; Bacteria/genetics/classification ; *Microbiota ; Genes, Bacterial ; },
abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.},
}

China
*Soil Microbiology
*Metals, Heavy/analysis
*Soil Pollutants/analysis
Mining
*Environmental Monitoring
Manganese/analysis
Agriculture
Soil/chemistry
Bacteria/genetics/classification
*Microbiota
Genes, Bacterial

@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {690-703},
pmid = {41699270},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Dysbiosis/microbiology/immunology ; Mice ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Ethiopia ; Male ; *HIV Infections/immunology/microbiology/complications ; Israel ; *Opportunistic Infections/immunology/microbiology ; Cryptosporidiosis/immunology/microbiology ; Adult ; CD4-Positive T-Lymphocytes/immunology ; Metagenomics ; Middle Aged ; Disease Susceptibility ; Cryptosporidium parvum ; Intestinal Mucosa/immunology ; },
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
Dysbiosis/microbiology/immunology
Mice
Fecal Microbiota Transplantation
Feces/microbiology
Female
Ethiopia
Male
*HIV Infections/immunology/microbiology/complications
Israel
*Opportunistic Infections/immunology/microbiology
Cryptosporidiosis/immunology/microbiology
Adult
CD4-Positive T-Lymphocytes/immunology
Metagenomics
Middle Aged
Disease Susceptibility
Cryptosporidium parvum
Intestinal Mucosa/immunology

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
mesh = {*Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; Microbiota/genetics ; Biodiversity ; DNA, Bacterial/genetics ; *Alphaproteobacteria/classification/genetics ; Lichens/microbiology ; Bacteria/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

*Phylogeny
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Plant Leaves/microbiology
Microbiota/genetics
Biodiversity
DNA, Bacterial/genetics
*Alphaproteobacteria/classification/genetics
Lichens/microbiology
Bacteria/classification/genetics
Sequence Analysis, DNA

@article {pmid41668418,
year = {2026},
author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S},
title = {Recent Microbial Evolutionary Insights From Metagenomics.},
journal = {Genome biology and evolution},
volume = {18},
number = {3},
pages = {},
pmid = {41668418},
issn = {1759-6653},
support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; },
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Evolution, Molecular ; Humans ; *Biological Evolution ; Phylogeny ; },
abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.},
}

*Metagenomics/methods
*Microbiota/genetics
*Evolution, Molecular
Humans
*Biological Evolution
Phylogeny

@article {pmid41655417,
year = {2026},
author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P},
title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.},
journal = {Water research},
volume = {294},
number = {},
pages = {125493},
doi = {10.1016/j.watres.2026.125493},
pmid = {41655417},
issn = {1879-2448},
mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Humans ; Human Activities ; Microbiota ; China ; Nitrogen ; Bacteria/genetics ; },
abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.},
}

*Groundwater/microbiology/chemistry
Metagenomics
Humans
Human Activities
Microbiota
China
Nitrogen
Bacteria/genetics

@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {664-677},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Humans ; Glomerular Filtration Rate ; Male ; Female ; Feces/microbiology ; Middle Aged ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; Cresols/metabolism ; Biomarkers ; Disease Progression ; Adult ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}

*Renal Insufficiency, Chronic/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Humans
Glomerular Filtration Rate
Male
Female
Feces/microbiology
Middle Aged
Dysbiosis/microbiology
*Kidney/physiopathology
Bacteria/classification/genetics/isolation & purification
Metagenomics
Aged
Cresols/metabolism
Biomarkers
Disease Progression
Adult

@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Humans ; Ethiopia/epidemiology ; *Gastrointestinal Microbiome ; Child, Preschool ; Female ; Male ; Feces/microbiology ; *Urban Population ; *Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Life Style ; *Bacteria/classification/genetics ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}

Humans
Ethiopia/epidemiology
*Gastrointestinal Microbiome
Child, Preschool
Female
Male
Feces/microbiology
*Urban Population
*Diet, Western/adverse effects
RNA, Ribosomal, 16S/genetics
Metagenomics
*Life Style
*Bacteria/classification/genetics

@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617724},
issn = {2052-4463},
mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/genetics ; *Microbiota ; *Genome, Fungal ; Metagenome ; },
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}

*Symbiosis
*Lichens/microbiology
*Ascomycota/genetics
*Microbiota
*Genome, Fungal
Metagenome

@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
mesh = {*Biosensing Techniques/methods ; *Microbiota ; Synthetic Biology ; },
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}

*Biosensing Techniques/methods
*Microbiota
Synthetic Biology

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Thailand ; *Prebiotics/administration & dosage ; Adult ; *Diet ; Fatty Acids, Volatile/metabolism ; Male ; Female ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics ; Models, Biological ; Young Adult ; Middle Aged ; Systems Biology ; Southeast Asian People ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

Humans
*Gastrointestinal Microbiome
Thailand
*Prebiotics/administration & dosage
Adult
*Diet
Fatty Acids, Volatile/metabolism
Male
Female
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics
Models, Biological
Young Adult
Middle Aged
Systems Biology
Southeast Asian People

@article {pmid41579975,
year = {2026},
author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A},
title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.},
journal = {Free radical biology & medicine},
volume = {246},
number = {},
pages = {518-530},
doi = {10.1016/j.freeradbiomed.2026.01.034},
pmid = {41579975},
issn = {1873-4596},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *Pyruvaldehyde/metabolism/blood ; *Glycation End Products, Advanced/metabolism/blood ; *Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology ; Male ; Female ; Feces/chemistry/microbiology ; Middle Aged ; Glyoxal/metabolism ; Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Gastrointestinal Microbiome ; Deoxyglucose/analogs & derivatives/metabolism ; Metabolomics ; Receptor for Advanced Glycation End Products/genetics/metabolism ; },
abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.},
}

Humans
*Pyruvaldehyde/metabolism/blood
*Glycation End Products, Advanced/metabolism/blood
*Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology
Male
Female
Feces/chemistry/microbiology
Middle Aged
Glyoxal/metabolism
Aged
Lactoylglutathione Lyase/genetics/metabolism
Gastrointestinal Microbiome
Deoxyglucose/analogs & derivatives/metabolism
Metabolomics
Receptor for Advanced Glycation End Products/genetics/metabolism

@article {pmid41570514,
year = {2026},
author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T},
title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119288},
doi = {10.1016/j.marpolbul.2026.119288},
pmid = {41570514},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Microbiota ; *Nitrogen Cycle ; Metagenomics ; *Metagenome ; Nitrogen/metabolism ; Denitrification ; Bacteria ; Ecosystem ; },
abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.},
}

*Lakes/microbiology
*Microbiota
*Nitrogen Cycle
Metagenomics
*Metagenome
Nitrogen/metabolism
Denitrification
Bacteria
Ecosystem

@article {pmid41565819,
year = {2026},
author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N},
title = {Baby-to-baby strain transmission shapes the developing gut microbiome.},
journal = {Nature},
volume = {651},
number = {8104},
pages = {191-200},
pmid = {41565819},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation & purification/drug effects ; Metagenomics ; },
abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics/physiology
Infant
Female
Feces/microbiology
Male
Infant, Newborn
Longitudinal Studies
Anti-Bacterial Agents/pharmacology
Siblings
Adult
Bacteria/classification/genetics/isolation & purification/drug effects
Metagenomics

@article {pmid41558447,
year = {2026},
author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K},
title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119293},
doi = {10.1016/j.marpolbul.2026.119293},
pmid = {41558447},
issn = {1879-3363},
mesh = {*Archaea ; *Oxygen/analysis ; China ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Eutrophication ; Microbiota ; Bacteria ; Proteomics ; Multiomics ; },
abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed ‌integrated multi-omics‌ approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.},
}

*Archaea
*Oxygen/analysis
China
Seawater/microbiology/chemistry
Nitrogen/metabolism
Eutrophication
Microbiota
Bacteria
Proteomics
Multiomics

@article {pmid41387308,
year = {2026},
author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R},
title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {12},
pages = {e17747},
pmid = {41387308},
issn = {2198-3844},
support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; },
mesh = {*Aspirin/adverse effects/toxicity/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Mice ; Male ; Intestines/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; *Carboxylesterase/metabolism ; *Carboxylic Ester Hydrolases/metabolism ; *Intestinal Diseases/chemically induced/microbiology ; },
abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.},
}

*Aspirin/adverse effects/toxicity/metabolism
Animals
*Gastrointestinal Microbiome/physiology/drug effects
Mice
Male
Intestines/drug effects
Disease Models, Animal
Mice, Inbred C57BL
*Carboxylesterase/metabolism
*Carboxylic Ester Hydrolases/metabolism
*Intestinal Diseases/chemically induced/microbiology

@article {pmid41350118,
year = {2026},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {55},
number = {3},
pages = {368-380},
pmid = {41350118},
issn = {1600-0714},
mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; Male ; *Microbiota/genetics ; *Mouth Neoplasms/microbiology/pathology ; Female ; Middle Aged ; Aged ; Saliva/microbiology ; Case-Control Studies ; Adult ; *Mouth/microbiology ; DNA, Bacterial ; },
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.

METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.

RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.

CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}

Humans
*Carcinoma, Squamous Cell/microbiology/pathology
Male
*Microbiota/genetics
*Mouth Neoplasms/microbiology/pathology
Female
Middle Aged
Aged
Saliva/microbiology
Case-Control Studies
Adult
*Mouth/microbiology
DNA, Bacterial

@article {pmid41078118,
year = {2026},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {24},
number = {3},
pages = {1189-1203},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Microbiota/genetics ; *Plants/microbiology/genetics ; *Metagenomics/methods ; *DNA, Plant/genetics/isolation & purification ; CRISPR-Cas Systems ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}

*Microbiota/genetics
*Plants/microbiology/genetics
*Metagenomics/methods
*DNA, Plant/genetics/isolation & purification
CRISPR-Cas Systems

@article {pmid41078079,
year = {2026},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {81},
number = {3},
pages = {764-780},
pmid = {41078079},
issn = {1398-9995},
support = {//the Harvard University William F. Milton Fund/ ; R01 AI127507/AI/NIAID NIH HHS/United States ; R01 ES036966/ES/NIEHS NIH HHS/United States ; R01 AI148338/AI/NIAID NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //American Lung Association Innovation Award/ ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; //Massachusetts General Hospital/ ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Bronchiolitis/microbiology/genetics/etiology ; Infant ; *Microbiota ; *Nasopharynx/microbiology ; Female ; Male ; DNA Methylation ; *Epigenome ; Prospective Studies ; Genome-Wide Association Study ; Severity of Illness Index ; Asthma ; Infant, Newborn ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.

METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age < 1 year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24 h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR] < 0.05), regions (mbDMRs, FDR < 0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6 years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR < 0.10).

RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).

CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}

Humans
*Bronchiolitis/microbiology/genetics/etiology
Infant
*Microbiota
*Nasopharynx/microbiology
Female
Male
DNA Methylation
*Epigenome
Prospective Studies
Genome-Wide Association Study
Severity of Illness Index
Asthma
Infant, Newborn

@article {pmid41015495,
year = {2026},
author = {Castells-Nobau, A and Fumagalli, A and Del Castillo-Izquierdo, Á and Rosell-Díaz, M and de la Vega-Correa, L and Samulėnaitė, S and Motger-Albertí, A and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Burokas, A and Coll, C and Zapata-Tona, C and Perez-Brocal, V and Ramio, L and Moya, A and Swann, J and Martín-García, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Gut microbial modulation of 3-hydroxyanthranilic acid and dopaminergic signalling influences attention in obesity.},
journal = {Gut},
volume = {75},
number = {4},
pages = {705-724},
doi = {10.1136/gutjnl-2025-336391},
pmid = {41015495},
issn = {1468-3288},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Obesity/metabolism/microbiology/psychology ; Mice ; *3-Hydroxyanthranilic Acid/metabolism ; Tryptophan/metabolism/blood ; Humans ; Male ; Fecal Microbiota Transplantation ; Drosophila melanogaster ; Female ; *Dopamine/metabolism ; Metagenomics ; Mice, Inbred C57BL ; Signal Transduction ; ortho-Aminobenzoates/metabolism ; Metabolomics ; },
abstract = {BACKGROUND: Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood.

OBJECTIVE: To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention.

DESIGN: We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster.

RESULTS: Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation.

CONCLUSIONS: We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Obesity/metabolism/microbiology/psychology
Mice
*3-Hydroxyanthranilic Acid/metabolism
Tryptophan/metabolism/blood
Humans
Male
Fecal Microbiota Transplantation
Drosophila melanogaster
Female
*Dopamine/metabolism
Metagenomics
Mice, Inbred C57BL
Signal Transduction
ortho-Aminobenzoates/metabolism
Metabolomics

@article {pmid40696533,
year = {2025},
author = {Liu, W and Wang, J and Xue, Y and Li, J and Huang, Y and Zhu, S and Wang, L and Wang, G and Chen, W and Zhao, J},
title = {The impact of Bifidobacterium longum CCFM1112 on chronic constipation: a randomised, double-blind, placebo-controlled study.},
journal = {Beneficial microbes},
volume = {17},
number = {2},
pages = {109-125},
doi = {10.1163/18762891-bja00085},
pmid = {40696533},
issn = {1876-2891},
mesh = {Humans ; *Constipation/therapy/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; Male ; Female ; *Bifidobacterium longum/physiology ; Middle Aged ; Adult ; Gastrointestinal Microbiome ; Quality of Life ; Feces/microbiology/chemistry ; Chronic Disease/therapy ; Treatment Outcome ; },
abstract = {A mounting body of evidence suggests that probiotics may mitigate constipation through their favourable modulation of gut microbiota and its metabolic byproducts. The precise mechanisms underlying this effect remain to be fully elucidated. This randomised, double-blind, placebo-controlled study investigates the clinical efficacy of Bifidobacterium longum (B. longum) CCFM1112 in treating chronic constipation. Fifty-six volunteers diagnosed with chronic constipation according to the Rome IV criteria were randomly assigned to either the B. longum CCFM1112 group or a placebo group for a 4-week intervention. Key outcomes measured included weekly spontaneous bowel movements (SBM), stool consistency (Bristol Stool Form Scale [BSFS]), Patient Assessment of Constipation-Symptoms (PAC-SYM) questionnaire, and Quality of Life (PAC-QOL) questionnaire. In addition, gut microbiota was detected using metagenomic sequencing, and non targeted metabolomics was used to detect fecal and serum metabolites. Results demonstrated that B. longum CCFM1112 significantly reduced PAC-QOL scores and improved BSFS in patients with chronic constipation. Correlation analyses revealed that B. longum CCFM1112 significantly increased the abundance of the genera Blautia, Anaerobutyricum, and Streptococcus. Furthermore, the abundance of species, including Blautia massiliensis, Blautia sp. SC05B48, Anaerobutyricum hallii, and Streptococcus salivarius, was also significantly elevated. Furthermore, it elevated fecal levels of linoleic acid, gamma-aminobutyric acid (GABA), and arachidonic acid, while increasing L-glutamic acid and decreasing adenosine in serum. Our research findings provide evidence that the intake of B. longum CCFM1112 can alleviate constipation.},
}

Humans
*Constipation/therapy/microbiology
*Probiotics/administration & dosage/therapeutic use
Double-Blind Method
Male
Female
*Bifidobacterium longum/physiology
Middle Aged
Adult
Gastrointestinal Microbiome
Quality of Life
Feces/microbiology/chemistry
Chronic Disease/therapy
Treatment Outcome

@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; },
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

Animals
*Lacticaseibacillus rhamnosus/physiology
*Probiotics/pharmacology
Mice
*Lipid Metabolism/drug effects
Male
*Gastrointestinal Microbiome
*Lipopolysaccharides/biosynthesis/metabolism
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
*Non-alcoholic Fatty Liver Disease/metabolism
*Metabolic Diseases/metabolism

@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41775849},
issn = {2045-2322},
abstract = {UNLABELLED: Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41937-x.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/administration & dosage ; Disulfides ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed/analysis ; *Drug Resistance, Microbial/genetics ; Diet/veterinary ; *Fishes/growth & development/microbiology ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}

Animals
*Sulfinic Acids/pharmacology/administration & dosage
Disulfides
*Antioxidants/metabolism
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Animal Feed/analysis
*Drug Resistance, Microbial/genetics
Diet/veterinary
*Fishes/growth & development/microbiology

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/complications ; *HIV Infections/microbiology/complications ; Male ; Female ; *Bacterial Translocation ; *Coinfection/microbiology/virology ; Middle Aged ; Adult ; Lipopolysaccharide Receptors/blood ; Lipopolysaccharides/blood ; Feces/microbiology ; SARS-CoV-2 ; Cohort Studies ; Severity of Illness Index ; Haptoglobins ; Protein Precursors/blood ; },
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

Humans
*Gastrointestinal Microbiome
*COVID-19/microbiology/complications
*HIV Infections/microbiology/complications
Male
Female
*Bacterial Translocation
*Coinfection/microbiology/virology
Middle Aged
Adult
Lipopolysaccharide Receptors/blood
Lipopolysaccharides/blood
Feces/microbiology
SARS-CoV-2
Cohort Studies
Severity of Illness Index
Haptoglobins
Protein Precursors/blood

@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Lactobacillus/physiology ; *Ileum/metabolism/microbiology ; Mice ; *Gallstones/microbiology/prevention & control/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; *Probiotics/administration & dosage ; Disease Models, Animal ; Colon/microbiology ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}

Animals
*Lactobacillus/physiology
*Ileum/metabolism/microbiology
Mice
*Gallstones/microbiology/prevention & control/metabolism
Mice, Inbred C57BL
*Gastrointestinal Microbiome
Male
*Probiotics/administration & dosage
Disease Models, Animal
Colon/microbiology

@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
pmid = {41758194},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/pharmacology/therapeutic use/pharmacokinetics ; Dysbiosis/chemically induced/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; Animals ; Metabolomics ; Neoplasms/drug therapy ; },
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Antimetabolites/pharmacology/therapeutic use/pharmacokinetics
Dysbiosis/chemically induced/microbiology
Bacteria/metabolism/drug effects/genetics/classification
Animals
Metabolomics
Neoplasms/drug therapy

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
mesh = {*Biofilms/growth & development ; Humans ; Pilot Projects ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Biodiversity ; Archaea/genetics/isolation & purification/classification ; Fungi/genetics/classification/isolation & purification ; Male ; Viruses/classification/genetics/isolation & purification ; Female ; Middle Aged ; },
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

*Biofilms/growth & development
Humans
Pilot Projects
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Microbiota
*Biodiversity
Archaea/genetics/isolation & purification/classification
Fungi/genetics/classification/isolation & purification
Male
Viruses/classification/genetics/isolation & purification
Female
Middle Aged

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
mesh = {Humans ; Child, Preschool ; *Choledochal Cyst/microbiology ; Infant ; Male ; Female ; Child ; Age Factors ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; },
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

Humans
Child, Preschool
*Choledochal Cyst/microbiology
Infant
Male
Female
Child
Age Factors
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Biliary Tract/microbiology

@article {pmid41754175,
year = {2026},
author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H},
title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754175},
issn = {2072-6643},
support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Methylamines/metabolism/blood ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Choline/administration & dosage/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism/etiology ; Mice ; *Metagenomics ; *Machine Learning ; Liver/metabolism/pathology ; Feces/microbiology ; },
abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.

METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.

RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.

CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.},
}

Animals
*Methylamines/metabolism/blood
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
*Choline/administration & dosage/metabolism
*Gastrointestinal Microbiome
*Obesity/microbiology/metabolism/etiology
Mice
*Metagenomics
*Machine Learning
Liver/metabolism/pathology
Feces/microbiology

@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Milk ; Animals ; Feces/microbiology/chemistry ; Adult ; Bacteroides ; *Body Weight ; Obesity/microbiology/diet therapy ; Middle Aged ; Streptococcus thermophilus ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
*Milk
Animals
Feces/microbiology/chemistry
Adult
Bacteroides
*Body Weight
Obesity/microbiology/diet therapy
Middle Aged
Streptococcus thermophilus

@article {pmid41752220,
year = {2026},
author = {Kareem, HA and Khan, MF},
title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752220},
issn = {1422-0067},
support = {82930-NP//University College Dublin Internal Fund/ ; },
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Soil Pollutants/metabolism ; *Fluorocarbons/metabolism ; Soil Microbiology ; *Environmental Restoration and Remediation/methods ; },
abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.},
}

Biodegradation, Environmental
*Microbial Consortia
*Soil Pollutants/metabolism
*Fluorocarbons/metabolism
Soil Microbiology
*Environmental Restoration and Remediation/methods

@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
mesh = {*Colorectal Neoplasms/epidemiology/genetics/microbiology ; Humans ; *Fusobacterium nucleatum/genetics ; *Polyketides/metabolism ; *Peptides/metabolism ; *Gastrointestinal Microbiome ; Mutation ; *Bacteriocins/metabolism/genetics ; *Microbiota ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}

*Colorectal Neoplasms/epidemiology/genetics/microbiology
Humans
*Fusobacterium nucleatum/genetics
*Polyketides/metabolism
*Peptides/metabolism
*Gastrointestinal Microbiome
Mutation
*Bacteriocins/metabolism/genetics
*Microbiota

@article {pmid41746975,
year = {2026},
author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C},
title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0343817},
pmid = {41746975},
issn = {1932-6203},
mesh = {Humans ; *Tacrolimus/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Liver Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Adult ; Feces/microbiology ; Aged ; Dysbiosis ; Transplant Recipients ; Tandem Mass Spectrometry ; Metabolome/drug effects ; },
abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.

METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.

RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.

CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.},
}

Humans
*Tacrolimus/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Liver Transplantation/adverse effects
Male
Female
Middle Aged
*Immunosuppressive Agents/therapeutic use/pharmacology
Adult
Feces/microbiology
Aged
Dysbiosis
Transplant Recipients
Tandem Mass Spectrometry
Metabolome/drug effects

@article {pmid41729067,
year = {2026},
author = {Liu, Y and Zhang, T and Liu, J and Dong, X},
title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {8},
pages = {6824-6839},
doi = {10.1021/acs.jafc.5c14510},
pmid = {41729067},
issn = {1520-5118},
mesh = {*Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; *Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics ; Probiotics/metabolism ; Humans ; *Polymers/metabolism/chemistry ; Feces/microbiology ; *Lactobacillaceae/metabolism/genetics/isolation & purification ; Animals ; },
abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.},
}

*Proanthocyanidins/metabolism/chemistry
*Caffeic Acids/metabolism
Fermentation
*Gastrointestinal Microbiome
*Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics
Probiotics/metabolism
Humans
*Polymers/metabolism/chemistry
Feces/microbiology
*Lactobacillaceae/metabolism/genetics/isolation & purification
Animals

@article {pmid41719987,
year = {2026},
author = {Dang, X and Xu, S},
title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119906},
doi = {10.1016/j.ecoenv.2026.119906},
pmid = {41719987},
issn = {1090-2414},
mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects ; *Behavior, Animal/drug effects ; Molecular Docking Simulation ; Diabetes Mellitus, Experimental ; *Alkanesulfonic Acids/toxicity ; Salmonella enterica ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; Molecular Dynamics Simulation ; Colon/microbiology ; Fluorobenzenes ; },
abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.},
}

Animals
Male
Mice
Hippocampus/drug effects
*Behavior, Animal/drug effects
Molecular Docking Simulation
Diabetes Mellitus, Experimental
*Alkanesulfonic Acids/toxicity
Salmonella enterica
Gastrointestinal Microbiome/drug effects
*Environmental Pollutants/toxicity
Molecular Dynamics Simulation
Colon/microbiology
Fluorobenzenes

@article {pmid41715225,
year = {2026},
author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M},
title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41715225},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Sheep/microbiology/physiology/blood ; *Temperament/physiology ; *Vocalization, Animal/physiology ; Rumen/microbiology ; *Metabolome ; Female ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; gamma-Aminobutyric Acid/metabolism ; },
abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.

METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.

RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.

CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Sheep/microbiology/physiology/blood
*Temperament/physiology
*Vocalization, Animal/physiology
Rumen/microbiology
*Metabolome
Female
Metagenomics
Bacteria/classification/genetics/isolation & purification
gamma-Aminobutyric Acid/metabolism

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
mesh = {Methane/metabolism ; Wastewater ; Microbiota ; Acetates/metabolism ; },
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

Methane/metabolism
Wastewater
Microbiota
Acetates/metabolism

@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {44},
number = {4},
pages = {673-681},
pmid = {41669888},
issn = {1473-5598},
mesh = {Humans ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; Cohort Studies ; },
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}

Humans
*Hypertension/epidemiology/microbiology
Middle Aged
Female
Male
*Gastrointestinal Microbiome
Adult
Aged
Prospective Studies
Finland/epidemiology
Incidence
Risk Factors
Cohort Studies

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household environmental characteristics influence the house dust metagenome.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
mesh = {*Dust/analysis ; *Metagenome ; Humans ; *Microbiota ; *Family Characteristics ; Housing ; *Air Pollution, Indoor/analysis ; *Environmental Exposure ; },
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

*Dust/analysis
*Metagenome
Humans
*Microbiota
*Family Characteristics
Housing
*Air Pollution, Indoor/analysis
*Environmental Exposure

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0226425},
pmid = {41636495},
issn = {2165-0497},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
mesh = {Humans ; Female ; *Tears/chemistry/metabolism ; Male ; *Dry Eye Syndromes/microbiology/etiology ; *Proteome/analysis ; *Microbiota ; Adult ; *Contact Lenses/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Middle Aged ; Eye Proteins ; },
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

Humans
Female
*Tears/chemistry/metabolism
Male
*Dry Eye Syndromes/microbiology/etiology
*Proteome/analysis
*Microbiota
Adult
*Contact Lenses/adverse effects
Bacteria/classification/genetics/isolation & purification
Young Adult
Middle Aged
Eye Proteins

@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41634815},
issn = {2049-2618},
mesh = {*Triticum/growth & development/microbiology/physiology ; *Droughts ; *Caragana/microbiology ; *Plant Roots/microbiology ; Biofilms/growth & development ; *Microbiota ; Desert Climate ; Quorum Sensing ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Drought Resistance ; },
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}

*Triticum/growth & development/microbiology/physiology
*Droughts
*Caragana/microbiology
*Plant Roots/microbiology
Biofilms/growth & development
*Microbiota
Desert Climate
Quorum Sensing
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
Drought Resistance

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; Fresh Water ; *Fishes/microbiology/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

Animals
*Skin/microbiology
*Metagenomics/methods
Fresh Water
*Fishes/microbiology/genetics
Phylogeny
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Microbiota/genetics

@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617733},
issn = {2052-4463},
mesh = {Pacific Ocean ; *Metagenomics ; *Metagenome ; *Chlorophyll/analysis ; *Seawater/microbiology ; *Microbiota ; },
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}

Pacific Ocean
*Metagenomics
*Metagenome
*Chlorophyll/analysis
*Seawater/microbiology
*Microbiota

@article {pmid41617710,
year = {2026},
author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F},
title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617710},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Plastids/genetics/classification ; *Metagenomics/methods ; Phylogeny ; Symbiosis/genetics ; Cyanobacteria/genetics/classification ; Biodiversity ; Genetic Variation ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Genome, Plastid ; Alveolata/genetics ; Photosynthesis/genetics ; Evolution, Molecular ; },
abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.},
}

*Plastids/genetics/classification
*Metagenomics/methods
Phylogeny
Symbiosis/genetics
Cyanobacteria/genetics/classification
Biodiversity
Genetic Variation
Haptophyta/genetics/classification
Cryptophyta/genetics/classification
Genome, Plastid
Alveolata/genetics
Photosynthesis/genetics
Evolution, Molecular

@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxalates/metabolism ; *Kidney/metabolism ; Hyperoxaluria/metabolism ; Disease Management ; },
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Oxalates/metabolism
*Kidney/metabolism
Hyperoxaluria/metabolism
Disease Management

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

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

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

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

@article {pmid41468749,
year = {2026},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
pmid = {41468749},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology ; *Particulate Matter/analysis ; *Housing, Animal ; Metagenomics ; *Microbiota ; Risk Assessment ; *Air Microbiology ; Aerosols/analysis ; *Air Pollutants/analysis ; Bacteria/isolation & purification/classification ; Age Factors ; Animal Husbandry ; },
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}

Animals
*Chickens/microbiology/physiology
*Particulate Matter/analysis
*Housing, Animal
Metagenomics
*Microbiota
Risk Assessment
*Air Microbiology
Aerosols/analysis
*Air Pollutants/analysis
Bacteria/isolation & purification/classification
Age Factors
Animal Husbandry

@article {pmid41413233,
year = {2026},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {49},
number = {3},
pages = {958-968},
pmid = {41413233},
issn = {1348-4214},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Blood Pressure/physiology ; *Polyamines/metabolism ; Female ; *Hypertension/microbiology/metabolism/physiopathology ; Aged ; Adult ; Feces/microbiology ; },
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

Humans
*Gastrointestinal Microbiome/physiology
Middle Aged
Male
*Blood Pressure/physiology
*Polyamines/metabolism
Female
*Hypertension/microbiology/metabolism/physiopathology
Aged
Adult
Feces/microbiology

@article {pmid41401693,
year = {2026},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
pmid = {41401693},
issn = {1525-3171},
mesh = {China/epidemiology ; Animals ; *Virome ; Metagenomics ; *Galliformes/virology ; *Metagenome ; },
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}

China/epidemiology
Animals
*Virome
Metagenomics
*Galliformes/virology
*Metagenome

@article {pmid41364878,
year = {2026},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma.},
journal = {Blood advances},
volume = {10},
number = {5},
pages = {1634-1645},
pmid = {41364878},
issn = {2473-9537},
mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Immunotherapy, Adoptive/adverse effects/methods ; Aged ; Biomarkers ; Treatment Outcome ; Adult ; Recurrence ; },
abstract = {CD19 chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (R/R-DLBCL), but challenges such as posttreatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from patients with R/R-DLBCL were analyzed at apheresis (47 samples) and 1 month after infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly-diagnosed DLBCL, R/R-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders had higher levels of Bacteroides fragilis, whereas nonresponders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in R/R-DLBCL.},
}

Humans
*Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Immunotherapy, Adoptive/adverse effects/methods
Aged
Biomarkers
Treatment Outcome
Adult
Recurrence

@article {pmid41093027,
year = {2026},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
mesh = {Serine/analogs & derivatives/analogs & derivatives ; Quorum Sensing ; Microbial Consortia ; Microbiota ; *Photobioreactors/microbiology ; Microalgae/physiology ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Biomass ; Membranes, Artificial ; 4-Butyrolactone/analogs & derivatives/metabolism ; Bacteria/metabolism ; Metagenomics ; Chlorella/physiology ; Water Purification/methods ; },
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}

Serine/analogs & derivatives/analogs & derivatives
Quorum Sensing
Microbial Consortia
Microbiota
*Photobioreactors/microbiology
Microalgae/physiology
Nitrogen/analysis/metabolism
Phosphorus/analysis/metabolism
Biomass
Membranes, Artificial
4-Butyrolactone/analogs & derivatives/metabolism
Bacteria/metabolism
Metagenomics
Chlorella/physiology
Water Purification/methods

@article {pmid40814761,
year = {2026},
author = {Qin, P and Kragsnaes, MS and Holm, DK and Horn, HC and Nilsson, AC and Kjeldsen, J and Kristiansen, K and Ellingsen, T},
title = {Clinical Significance of Gut Microbiota Community Types for Long-Term Response to Fecal Microbiota Transplantation in Patients With Psoriatic Arthritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {78},
number = {2},
pages = {320-331},
pmid = {40814761},
issn = {2326-5205},
support = {Sundhedsdonationer 2022-0026//Sygeforsikringen "danmark"/ ; //Fabrikant Vilhelm Pedersen's Mindelegat (on recommendation by the Novo Nordisk Foundation)/ ; //Medicine Fund of the Danish Regions (Regionernes Medicin- og behandlingspulje)/ ; //University of Southern Denmark Research Fund/ ; //the Danish Rheumatism Association/ ; //the Danish Psoriasis Research Foundation/ ; //Research Fund of Odense University Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; *Arthritis, Psoriatic/therapy/microbiology ; Bacteroides ; Adult ; Prevotella ; Treatment Outcome ; Feces/microbiology ; Clinical Relevance ; },
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) holds promises as a beneficial supplement to methotrexate in patients with psoriatic arthritis (PsA). We therefore investigated how gut bacterial signatures in patients and donor strain engraftment were associated with long-term response to FMT.

METHODS: This exploratory study is based on the FLORA trial cohort, encompassing 31 patients with moderate-to-high PsA disease activity and four FMT donors. Of the 15 patients receiving one single-donor FMT, 13 were included in the per-protocol (PP) population. Stool samples were collected before and after FMT (week 4, 12, and 26). We performed shotgun metagenomics to characterize gut microbiota features.

RESULTS: At baseline, 17 patients (55%) had a gut microbiota community type dominated by the Bacteroides genus (B-type), whereas 14 (45%) had a Prevotella-driven community type (P-type). The B- and P-type patients did not differ in disease activity or demographics, but the B-type had a significantly higher species diversity compared to the P-type (P = 0.005). In the PP population, five of seven B-type patients versus none of six P-type patients (P = 0.021) achieved a long-term clinical beneficial response at week 26. Bacterial strain richness increased significantly from baseline to week 4 and week 26 in B-type (P = 0.016), but not in P-type, patients. Eighteen engrafted strains persisted only in B-type recipients by week 26, including a Bacteroides clarus strain, which demonstrated a negative effect size regarding arthritis pain and the patients' global assessment of disease.

CONCLUSION: Recipients with a Bacteroides-dominated community structure were more likely to achieve long-term beneficial response following one FMT.},
}

Humans
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation
Male
Female
Middle Aged
*Arthritis, Psoriatic/therapy/microbiology
Bacteroides
Adult
Prevotella
Treatment Outcome
Feces/microbiology
Clinical Relevance

@article {pmid40554061,
year = {2026},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {81},
number = {},
pages = {897-914},
pmid = {40554061},
issn = {2090-1224},
mesh = {Male ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Testis/drug effects/metabolism ; Mice ; *Chenodeoxycholic Acid/metabolism ; *Alkanesulfonic Acids/toxicity ; *Spermatogenesis/drug effects ; *Fluorocarbons/toxicity ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Metabolome/drug effects ; },
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.

OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.

METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.

RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.

CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}

Male
Animals
*Gastrointestinal Microbiome/drug effects
*Testis/drug effects/metabolism
Mice
*Chenodeoxycholic Acid/metabolism
*Alkanesulfonic Acids/toxicity
*Spermatogenesis/drug effects
*Fluorocarbons/toxicity
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Fecal Microbiota Transplantation
Metabolome/drug effects

@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}

@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science & technology},
volume = {59},
number = {43},
pages = {23275-23288},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
mesh = {*Extracellular Vesicles/metabolism ; *Manganese/metabolism ; Electron Transport ; Soil Microbiology ; Metagenomics ; *Shewanella/metabolism ; Biofilms ; Microbiota ; },
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}

*Extracellular Vesicles/metabolism
*Manganese/metabolism
Electron Transport
Soil Microbiology
Metagenomics
*Shewanella/metabolism
Biofilms
Microbiota

@article {pmid41747902,
year = {2026},
author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S},
title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134278},
doi = {10.1016/j.biortech.2026.134278},
pmid = {41747902},
issn = {1873-2976},
abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.},
}

@article {pmid41736978,
year = {2026},
author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH},
title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73137},
pmid = {41736978},
issn = {2045-7758},
abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.},
}

@article {pmid41736795,
year = {2026},
author = {Pan, H and Wu, L and Sheng, S},
title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771312},
pmid = {41736795},
issn = {2235-2988},
mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; *Wound Healing ; },
abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.

METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.

RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.

DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.},
}

Humans
Female
*Postmenopause
*Gastrointestinal Microbiome/genetics
Aged
Middle Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
*Wound Healing

@article {pmid41736790,
year = {2026},
author = {Yu, S and Niu, H and Zhang, Y and Yu, L and Zhang, Q and Liu, X and Sang, Y and Wang, R and Zhang, M},
title = {Characterization of gut microbiota in patients with diabetic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1713005},
pmid = {41736790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Diabetic Nephropathies/microbiology ; Feces/microbiology ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus (DM). Although dysbiosis of the gut microbiota in DKD has been reported, the specific microbial species associated with disease progression from DM to DKD remain insufficiently defined.

METHODS: We conducted shotgun metagenomic sequencing on fecal samples from 55 healthy participants, 47 patients with DM, and 38 patients with DKD. Gut microbiota diversity, composition, and functional pathways were compared across groups; correlations with glycemic and renal indices were evaluated.

RESULTS: Overall alpha-diversity showed no significantly difference between DKD and healthy controls; however, the simpson's index was higher in DKD than in DM (p < 0.05). There was a difference in beta-diversity between DKD and the healthy control (p = 0.002), but no significant difference was observed between the DKD and DM group. Bacteria significantly enriched in DM/DKD include Mediterraneibacter, Enterocloster, Shigella, Limosilactobacillus, and Thomasclavelia, which showed positive correlations with glycemic indicators (HbA1c, fasting blood glucose) and renal indicators (BUN, UACR). In contrast, health-enriched bacteria, Phocaeicola, Faecalibacterium, Lachnospira, Agathobacter, Odoribacter, and Paraprevotella were negatively correlated with these parameters. Functional analysis revealed that compared to the DM group, the DKD group enriched pathways related to aromatic amino acid biosynthesis (phenylalanine, tyrosine, tryptophan), biofilm formation, and lipopolysaccharide biosynthesis. Gut microbial shifts along the DM-DKD correlates with adverse glycemic and renal phenotypes, as well as functional characteristics associated with inflammation and barrier injury. These findings suggest that microbially driven metabolic and structural pathways represent potential targets for mitigating the progression of DKD.

CONCLUSION: This study elucidates the distinct characteristics of the gut microbiota in DKD patients and highlights potential microbial markers involved in the progression from DM to DKD.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
Middle Aged
*Diabetic Nephropathies/microbiology
Feces/microbiology
Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid41736479,
year = {2026},
author = {Kong, S and Ning, Z and Chen, Z and Zhang, M},
title = {Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {3},
pages = {e70318},
doi = {10.1002/wer.70318},
pmid = {41736479},
issn = {1554-7531},
support = {252S7601D//Hebei Province Science and Technology Support Program/ ; 242S4201Z//Hebei Province Science and Technology Support Program/ ; },
mesh = {*Groundwater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Propane/analogs & derivatives/metabolism ; *Microbial Consortia ; },
abstract = {1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely exacerbated groundwater environment deterioration. Due to the lack of effective natural attenuation pathways, TCP typically exhibits a fate of persistent retention within aquifers. To address this challenge, instead of relying on limited specific strains, this study focused on exploring broad-spectrum co-metabolic substrates to enhance the degradation efficiency of a non-Dehalogenimonas synergistic consortium optimized through long-term directed domestication. Results indicated that the average degradation rate of the domesticated consortium increased to 19.06 μmol L[-1] d[-1], achieving complete removal within 3.5 days, thereby effectively altering the environmental persistence of TCP. Microbial community and metagenomic analyses revealed that this transformation process was driven by a synergistic alliance comprising Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination". Crucially, the consortium demonstrated exceptional broad-spectrum adaptability to various co-metabolic substrates, where sodium acetate and lactate significantly enhanced the degradation efficiency. This study confirms that utilizing suitable co-metabolic substrates can effectively activate the non-Dehalogenimonas consortium to regulate the migration and fate of pollutants in complex groundwater environments, offering an efficient bioremediation strategy to arrest groundwater contamination.},
}

*Groundwater/chemistry/microbiology
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Propane/analogs & derivatives/metabolism
*Microbial Consortia

@article {pmid41736423,
year = {2026},
author = {Dongqi, LI and Tongxing, W and Zixuan, W and Yihui, Y and Jie, LI and Jiaojiao, GU and Cuiru, LI and Aili, W and Lingling, S and Yongjie, M and Zeyu, Z and Yunlong, H and Huailin, G},
title = {Improving glucose tolerance in obese rats: the role of Jinlida granules () in gut microbiota modulation.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {1},
pages = {62-72},
pmid = {41736423},
issn = {2589-451X},
support = {2017YFC700500//National Key Research and Development Program 'Modernization Research of Traditional Chinese Medicine': Cardiovascular Event Chain (Metabolic Syndrome, Atherosclerosis, Myocardial Infarction, Arrhythmia, Heart Failure)/ ; 223777155D//Key R&D Program of Hebei: Traditional Chinese Medicine Innovation Project: Clinical Research on the Treatment of Diabetes Foot with Collateral Drugs and the Mechanism of Its Influence on Collateral Vessel Reconstruction/ ; 2023179//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Jinlida Granules in Treating Intestinal Dysfunction of diabetes and Its Effect on Short Chain Fatty Acids/ ; 2018200//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Tongluo Therapy for Diabetes Foot and Its Influence on Microcirculation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Rats ; *Obesity/drug therapy/microbiology/metabolism/genetics ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Humans ; Glucose Tolerance Test ; Diet, High-Fat/adverse effects ; Zonula Occludens-1 Protein/metabolism/genetics ; Claudin-1/metabolism/genetics ; Blood Glucose/metabolism ; },
abstract = {OBJECTIVE: To investigate the effects of Jinlida granules (, JLD) on body weight, glucose tolerance, intestinal inflammation and barrier function in high-fat diet (HFD)-induced obese rats and explore the regulation of the gut microbiota as a potential treatment mechanism.

METHODS: Sprague-Dawley rats were divided into control, HFD, low-dose JLD (L-JLD), high-dose JLD (H-JLD), and sitagliptin groups. The rats, with the exception of those in the control group, were fed a HFD to establish an obesity model while simultaneously receiving 0.5% carboxymethyl cellulose, L-JLD, H-JLD or sitagliptin for 25 weeks. We assessed body weight, conducted oral glucose tolerance tests, and analysed faecal samples using metagenomic sequencing. Haematoxylin-eosin (HE), Masson and immunohistochemical (IHC) staining were employed to evaluate histological changes in the colon tissue. Immunofluorescence (IF) staining was used to measure the expression levels of Zonula occludens-1 (ZO-1) and Claudin-1 in colon tissue. The colon tissue was also subjected to transcriptomic evaluation.

RESULTS: JLD treatment significantly reduced body weight and enhanced glucose tolerance in obese rats. It alleviated colonic tissue damage, decreased collagen deposition, inhibited macrophage infiltration, and increased the expression of the tight junction proteins ZO-1 and Claudin-1. Metagenomic analysis revealed JLD-induced shifts in the gut microbiota composition (increasing the abundance of Turicibacter, Faecalibaculum, Coriobacteriaceae and Lactobacillus reuteri), enriching beneficial bacteria and metabolic pathways (increasing the biosynthesis of various secondary metabolites, ascorbate and aldarate metabolism, oxidative phosphorylation, C5-branched dibasic acid metabolism and beta-alanine metabolism). Transcriptomic analysis revealed downregulation of inflammatory and immune pathways (inhibition of the tumour necrosis factor signalling pathway, advanced glycation end products-receptor for advanced glycation end products signalling pathway, toll-like receptor signalling pathway, and interleukin-17 signalling pathway), suggesting a comprehensive modulatory effect of JLD on intestinal health and metabolic function.

CONCLUSIONS: JLD granules effectively improve glucose tolerance and ameliorate obesity-related intestinal dysfunctions in HFD-induced obese rats. These benefits are likely mediated through the modulation of the gut microbiota, the suppression of intestinal inflammation, the enhancement of barrier function, and the attenuation of proinflammatory pathways. Our findings offer novel insights into the therapeutic potential of JLD, emphasizing its role in integrating gut microbiota management into the treatment of metabolic disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
Rats
*Obesity/drug therapy/microbiology/metabolism/genetics
Male
*Drugs, Chinese Herbal/administration & dosage
Humans
Glucose Tolerance Test
Diet, High-Fat/adverse effects
Zonula Occludens-1 Protein/metabolism/genetics
Claudin-1/metabolism/genetics
Blood Glucose/metabolism

@article {pmid41734489,
year = {2026},
author = {Sabatino, R and Gini, C and Borgomaneiro, G and Sbaffi, T and Corno, G and Sun, K and Zhang, XH and Di Cesare, A},
title = {Sinking particles as repository of antimicrobial resistome diversity in the Sansha Yongle Blue Hole.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181585},
doi = {10.1016/j.scitotenv.2026.181585},
pmid = {41734489},
issn = {1879-1026},
abstract = {The aquatic environment plays a central role in the selection and spread of antimicrobial resistance genes (ARGs). Using metagenomic approaches, several studies have provided a comprehensive view of the antimicrobial resistome across different aquatic ecosystems. However, unique aquatic systems, such as oceanic blue holes, remain largely unexplored. Free-living and particle-associated samples from the Sansha Yongle Blue Hole (South China Sea) were analyzed by shotgun metagenomics to characterize the antimicrobial resistome and the potential mobility of detected ARGs. The diversity of the antimicrobial resistome significantly decreased with increasing water depth. This trend was driven by the free-living bacterial community, whereas it remained stable in particle-associated communities. Additionally, the latter showed a higher frequency of co-occurring ARGs and mobile genetic elements on the same contigs, with a frequent plasmid localization of these genes. Overall, particle-associated bacteria proved essential for sustaining antimicrobial resistome diversity. Furthermore, these findings suggest that horizontal transfer of ARG may be more frequent within particle-associated communities along the water column of the blue holes, potentially contributing to the persistence of resistances in deep marine waters.},
}

@article {pmid41731616,
year = {2026},
author = {Fan, S and Lu, J and Cui, H and Ding, W and Li, S and Sun, J and Li, YX and Zhang, W},
title = {Unlocking the unexplored AMPSphere in marine rare species.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02326-0},
pmid = {41731616},
issn = {2049-2618},
abstract = {BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action.

RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (< 0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems.

CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.},
}

@article {pmid41729207,
year = {2026},
author = {Gouda, MNR and Subramanian, S},
title = {Functional Genomics and Enzymatic Diversity of Gut Bacteria in Apis mellifera: A Multi-Approach Study from India.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41729207},
issn = {1432-0991},
mesh = {Bees/microbiology ; Animals ; India ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/enzymology/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Phylogeny ; Genomics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The gut microbiota of the western honey bee Apis mellifera plays a vital role in host nutrition, digestion, immunity, and overall colony health. Although the functional and enzymatic capabilities of bee-associated microbes are increasingly recognized, studies integrating culture-dependent screening with metagenomic functional profiling remain scarce. This study characterizes the gut bacterial communities of forager and hive bees from the Indian subcontinent using cultivation, 16S rRNA gene sequencing, enzyme assays, and metagenomic analysis. A total of 165 isolates were obtained, yielding 85 unique strains deposited in GenBank. Metagenomic assembly generated 7.78 million non-redundant genes, including 11,050 KEGG-annotated and 2.43 million CAZy-annotated genes. Forager bees showed pronounced enrichment of carbohydrate-processing pathways such as glycolysis/gluconeogenesis (22.9%), galactose metabolism (4.42%), starch and sucrose metabolism, and ABC transporters (9.80%), consistent with their nectar- and pollen-rich diet. Culture-based biochemical assays revealed substantial enzymatic diversity among isolates belonging to Bacillus, Enterobacter, Serratia, Cedecea, Clostridium, Lysinibacillus, and Aneurinibacillus. High invertase activities were recorded in Xanthomonas sp. HAmf44 (2.509 U/mg), Clostridium argentinense HAmf20 (2.470 U/mg), Lysinibacillus fusiformis HAmh15 (2.509 U/mg), and Bacillus paralicheniformis HAmh05 (2.333 U/mg). Strong lipolytic activities were observed in Cedecea davisae HAmf19 (6.062 U/mg), Pseudomonas aeruginosa HAmh21 (5.927 U/mg), and Enterobacter cloacae HAmf26 (3.349 U/mg). Significant variation among isolates (p = 0.001) underscored the functional diversity of the gut microbiota. Integrating KEGG orthologs with species abundance revealed that dominant taxa-including Gilliamella, Snodgrassella, Lactobacillus, and Bifidobacterium-drive key metabolic pathways. Overall, this study provides the first combined enzymatic and metagenomic assessment of A. mellifera gut microbiota from India and identifies high-performing strains with probiotic potential to enhance honey bee nutrition and colony productivity.},
}

Bees/microbiology
Animals
India
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/enzymology/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics
Phylogeny
Genomics
Bacterial Proteins/genetics/metabolism

@article {pmid41686173,
year = {2026},
author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S},
title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14443},
pmid = {41686173},
issn = {1520-5118},
abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.},
}

@article {pmid41562342,
year = {2026},
author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J},
title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/1b8sv1},
pmid = {41562342},
issn = {0392-856X},
abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.

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

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

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

@article {pmid40990531,
year = {2025},
author = {Del Carratore, F and Breitling, R},
title = {Engineering microbiomes for natural product discovery and production.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00038f},
pmid = {40990531},
issn = {1460-4752},
abstract = {Covering: 2021 to 2025Microbial communities represent a vast and largely untapped source of natural products with potential applications in various fields, including medicine, agriculture, and the biomanufacturing industry. Secondary metabolites play a crucial role in mediating interspecies interactions within these communities, influencing their structure and function. Recent advances in microbial genetic engineering and multi-omics technologies have enabled the harnessing of these interactions for enhanced natural product discovery and production. These techniques, coupled with systems biology and mathematical modelling, allow for the rational design and manipulation of microbial consortia to elicit the expression of cryptic biosynthetic gene clusters and to optimize the production of desired compounds. Additionally, direct mining of microbiomes using metagenomics, metatranscriptomics, and metabolomics has revealed a wealth of novel biosynthetic gene clusters and secondary metabolites with potential therapeutic and industrial value. Despite the challenges associated with cultivating and characterizing diverse microbial species, ongoing advancements in computational tools and data analysis are rapidly expanding our ability to explore and exploit the seemingly inexhaustible reservoir of natural products hidden within microbial communities.},
}

@article {pmid41724868,
year = {2026},
author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR},
title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.},
journal = {Archives of virology},
volume = {171},
number = {3},
pages = {},
pmid = {41724868},
issn = {1432-8798},
mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; *Carcinoma, Lewis Lung/complications/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Male ; },
abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.},
}

Animals
*Cachexia/virology/etiology/microbiology
*Dysbiosis/virology
*Virome
Mice
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Disease Models, Animal
*Carcinoma, Lewis Lung/complications/virology
*DNA Viruses/genetics/classification/isolation & purification
Male

@article {pmid41722974,
year = {2026},
author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J},
title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.},
journal = {Food microbiology},
volume = {137},
number = {},
pages = {105022},
doi = {10.1016/j.fm.2025.105022},
pmid = {41722974},
issn = {1095-9998},
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Morus/microbiology/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Microbiota ; Temperature ; Hydrogen-Ion Concentration ; Ethanol/metabolism ; Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Acids/metabolism ; Lactobacillus/metabolism/genetics ; Stress, Physiological ; Multiomics ; },
abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.},
}

Fermentation
*Wine/microbiology/analysis
*Morus/microbiology/metabolism
Saccharomyces cerevisiae/metabolism/genetics
*Microbiota
Temperature
Hydrogen-Ion Concentration
Ethanol/metabolism
Metabolomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
*Acids/metabolism
Lactobacillus/metabolism/genetics
Stress, Physiological
Multiomics

@article {pmid41718551,
year = {2026},
author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E},
title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630482},
pmid = {41718551},
issn = {1949-0984},
mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; MicroRNAs/metabolism/genetics ; Caco-2 Cells ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.},
}

Humans
*Extracellular Vesicles/metabolism/genetics
MicroRNAs/metabolism/genetics
Caco-2 Cells
*RNA, Bacterial/metabolism/genetics
*Epithelial Cells/microbiology/metabolism
*Gastrointestinal Microbiome

@article {pmid41615027,
year = {2025},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Microbiota ; *Archaea/genetics/classification/isolation & purification/growth & development ; },
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

*Metagenomics/methods
*Artificial Intelligence
*Bacteria/genetics/classification/isolation & purification/growth & development
Microbiota
*Archaea/genetics/classification/isolation & purification/growth & development

@article {pmid41537582,
year = {2026},
author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D},
title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.},
journal = {mSphere},
volume = {11},
number = {2},
pages = {e0084225},
doi = {10.1128/msphere.00842-25},
pmid = {41537582},
issn = {2379-5042},
support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Acinetobacter/genetics/classification/isolation & purification ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.},
}

*Solanum lycopersicum/microbiology/growth & development
*Acinetobacter/genetics/classification/isolation & purification
Soil Microbiology
*Microbiota
Rhizosphere
Metagenomics
Plant Roots/microbiology
Metagenome

@article {pmid41460655,
year = {2026},
author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE},
title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {109},
number = {4},
pages = {1542-1557},
doi = {10.1177/13872877251407700},
pmid = {41460655},
issn = {1875-8908},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolomics/methods ; *Artificial Intelligence ; Biomarkers/metabolism ; *Metagenomics/methods ; *Brain/metabolism ; Dysbiosis/metabolism ; },
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.},
}

Humans
*Alzheimer Disease/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
*Metabolomics/methods
*Artificial Intelligence
Biomarkers/metabolism
*Metagenomics/methods
*Brain/metabolism
Dysbiosis/metabolism

@article {pmid40782151,
year = {2026},
author = {Kumari, P and Tripathi, BM and Eo, KY and Kimura, J and Yamamoto, N},
title = {Spatioseasonal Comparison of Fecal Resistome and Pathogenome of Raccoon Dogs in Korea.},
journal = {EcoHealth},
volume = {23},
number = {1},
pages = {71-83},
pmid = {40782151},
issn = {1612-9210},
support = {2021R1F1A1060259//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Raccoon Dogs/microbiology ; *Feces/microbiology ; Republic of Korea ; Seasons ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; },
abstract = {The raccoon dog (Nyctereutes procyonoides) is a medium-sized omnivore native to Asia. Because they live close to human habitation, and therefore, there is likely bidirectional influence between raccoon dogs and humans, it is important to investigate their potential risks. Here, to identify potential risks of carriage of antimicrobial resistance (AMR) and human pathogens by raccoon dogs, we investigated spatioseasonal patterns of fecal resistome (collection of antimicrobial resistance genes: ARGs), pathogenome (collection of virulence factor genes: VFGs), and microbiome (collection of bacterial species) of raccoon dogs inhabiting an urban forest area and a rural rice paddy area in Korea. Metagenomic sequencing revealed that the compositions of fecal resistome, pathogenome, and microbiome were all patterned by season, and we hypothesize that the observed patterns are due to seasonal changes in the diet of omnivorous raccoon dogs. Furthermore, although less pronounced than the seasonal differences, we also observed the geographical differences in the resistome, with aminoglycoside resistance genes being more prevalent in the rural area, which may reflect the geographical difference in selective pressures for AMR emergence, such as the use of manure that may contain antimicrobials in rice cultivation in agricultural areas. Additionally, our network analysis revealed that specific antimicrobial resistance genes were linked to specific bacterial pathogens, e.g., tetA-P to Clostridium. Overall, our study successfully revealed for the first time that not only the microbiome, but also the resistome and pathogenome of wild animals change spatioseasonally, and that the risk of AMR in bacterial pathogens laden by raccoon dogs is spatioseasonal.},
}

Animals
*Raccoon Dogs/microbiology
*Feces/microbiology
Republic of Korea
Seasons
*Drug Resistance, Bacterial/genetics
Gastrointestinal Microbiome

@article {pmid41722379,
year = {2026},
author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM},
title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.},
journal = {The Science of the total environment},
volume = {1020},
number = {},
pages = {181545},
doi = {10.1016/j.scitotenv.2026.181545},
pmid = {41722379},
issn = {1879-1026},
abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.},
}

@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
mesh = {Serbia ; *Microbiota ; Seasons ; *Air Microbiology ; Environmental Monitoring ; Air Pollution/statistics & numerical data ; *Drug Resistance, Microbial/genetics ; *Air Pollutants/analysis ; },
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}

Serbia
*Microbiota
Seasons
*Air Microbiology
Environmental Monitoring
Air Pollution/statistics & numerical data
*Drug Resistance, Microbial/genetics
*Air Pollutants/analysis

@article {pmid41666834,
year = {2026},
author = {S, H and A, P},
title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107903},
doi = {10.1016/j.marenvres.2026.107903},
pmid = {41666834},
issn = {1879-0291},
mesh = {*Carbon Sequestration ; *Seawater/microbiology ; Seasons ; Metagenomics ; *Microbiota ; Bacteria ; *Environmental Monitoring ; Cyanobacteria ; *Water Microbiology ; },
abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.},
}

*Carbon Sequestration
*Seawater/microbiology
Seasons
Metagenomics
*Microbiota
Bacteria
*Environmental Monitoring
Cyanobacteria
*Water Microbiology

@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
mesh = {Animals ; Cats ; *Pets/microbiology ; *Ownership ; Humans ; *Gastrointestinal Microbiome ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; },
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}

Animals
Cats
*Pets/microbiology
*Ownership
Humans
*Gastrointestinal Microbiome
*Drug Resistance, Microbial/genetics
Feces/microbiology

@article {pmid41387121,
year = {2026},
author = {Ji, Y and Liu, X and Zhao, S and Zhou, S and Yang, Y and Zhang, P and Shi, Y and Qin, W and Zhu, G and Zhu, Y and Gao, Y and Jiang, J and Wang, B},
title = {Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {11},
pages = {e09416},
doi = {10.1002/advs.202509416},
pmid = {41387121},
issn = {2198-3844},
support = {U22A20590//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; 42477318//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; 2025YFE0103900//National Key R&D Program of China/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; BX20240168//China National Postdoctoral Program for Innovative Talents/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {Phylogeny ; *Host Microbial Interactions/genetics/physiology ; *Bacteria/genetics/classification ; Metagenome/genetics ; Ecosystem ; Biodiversity ; Metagenomics/methods ; },
abstract = {Patescibacteriota, also known as Candidate Phyla Radiation (CPR), is a diverse clade of ultra-small bacteria with an epibiotic lifestyle. Despite their ubiquity across diverse ecosystems and ecological importance in microbial networks, the global distribution of Patescibacteriota and functional interactions with their host organisms remain largely unknown. Here, by leveraging comprehensive Patescibacteriota genomic resources and global multi-habitat metagenomic datasets, it is demonstrated that ribosomal protein S3 (rpS3) as a reliable phylogenetic marker, enabling accurate recovery of Patescibacteriota diversity from short-read metagenomes. Using this framework, extensive taxonomic diversity and pronounced community heterogeneity are uncovered across eight ecosystems. Through network analysis and genome-wide functional screening, habitat-specific co-occurrence patterns are also revealed between Patescibacteriota and host-associated bacteria, especially potential functional synergies mediated by metabolic pathway cascades. Notably, Patescibacteriota-encoded NirK may assist sulfate-reducing bacteria in resisting nitrite stress, while NorB can mitigate nitric oxide toxicity for complete ammonia-oxidizing bacteria. Taken together, this study highlights the underappreciated diversity of Patescibacteriota and elucidates its important role in supporting host metabolism through complementary biochemical functions, offering new insights into its ecological significance and evolutionary adaptations in the global ecosystem.},
}

Phylogeny
*Host Microbial Interactions/genetics/physiology
*Bacteria/genetics/classification
Metagenome/genetics
Ecosystem
Biodiversity
Metagenomics/methods

@article {pmid41721873,
year = {2026},
author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S},
title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41721873},
issn = {1573-4978},
mesh = {*Geologic Sediments/microbiology ; Metagenomics/methods ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Fungi/genetics ; Microbiota/genetics ; Bacteria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.

METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.

CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.},
}

*Geologic Sediments/microbiology
Metagenomics/methods
Biodiversity
Nitrogen/metabolism
Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Fungi/genetics
Microbiota/genetics
Bacteria/genetics
Phylogeny

@article {pmid41715233,
year = {2026},
author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL},
title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {72},
pmid = {41715233},
issn = {2049-2618},
support = {Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; },
mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; },
abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.

RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.},
}

Metagenome
*Rumen/enzymology/microbiology
Animals
*Cattle/microbiology
Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Fatty Acids, Volatile/biosynthesis
*Methane/biosynthesis
Hydrogen/metabolism
Metabolic Networks and Pathways/drug effects

@article {pmid41714786,
year = {2026},
author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S},
title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40561-z},
pmid = {41714786},
issn = {2045-2322},
}

@article {pmid41671795,
year = {2026},
author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B},
title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134181},
doi = {10.1016/j.biortech.2026.134181},
pmid = {41671795},
issn = {1873-2976},
mesh = {*Denitrification/drug effects ; *Sulfamethoxazole/pharmacology ; *Ammonium Compounds/metabolism ; Oxidation-Reduction/drug effects ; Anaerobiosis/drug effects ; Nitrogen/metabolism ; Bioreactors/microbiology ; Microbiota ; },
abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.},
}

*Denitrification/drug effects
*Sulfamethoxazole/pharmacology
*Ammonium Compounds/metabolism
Oxidation-Reduction/drug effects
Anaerobiosis/drug effects
Nitrogen/metabolism
Bioreactors/microbiology
Microbiota