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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {2438-2451},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
mesh = {*Silage/analysis/microbiology ; Fermentation ; Animals ; Rumen/metabolism/microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Lactiplantibacillus plantarum/metabolism ; Animal Feed/analysis ; Digestion ; Gastrointestinal Microbiome ; },
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}

*Silage/analysis/microbiology
Fermentation
Animals
Rumen/metabolism/microbiology
Bacteria/genetics/classification/metabolism/isolation & purification
*Lactiplantibacillus plantarum/metabolism
Animal Feed/analysis
Digestion
Gastrointestinal Microbiome

@article {pmid41478124,
year = {2026},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
mesh = {*Rhizosphere ; Mining ; *Antimony/toxicity ; *Microbiota ; *Soil Pollutants/toxicity ; Adaptation, Physiological ; Soil Microbiology ; Plant Roots/microbiology/growth & development ; },
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}

*Rhizosphere
Mining
*Antimony/toxicity
*Microbiota
*Soil Pollutants/toxicity
Adaptation, Physiological
Soil Microbiology
Plant Roots/microbiology/growth & development

@article {pmid41453903,
year = {2025},
author = {Lin, Z and Li, S and Liu, M and Li, J and Liu, F and Cao, J and Chen, S and Huang, K and Wang, Y and Li, H and Wang, Y and Yang, B and Xing, D and Wang, Q and Ji, X and Bai, X and Hu, D and Zhang, M and Guo, D and Huang, J and Geng, B and Gu, D and Lu, X},
title = {Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {808},
pmid = {41453903},
issn = {2041-1723},
support = {91857118//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 12126602//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Hypertension/metabolism/microbiology ; Male ; *Carnitine/analogs & derivatives/metabolism/blood ; *Blood Pressure/drug effects/physiology ; Female ; *Sodium Chloride, Dietary/adverse effects ; Middle Aged ; Animals ; Rats ; Feces/microbiology ; Metabolome ; },
abstract = {This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt, and high-salt interventions. SSBP was assessed and used as the primary outcome, and fecal shotgun metagenome and plasma targeted metabolome were measured. We found that high salt significantly altered 85 gut-microbial species (p < 9.42 × 10[-5]) and 70 metabolites (p < 2.26 × 10[-4]). Among them, the changes in 22 species and 8 metabolites were associated with SSBP (p < 0.05), and a gut microbiota-acylcarnitine network implicated in SSBP was identified, with a gut microbiota-derived metabolite, isovalerylcarnitine, as the core metabolite. Isovalerylcarnitine was also inversely associated with SSBP in the GenSalt study (p = 0.0102). Importantly, increased isovalerylcarnitine attenuated SS hypertension and improved endothelial function in rats, and was associated with reduced risk (ranging from 13% to 19%) of BP progression and incident hypertension in a prospective cohort (n = 3907, median follow-up = 5.5 years). This study demonstrated that the gut-acylcarnitine axis may play roles in the development of SS hypertension. Trial number: ChiCTR1900025171.},
}

*Gastrointestinal Microbiome/physiology/drug effects
Humans
*Hypertension/metabolism/microbiology
Male
*Carnitine/analogs & derivatives/metabolism/blood
*Blood Pressure/drug effects/physiology
Female
*Sodium Chloride, Dietary/adverse effects
Middle Aged
Animals
Rats
Feces/microbiology
Metabolome

@article {pmid41448087,
year = {2026},
author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M},
title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140887},
doi = {10.1016/j.jhazmat.2025.140887},
pmid = {41448087},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Metformin/pharmacology ; *Microbiota/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics/drug effects ; },
abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.},
}

*Sewage/microbiology
*Gene Transfer, Horizontal/drug effects
*Metformin/pharmacology
*Microbiota/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
Genes, Bacterial
*Drug Resistance, Bacterial/genetics/drug effects

@article {pmid41421350,
year = {2026},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {7},
number = {1},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
mesh = {*Autism Spectrum Disorder/microbiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Host Microbial Interactions/genetics ; Metagenomics/methods ; Male ; Female ; Genomics/methods ; Polymorphism, Single Nucleotide/genetics ; Dysbiosis/microbiology ; Metabolomics/methods ; Genetic Variation ; Multiomics ; },
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

*Autism Spectrum Disorder/microbiology/genetics/metabolism
Humans
*Gastrointestinal Microbiome/genetics
Child
*Host Microbial Interactions/genetics
Metagenomics/methods
Male
Female
Genomics/methods
Polymorphism, Single Nucleotide/genetics
Dysbiosis/microbiology
Metabolomics/methods
Genetic Variation
Multiomics

@article {pmid41412053,
year = {2026},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; Pacific Ocean ; *Temperature ; Halogenation ; Phylogeny ; *Bacteria/genetics/metabolism ; Microbiota ; },
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

*Geologic Sediments/microbiology
Pacific Ocean
*Temperature
Halogenation
Phylogeny
*Bacteria/genetics/metabolism
Microbiota

@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {40},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology/metabolism ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fermentation ; Metabolome ; Metabolomics ; Metagenomics ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}

Animals
*Rumen/microbiology/metabolism
Sheep/microbiology/metabolism
*Animal Feed/analysis
*Diet/veterinary
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Fermentation
Metabolome
Metabolomics
Metagenomics

@article {pmid41398277,
year = {2025},
author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H},
title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {16},
pmid = {41398277},
issn = {1741-7007},
support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&D Program of China/ ; 2022YFC2805505//the National Key R&D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics ; Metagenome ; *Water Microbiology ; },
abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.

RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553 m) and sediments (3060-9232 m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher ɑ-diversity than the deep-sea waters and sediments (p < 0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.

CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.},
}

*Geologic Sediments/microbiology
*Microbiota
*Seawater/microbiology
*Bacteria/classification/genetics
Metagenome
*Water Microbiology

@article {pmid41391314,
year = {2026},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Nitrogen Cycle ; *Microplastics/toxicity ; Ecosystem ; *Water Pollutants, Chemical/toxicity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Polyethylene ; },
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}

*Geologic Sediments/microbiology/chemistry
*Nitrogen Cycle
*Microplastics/toxicity
Ecosystem
*Water Pollutants, Chemical/toxicity
RNA, Ribosomal, 16S/genetics
Microbiota
Bacteria/genetics/metabolism
Nitrogen/metabolism
Polyethylene

@article {pmid41371144,
year = {2026},
author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y},
title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140716},
doi = {10.1016/j.jhazmat.2025.140716},
pmid = {41371144},
issn = {1873-3336},
mesh = {*Microbial Consortia ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Trichloroethanes/metabolism ; Chloroflexi/metabolism/genetics ; Halogenation ; Bacteria/metabolism/genetics ; },
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.},
}

*Microbial Consortia
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Trichloroethanes/metabolism
Chloroflexi/metabolism/genetics
Halogenation
Bacteria/metabolism/genetics

@article {pmid41371128,
year = {2026},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal/drug effects ; Aquaculture ; *Gastrointestinal Microbiome/drug effects ; *Enrofloxacin/pharmacology ; Animals ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Fatty Acids, Volatile/metabolism ; Bacteriophages/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; },
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}

*Gene Transfer, Horizontal/drug effects
Aquaculture
*Gastrointestinal Microbiome/drug effects
*Enrofloxacin/pharmacology
Animals
*Anti-Bacterial Agents/pharmacology
Plasmids/genetics
*Drug Resistance, Bacterial/genetics
Fatty Acids, Volatile/metabolism
Bacteriophages/genetics
Bacteria/genetics/drug effects
Genes, Bacterial
Drug Resistance, Microbial/genetics

@article {pmid41352011,
year = {2026},
author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X},
title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140640},
doi = {10.1016/j.jhazmat.2025.140640},
pmid = {41352011},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Hydrocarbons, Chlorinated/metabolism ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Microbiota ; },
abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.},
}

*Soil Pollutants/metabolism
Biodegradation, Environmental
*Soil Microbiology
*Hydrocarbons, Chlorinated/metabolism
*Bacteria/metabolism/genetics
*Archaea/metabolism/genetics
Microbiota

@article {pmid41339548,
year = {2026},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {649},
number = {8098},
pages = {971-981},
pmid = {41339548},
issn = {1476-4687},
mesh = {Denmark ; *Microbiota/genetics ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Humans ; Ecosystem ; Biodiversity ; *Environmental Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}

Denmark
*Microbiota/genetics
Metagenome/genetics
RNA, Ribosomal, 16S/genetics
Phylogeny
Humans
Ecosystem
Biodiversity
*Environmental Microbiology
Agriculture
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid41260011,
year = {2026},
author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J},
title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119004},
doi = {10.1016/j.marpolbul.2025.119004},
pmid = {41260011},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Freezing ; *Bacteria/classification ; Seasons ; Ecosystem ; *Microbiota ; Ice Cover ; Geologic Sediments/microbiology ; Nitrogen ; },
abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.},
}

*Lakes/microbiology
*Nitrogen Cycle
*Freezing
*Bacteria/classification
Seasons
Ecosystem
*Microbiota
Ice Cover
Geologic Sediments/microbiology
Nitrogen

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

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

@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70124},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}

@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {2586},
pmid = {41430427},
issn = {2045-2322},
mesh = {Italy ; *Metals, Heavy/analysis ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants/analysis ; *Soil/chemistry ; Environmental Monitoring/methods ; Metagenomics ; Models, Statistical ; },
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}

Italy
*Metals, Heavy/analysis
*Soil Microbiology
*Microbiota
*Soil Pollutants/analysis
*Soil/chemistry
Environmental Monitoring/methods
Metagenomics
Models, Statistical

@article {pmid41395946,
year = {2026},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; IDN/20/024//Internal funds KU Leuven/ ; },
mesh = {Humans ; *Virome/genetics ; *Skin/virology/microbiology ; Male ; Female ; Adult ; *Hidradenitis Suppurativa/virology/microbiology ; Middle Aged ; Microbiota ; Bacteriophages/genetics ; Metagenomics ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

Humans
*Virome/genetics
*Skin/virology/microbiology
Male
Female
Adult
*Hidradenitis Suppurativa/virology/microbiology
Middle Aged
Microbiota
Bacteriophages/genetics
Metagenomics

@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {118},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
mesh = {Humans ; *Pulpitis/microbiology ; Adult ; *Metagenomics ; Adolescent ; Young Adult ; *High-Throughput Nucleotide Sequencing ; Male ; *Microbiota/genetics ; Chronic Disease ; Female ; *Dental Pulp/microbiology ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.

METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906 million paired-end reads per specimen.

RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.

CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}

Humans
*Pulpitis/microbiology
Adult
*Metagenomics
Adolescent
Young Adult
*High-Throughput Nucleotide Sequencing
Male
*Microbiota/genetics
Chronic Disease
Female
*Dental Pulp/microbiology

@article {pmid41389008,
year = {2026},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics alter duodenal immune populations upon gluten exposure in mice: implications for non-coeliac gluten sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {330},
number = {2},
pages = {G137-G153},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Animals ; *Glutens/immunology ; *Anti-Bacterial Agents/pharmacology ; *Duodenum/immunology/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred BALB C ; Intestinal Mucosa/immunology/drug effects/microbiology ; Eosinophils/immunology/drug effects ; Male ; Feces/microbiology ; },
abstract = {A growing proportion of the non-celiac population experiences adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesized that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5 mg/kg) or PBS-vehicle daily for 5 days. Mice were then treated with a 3-mg wheat-gluten suspension, or vehicle, on days 4 and 5 before euthanasia on day 7. Duodenal immune cells were analyzed by histology and flow cytometry, whereas the duodenal MAM and fecal microbiome were characterized via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in feces, and resulted in altered microbial carbohydrate and lipid metabolism, compared with vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared with vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.NEW & NOTEWORTHY A mouse model examined how microbial modulation affects immune responses to gluten. Antibiotic treatment followed by gluten reintroduction reduced duodenal Staphylococcus and altered microbial carbohydrate and lipid metabolism pathways in the fecal microbiome. Antibiotics and gluten treatment resulted in increased abundance and activation of duodenal eosinophils and elevated γδ T-cells in the duodenal epithelium. These findings highlight the role the microbiome plays in gluten-induced immune responses, providing insights into mechanisms behind non-celiac gluten sensitivity.},
}

Animals
*Glutens/immunology
*Anti-Bacterial Agents/pharmacology
*Duodenum/immunology/drug effects/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred BALB C
Intestinal Mucosa/immunology/drug effects/microbiology
Eosinophils/immunology/drug effects
Male
Feces/microbiology

@article {pmid41387926,
year = {2025},
author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H},
title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {30},
pmid = {41387926},
issn = {2049-2618},
support = {32192463//The Major Program of National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Grassland ; *Gastrointestinal Microbiome ; Sheep/microbiology ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics/methods ; Poaceae ; *Nutrients/metabolism ; Fermentation ; Multiomics ; },
abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.

RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.

CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.},
}

Animals
*Rumen/microbiology/metabolism
Grassland
*Gastrointestinal Microbiome
Sheep/microbiology
Animal Feed/analysis
Bacteria/classification/genetics/isolation & purification/metabolism
Metagenomics/methods
Poaceae
*Nutrients/metabolism
Fermentation
Multiomics

@article {pmid41384736,
year = {2026},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0136425},
doi = {10.1128/msystems.01364-25},
pmid = {41384736},
issn = {2379-5077},
mesh = {Fermentation ; *Coffea/microbiology/metabolism/chemistry ; Metabolomics/methods ; Humans ; Metagenomics/methods ; Taste ; Metabolome ; Microbiota ; Coffee/microbiology ; },
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.

IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}

Fermentation
*Coffea/microbiology/metabolism/chemistry
Metabolomics/methods
Humans
Metagenomics/methods
Taste
Metabolome
Microbiota
Coffee/microbiology

@article {pmid41382192,
year = {2025},
author = {Xue, R and Li, Z and Qin, W and Wang, Y and Zhao, K and Liu, L and Bai, Y},
title = {Prolonged grazing reduces the diversity and weakens virus-host links of metagenome-assembled viral community in acidic karst soil.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {15},
pmid = {41382192},
issn = {1741-7007},
support = {41907025//National Natural Science Foundation of China/ ; 32160337//National Natural Science Foundation of China/ ; 2025ZNSFSC0202//Natural Science Foundation of Sichuan Province/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; *Soil/chemistry ; Biodiversity ; *Virome ; *Herbivory ; Bacteria/genetics ; Microbiota ; },
abstract = {BACKGROUND: Soil viruses are fundamental yet often overlooked components of terrestrial ecosystems, where they profoundly influence microbial diversity, community assembly, and biogeochemical cycling through predator-prey dynamics and the carriage of auxiliary metabolic genes (AMGs). However, the impact of human-driven land use change on viral communities and their functional potential remains poorly understood.

RESULTS: In this study, we analyzed viral diversity, virus-host linkage, and functional profiles of AMGs across different land management regimes in acidic karst soil after reclamation. The results showed that both bacterial and viral communities significantly differ across the four land management regimes, which are unused land, grazing pastureland, abandoned pastureland, and fertilized grazing pastureland. Grazing led to a lower viral diversity, a decrease in lysogenic viral abundance, and fewer virus-host linkages. The diversity and function of AMGs were also significantly affected by land management regimes, with grazing leading to a reduction in both AMGs diversity and relative abundance. Furthermore, both the bacterial community and soil physiochemical properties were essential factors that shaped viral diversity and lifestyle.

CONCLUSIONS: Overall, our findings indicate that inappropriate land use (long-term grazing) disrupts the virus-host balance, thereby altering the functional profiles of the soil viral community.},
}

*Soil Microbiology
*Metagenome
*Soil/chemistry
Biodiversity
*Virome
*Herbivory
Bacteria/genetics
Microbiota

@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
doi = {10.1111/1755-0998.70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}

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

@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}

*Metagenomics/methods
*Software
Workflow
*Computational Biology/methods
Microbiota

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

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

@article {pmid41459742,
year = {2026},
author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, S and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM},
title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf284},
pmid = {41459742},
issn = {1751-7370},
support = {RS-2022-RD010405//Cooperative Research Program for Agriculture Science and Technology Development/ ; //Rural Development Administration/ ; //National Research Foundation/ ; NRF-2021M3A9I5021439//Ministry of Science and ICT/ ; RS-2023-00219213//Ministry of Science and ICT/ ; KRIBB//Korea Research Institute of Bioscience and Biotechnology/ ; //Initiative Program, South Korea/ ; },
mesh = {*Oryza/genetics/microbiology/metabolism ; *Rhizosphere ; *Methane/metabolism ; *Nitrogen/metabolism ; *Microbiota ; Soil Microbiology ; Alleles ; *Crops, Agricultural/genetics ; Metagenomics ; Metagenome ; Plant Roots/microbiology ; Nitrogen Fixation ; Bacteria/genetics/metabolism/classification ; },
abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line Saeilmi particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation and promoting microbial nitrogen fixation. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. Our study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.},
}

*Oryza/genetics/microbiology/metabolism
*Rhizosphere
*Methane/metabolism
*Nitrogen/metabolism
*Microbiota
Soil Microbiology
Alleles
*Crops, Agricultural/genetics
Metagenomics
Metagenome
Plant Roots/microbiology
Nitrogen Fixation
Bacteria/genetics/metabolism/classification

@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {638},
pmid = {41388019},
issn = {2041-1723},
support = {K08 AI123494/AI/NIAID NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Cholera Vaccines/immunology/administration & dosage ; *Immunity, Innate/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; *Sphingolipids/metabolism/immunology ; Vibrio cholerae/immunology ; *Cholera/prevention & control/immunology/microbiology ; Administration, Oral ; Feces/microbiology ; Macrophages/immunology ; Bacteroides/metabolism/immunology ; Female ; Male ; Adult ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}

Humans
*Cholera Vaccines/immunology/administration & dosage
*Immunity, Innate/immunology
*Gastrointestinal Microbiome/immunology/genetics
*Sphingolipids/metabolism/immunology
Vibrio cholerae/immunology
*Cholera/prevention & control/immunology/microbiology
Administration, Oral
Feces/microbiology
Macrophages/immunology
Bacteroides/metabolism/immunology
Female
Male
Adult

@article {pmid41385957,
year = {2026},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
pmid = {41385957},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; },
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}

Animals
*Ducks/microbiology/physiology
*Gastrointestinal Microbiome
Domestication
*Adaptation, Physiological
Cecum/microbiology
Ileum/microbiology
*Metabolome
Metabolomics
Multiomics

@article {pmid41330454,
year = {2026},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, JX and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy ; *Dysbiosis/physiopathology/microbiology ; Animals ; Brain/physiopathology ; Probiotics/therapeutic use ; Sleep/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy
*Dysbiosis/physiopathology/microbiology
Animals
Brain/physiopathology
Probiotics/therapeutic use
Sleep/physiology
*Brain-Gut Axis/physiology

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

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

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

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41485252,
year = {2026},
author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M},
title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.},
journal = {International immunopharmacology},
volume = {171},
number = {},
pages = {116155},
doi = {10.1016/j.intimp.2025.116155},
pmid = {41485252},
issn = {1878-1705},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Cellular Senescence/drug effects ; Mice, Inbred C57BL ; *Tumor Suppressor Protein p53/metabolism ; Signal Transduction/drug effects ; Mice ; Dextran Sulfate ; Male ; Disease Models, Animal ; Cell Cycle/drug effects ; Humans ; Colon/drug effects/pathology ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.},
}

Animals
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology
*Gastrointestinal Microbiome/drug effects
Cellular Senescence/drug effects
Mice, Inbred C57BL
*Tumor Suppressor Protein p53/metabolism
Signal Transduction/drug effects
Mice
Dextran Sulfate
Male
Disease Models, Animal
Cell Cycle/drug effects
Humans
Colon/drug effects/pathology

@article {pmid41468674,
year = {2026},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica/microbiology/growth & development/metabolism ; *Metagenomics/methods ; Soil Microbiology ; Plant Roots/microbiology/chemistry ; *Metabolome ; Bacteria/classification/genetics/metabolism/isolation & purification ; Microbiota ; Soil/chemistry ; Coumarins/analysis/metabolism ; Quorum Sensing ; Metabolomics ; Acyl-Butyrolactones/metabolism ; },
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}

*Rhizosphere
*Angelica/microbiology/growth & development/metabolism
*Metagenomics/methods
Soil Microbiology
Plant Roots/microbiology/chemistry
*Metabolome
Bacteria/classification/genetics/metabolism/isolation & purification
Microbiota
Soil/chemistry
Coumarins/analysis/metabolism
Quorum Sensing
Metabolomics
Acyl-Butyrolactones/metabolism

@article {pmid41455311,
year = {2026},
author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS},
title = {Harnessing methane proxies to understand and mitigate enteric emissions from ruminant production systems.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181258},
doi = {10.1016/j.scitotenv.2025.181258},
pmid = {41455311},
issn = {1879-1026},
mesh = {*Methane/analysis/metabolism ; Animals ; *Ruminants/metabolism ; *Environmental Monitoring/methods ; *Animal Husbandry ; Rumen/microbiology ; Gastrointestinal Microbiome ; *Air Pollutants/analysis ; },
abstract = {Methane emissions from livestock, particularly ruminants, significantly contribute to global warming, necessitating the development of accurate methane monitoring systems. Direct methane measurement is technically complex, time-consuming, labour-intensive, and costly. Recent advances in methane inhibitors, such as 3-nitrooxy propanol and halogenated analogues, plant secondary compounds, including polyphenols and essential oils, to reduce methane emissions have necessitated the discovery of processes underlying rumen methane synthesis and inhibition. The identification of methane proxies, such as behavioural and input proxies (dry matter intake, neutral detergent fibre), microbial community proxies (rumen metagenome profiles), metabolic pathway proxies (fatty acids), molecular and genetic proxies (microbial genes), and downstream and non-invasive proxies (milk fatty acids and faecal lipidomes), is leading to more viable solutions. New developments in 'omic' techniques, including lipidomics, metagenomics and metatranscriptomics, have enabled the detection of proxies at the molecular level utilising rumen liquor, milk, blood, urine, and faeces. In addition to traditional methane proxies, rumen microbiota profiles, and specific genes involved in rumen methanogenesis (such as mcr and mrt, which encode methyl coenzyme reductase 1 and 2), these markers can be used to identify methane-producing pathways. Protozoa-associated methanogens (PAMs), propionate-producing bacteria, and methane-oxidising methanotrophs (Methylocystis sp.) are emerging as new proxies. Methane proxies provide scalable, affordable, and mechanistically insightful alternatives to conventional direct measuring techniques, which improve the understanding of rumen function and the biological causes of methane releases, enabling large-scale methane monitoring and will enable designing effective methane mitigation strategies in livestock production systems.},
}

*Methane/analysis/metabolism
Animals
*Ruminants/metabolism
*Environmental Monitoring/methods
*Animal Husbandry
Rumen/microbiology
Gastrointestinal Microbiome
*Air Pollutants/analysis

@article {pmid41389850,
year = {2026},
author = {Petrov, VA and Schade, S and Laczny, CC and Hällqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Parkinson Disease/diet therapy/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Inflammation/metabolism/diet therapy ; *Resistant Starch/administration & dosage ; *Starch ; Quality of Life ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; },
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids alongside a reduction in opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}

Humans
*Gastrointestinal Microbiome/physiology/drug effects
*Parkinson Disease/diet therapy/microbiology/metabolism
Male
Female
Aged
Middle Aged
Inflammation/metabolism/diet therapy
*Resistant Starch/administration & dosage
*Starch
Quality of Life
Dietary Fiber
Fatty Acids, Volatile/metabolism

@article {pmid41285454,
year = {2026},
author = {Safika, S and Nisa', C and Supratikno, and Cahyadi, DD},
title = {Gut microbiota profiling of Javan pangolin (Manis javanica).},
journal = {The Journal of veterinary medical science},
volume = {88},
number = {1},
pages = {191-195},
doi = {10.1292/jvms.25-0036},
pmid = {41285454},
issn = {1347-7439},
mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Pangolins/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; },
abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.},
}

Animals
*Gastrointestinal Microbiome
Feces/microbiology
*Pangolins/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Female

@article {pmid40275546,
year = {2025},
author = {Jungpraditphol, I and Sutthiboonyapan, P and Khamwachirapitak, C and Krasaesin, A and Srithanyarat, S and Porntaveetus, T and Wiriyakijja, P},
title = {Shotgun Metagenomics of Biofilm Microbiome in Oral Lichen Planus With Desquamative Gingivitis.},
journal = {Oral diseases},
volume = {31},
number = {11},
pages = {3069-3080},
doi = {10.1111/odi.15349},
pmid = {40275546},
issn = {1601-0825},
support = {68-032,68-059//Health Systems Research Institute/ ; HEA_FF_68_008_3200_001,HEA_FF_68_223_3200_015//Thailand Science Research and Innovation Chulalongkorn University/ ; DRF68_007//Faculty of Dentistry, Chulalongkorn University/ ; },
mesh = {Humans ; *Gingivitis/microbiology/complications ; *Lichen Planus, Oral/microbiology/complications ; *Biofilms ; *Metagenomics ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; Adult ; Dental Plaque/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {INTRODUCTION: Oral lichen planus (OLP) is a chronic inflammatory condition often associated with desquamative gingivitis (DG). The oral microbiome's role in OLP and DG (OLP-DG) is gaining recognition, but prior 16S rRNA studies lacked taxonomic resolution. This study introduced shotgun metagenomic sequencing to thoroughly compare the supragingival and subgingival plaque microbiomes of individuals with and without OLP-DG.

METHODS: Twenty-seven participants (9 OLP-DG, 18 non-OLP) were recruited. Supra- and subgingival plaque samples were collected separately. Genomic DNA was analyzed using shotgun metagenomic sequencing. Microbial abundance and diversity were assessed through bioinformatic and statistical analyses.

RESULTS: We observed significant changes in the supragingival and subgingival microbiomes in OLP-DG. Supragingival plaque showed reduced Corynebacteriaceae and Porphyromonadaceae, with enrichment of an unnamed Synergistaceae genus and three unnamed species (Candidatus Saccharibacteria bacterium oral taxon 955 and 488 and GGB10852_SGB17523). Subgingival plaque revealed increased Flavobacteriaceae and Rhodocyclaceae, and reduced Actinomycetaceae. Although alpha or beta diversity was not significantly different, common commensals like Corynebacterium matruchotii and Streptococcus mitis were less abundant in OLP-DG patients.

CONCLUSION: This first-time application of metagenomic sequencing revealed a distinct microbiome in OLP-DG, characterized by novel bacterial species and reduced commensals, suggesting a potential role in OLP-DG pathogenesis, and warranting further study.},
}

Humans
*Gingivitis/microbiology/complications
*Lichen Planus, Oral/microbiology/complications
*Biofilms
*Metagenomics
Male
Female
*Microbiota/genetics
Middle Aged
Adult
Dental Plaque/microbiology
RNA, Ribosomal, 16S

@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}

Animals
Male
*Lactiplantibacillus plantarum/physiology
*Probiotics/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects/physiology
Mice, Inbred C57BL
*Liver Diseases, Alcoholic/therapy/microbiology
Liver/metabolism
Mice
Dysbiosis
NF-E2-Related Factor 2/metabolism/genetics
Oxidative Stress
Bile Acids and Salts/metabolism
Disease Models, Animal

@article {pmid41499937,
year = {2026},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
mesh = {Humans ; *Parkinson Disease/drug therapy/microbiology/metabolism ; Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; Caco-2 Cells ; Animals ; *Methylamines/metabolism ; Rats ; *5-Hydroxytryptophan/metabolism ; PC12 Cells ; Male ; *Plant Extracts/pharmacology ; Female ; Faecalibacterium prausnitzii ; Aged ; },
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.

PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.

METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPKα signaling pathways.

RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPKα signaling.

CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPKα signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}

Humans
*Parkinson Disease/drug therapy/microbiology/metabolism
Gastrointestinal Microbiome/drug effects
*Probiotics/pharmacology
Caco-2 Cells
Animals
*Methylamines/metabolism
Rats
*5-Hydroxytryptophan/metabolism
PC12 Cells
Male
*Plant Extracts/pharmacology
Female
Faecalibacterium prausnitzii
Aged

@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
pmid = {41494287},
issn = {2213-2317},
mesh = {Animals ; *Citrobacter rodentium/drug effects/pathogenicity ; Oxidation-Reduction/drug effects ; Rats ; *Antioxidants/pharmacology/administration & dosage/chemistry ; *Colon/microbiology/drug effects/metabolism ; Delayed-Action Preparations/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy/metabolism ; Male ; Coumaric Acids/pharmacology/administration & dosage ; },
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}

Animals
*Citrobacter rodentium/drug effects/pathogenicity
Oxidation-Reduction/drug effects
Rats
*Antioxidants/pharmacology/administration & dosage/chemistry
*Colon/microbiology/drug effects/metabolism
Delayed-Action Preparations/pharmacology
*Gastrointestinal Microbiome/drug effects
*Enterobacteriaceae Infections/microbiology/drug therapy/metabolism
Male
Coumaric Acids/pharmacology/administration & dosage

@article {pmid41485293,
year = {2026},
author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H},
title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157744},
doi = {10.1016/j.phymed.2025.157744},
pmid = {41485293},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Pyridoxamine/metabolism/pharmacology ; *Diabetic Nephropathies/drug therapy/metabolism ; Mice ; Male ; Transforming Growth Factor beta/metabolism ; Glycation End Products, Advanced/metabolism ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; Fecal Microbiota Transplantation ; Receptor for Advanced Glycation End Products/metabolism ; Kidney/drug effects/metabolism ; Signal Transduction/drug effects ; Vitamin B 6/metabolism ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.

PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).

METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.

RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-κB-AP-1 axis and TGF-β receptor signaling, thereby suppressing NF-κB-driven inflammation and Smad2-mediated fibrosis.

CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Pyridoxamine/metabolism/pharmacology
*Diabetic Nephropathies/drug therapy/metabolism
Mice
Male
Transforming Growth Factor beta/metabolism
Glycation End Products, Advanced/metabolism
Mice, Inbred C57BL
*Drugs, Chinese Herbal/pharmacology
Fecal Microbiota Transplantation
Receptor for Advanced Glycation End Products/metabolism
Kidney/drug effects/metabolism
Signal Transduction/drug effects
Vitamin B 6/metabolism

@article {pmid41351981,
year = {2026},
author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X},
title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157610},
doi = {10.1016/j.phymed.2025.157610},
pmid = {41351981},
issn = {1618-095X},
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Male ; Mice ; *Reactive Oxygen Species/metabolism ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.

PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.

METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.

RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.

CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.},
}

Animals
*Drugs, Chinese Herbal/pharmacology
*Gastrointestinal Microbiome/drug effects
*Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism
*Receptors, Aryl Hydrocarbon/metabolism
Male
Mice
*Reactive Oxygen Species/metabolism
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Mice, Inbred C57BL
Signal Transduction/drug effects

@article {pmid41316726,
year = {2026},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D902-D911},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}

*Genome, Viral
*Virome/genetics
*Metagenome
*Viruses/genetics/classification
*Databases, Genetic
Metagenomics/methods
Open Reading Frames
Microbiota/genetics
Humans
Software
Molecular Sequence Annotation

@article {pmid41277537,
year = {2026},
author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH},
title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D734-D742},
pmid = {41277537},
issn = {1362-4962},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Disease/genetics ; Phenotype ; Software ; },
abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.},
}

Humans
*Gastrointestinal Microbiome/genetics
Biomarkers/analysis
RNA, Ribosomal, 16S/genetics
*Databases, Genetic
Metagenome/genetics
Metagenomics/methods
Disease/genetics
Phenotype
Software

@article {pmid41263098,
year = {2026},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D555-D563},
pmid = {41263098},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multigene Family ; Metagenome ; *Databases, Genetic ; Polysaccharides/metabolism ; Metagenomics/methods ; *Glycoside Hydrolases/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; Genome, Bacterial ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Multigene Family
Metagenome
*Databases, Genetic
Polysaccharides/metabolism
Metagenomics/methods
*Glycoside Hydrolases/genetics/metabolism
*Bacteria/genetics/enzymology/classification
Genome, Bacterial

@article {pmid41261745,
year = {2026},
author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z},
title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D925-D931},
pmid = {41261745},
issn = {1362-4962},
support = {2022FY100905//Science & Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; },
mesh = {*Virome/genetics ; Animals ; *Metagenomics/methods ; *Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Chiroptera/virology ; *Software ; Ticks/virology ; Zoonoses/virology ; Humans ; Culicidae/virology ; Animals, Wild/virology ; Rodentia/virology ; Metagenome ; Genome, Viral ; },
abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.},
}

*Virome/genetics
Animals
*Metagenomics/methods
*Viruses/genetics/classification
High-Throughput Nucleotide Sequencing
Chiroptera/virology
*Software
Ticks/virology
Zoonoses/virology
Humans
Culicidae/virology
Animals, Wild/virology
Rodentia/virology
Metagenome
Genome, Viral

@article {pmid41243980,
year = {2026},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1743-D1752},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI)/ ; //Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Autónoma de México/ ; },
mesh = {*Rhizosphere ; *Crops, Agricultural/microbiology ; *Microbiota/genetics ; Soil Microbiology ; *Metagenomics/methods ; Metagenome ; Software ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}

*Rhizosphere
*Crops, Agricultural/microbiology
*Microbiota/genetics
Soil Microbiology
*Metagenomics/methods
Metagenome
Software

@article {pmid41207298,
year = {2026},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D763-D775},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Metagenome
*Databases, Genetic
Molecular Sequence Annotation
Bacteria/genetics/classification
Software
Internet

@article {pmid41171125,
year = {2026},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D826-D834},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; ERC-AdG-669830/ERC_/European Research Council/International ; },
mesh = {*Metagenomics/methods ; Animals ; Humans ; *Databases, Genetic ; Metadata ; Metagenome ; Data Curation ; Gastrointestinal Microbiome/genetics ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}

*Metagenomics/methods
Animals
Humans
*Databases, Genetic
Metadata
Metagenome
Data Curation
Gastrointestinal Microbiome/genetics

@article {pmid40888850,
year = {2026},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1733-D1742},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Skłodowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}

*Plant Roots/microbiology
*Microbiota/genetics
*Databases, Protein
Metagenomics
Molecular Sequence Annotation
Metagenome

@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
doi = {10.4014/jmb.2510.10017},
pmid = {41539854},
issn = {1738-8872},
mesh = {*Clostridium Infections/microbiology/therapy/prevention & control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}

*Clostridium Infections/microbiology/therapy/prevention & control
Animals
*Clostridium/physiology/genetics
Gastrointestinal Microbiome
Mice
*Clostridioides difficile
Disease Models, Animal
Feces/microbiology
Metagenomics

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

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

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

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

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

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

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

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

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Aging/genetics/physiology ; *Longevity/genetics/physiology ; Aged ; Male ; Computational Biology ; Female ; Aged, 80 and over ; Feces/microbiology ; Metagenome/genetics ; Middle Aged ; },
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

Humans
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Aging/genetics/physiology
*Longevity/genetics/physiology
Aged
Male
Computational Biology
Female
Aged, 80 and over
Feces/microbiology
Metagenome/genetics
Middle Aged

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

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

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

*Wastewater/microbiology/virology
*Microbiota/genetics
*Bacteria/genetics/classification
*Drug Resistance, Microbial/genetics
*Viruses/genetics/classification/isolation & purification
Metagenomics/methods
*Eukaryota/genetics/classification
Metagenome
Genetic Variation

@article {pmid41468660,
year = {2026},
author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111600},
doi = {10.1016/j.ijfoodmicro.2025.111600},
pmid = {41468660},
issn = {1879-3460},
mesh = {Fermentation ; *Thiamethoxam/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Neonicotinoids/metabolism ; *Insecticides/metabolism ; *Vigna/microbiology/chemistry/metabolism ; Guanidines/metabolism ; Taste ; Metagenomics ; Multiomics ; Thiazoles ; },
abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.},
}

Fermentation
*Thiamethoxam/metabolism
*Microbiota
Biodegradation, Environmental
*Bacteria/metabolism/genetics/classification/isolation & purification
Neonicotinoids/metabolism
*Insecticides/metabolism
*Vigna/microbiology/chemistry/metabolism
Guanidines/metabolism
Taste
Metagenomics
Multiomics
Thiazoles

@article {pmid41388903,
year = {2026},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {2},
pages = {},
doi = {10.1093/femsec/fiaf127},
pmid = {41388903},
issn = {1574-6941},
support = {21-17322 M//Czech Science Foundation/ ; },
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Methane/metabolism ; Genome, Bacterial ; *Methylococcaceae/genetics/classification ; Geologic Sediments/microbiology ; Biodiversity ; Metagenome ; Ecosystem ; },
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterize the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulfur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognized species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}

*Phylogeny
RNA, Ribosomal, 16S/genetics
*Methane/metabolism
Genome, Bacterial
*Methylococcaceae/genetics/classification
Geologic Sediments/microbiology
Biodiversity
Metagenome
Ecosystem

@article {pmid40576662,
year = {2026},
author = {Goldschmidt, I and Kramer, M and Junge, N and Ouro-Djobo, N and Poets, A and Rathert, M and Geffers, R and Baumann, U and Hartleben, B and Schulze, KD and Woltemate, S and Vital, M},
title = {Short-term and long-term development of gut microbiota in children after liver transplantation-A prospective observational trial.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {32},
number = {2},
pages = {176-194},
doi = {10.1097/LVT.0000000000000659},
pmid = {40576662},
issn = {1527-6473},
mesh = {Humans ; *Liver Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Child ; Prospective Studies ; *Dysbiosis/microbiology ; Child, Preschool ; Adolescent ; *End Stage Liver Disease/surgery/microbiology ; Feces/microbiology ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Case-Control Studies ; Infant ; Graft Survival ; Treatment Outcome ; Follow-Up Studies ; Metagenomics ; Time Factors ; },
abstract = {In children, little is known about gut microbiota (GM) in end-stage liver disease and its association with graft function after pediatric liver transplantation (pLT). We analyzed GM composition and function in children before pLT, longitudinally post-pLT and in long-term survivors (LT-pLT) in order to assess the impact of disease severity, treatment, and pLT on GM and delineate associations with graft and patient health. Fecal samples (FS) of 29 children [17f (female), age 2.6 (0.2-15.7) years] awaiting pLT were included with longitudinal follow-ups until 12 months post-transplant in 18, and compared with 38 LT-pLT [21f, age 11 (2.7-17.7) years, 7.8 (1.0-17.0) years post-pLT] and 94 healthy controls (HCs). Samples were analyzed using quantitative 16S rRNA gene analyses combined with shotgun metagenomics (subset of samples). Pre-pLT patients showed reduced alpha-diversities and altered GM composition compared with LT-pLT and HC, associated with disease severity and anti-pruritic treatment with rifampicin. Dysbiosis increased after pLT and started to recover after 3M (months). Although bacterial concentrations, alpha diversity, and gene richness increased post-pLT, levels remained below those of HC. Abundances of key functions, for example, the capacity to synthesize butyrate, also remained reduced. Quantitative analyses revealed the true extent of differences between patients and HC that were underestimated using relative abundance data. GM diversity and functional capacities correlated negatively with transaminase levels mid-term and long-term after pLT. Random Forest analyses based on GM were able to predict hepatocellular damage at high accuracy (AUC: 0.89). We provide comprehensive, quantitative insights into GM composition and function before and after pLT. A link between GM alterations and (long-term) graft health was uncovered, providing possible targets to modulate GM function in order to increase graft and patient health.},
}

Humans
*Liver Transplantation/adverse effects
*Gastrointestinal Microbiome/genetics
Female
Male
Child
Prospective Studies
*Dysbiosis/microbiology
Child, Preschool
Adolescent
*End Stage Liver Disease/surgery/microbiology
Feces/microbiology
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Severity of Illness Index
Case-Control Studies
Infant
Graft Survival
Treatment Outcome
Follow-Up Studies
Metagenomics
Time Factors

@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
doi = {10.1080/19490976.2025.2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}

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

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

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

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

@article {pmid41406442,
year = {2026},
author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B},
title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0056},
pmid = {41406442},
issn = {1480-3275},
mesh = {Animals ; Temperature ; *Bacteria/genetics/classification/isolation & purification ; *Shellfish/microbiology ; RNA, Ribosomal, 16S/genetics ; *Food Storage ; China ; Fresh Water/microbiology ; Food Microbiology ; Microbiota ; },
abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4 °C) and room-temperature (25 °C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25 °C while Bacillota increased compared to 4 °C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.},
}

Animals
Temperature
*Bacteria/genetics/classification/isolation & purification
*Shellfish/microbiology
RNA, Ribosomal, 16S/genetics
*Food Storage
China
Fresh Water/microbiology
Food Microbiology
Microbiota

@article {pmid41398180,
year = {2025},
author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {14},
pmid = {41398180},
issn = {2055-5008},
support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Fetal Blood/virology ; Female ; *Virome ; *Infectious Disease Transmission, Vertical ; Pregnancy ; Phylogeny ; Infant, Newborn ; *Viruses/classification/genetics/isolation & purification ; *Maternal Health ; Metagenomics ; Adult ; Genome, Viral ; Health Status ; },
abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.},
}

Humans
*Fetal Blood/virology
Female
*Virome
*Infectious Disease Transmission, Vertical
Pregnancy
Phylogeny
Infant, Newborn
*Viruses/classification/genetics/isolation & purification
*Maternal Health
Metagenomics
Adult
Genome, Viral
Health Status

@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1801},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ketamine/adverse effects ; *Cystitis/chemically induced/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Rats ; Metabolomics/methods ; Male ; Rats, Sprague-Dawley ; Urinary Bladder/metabolism ; *Metabolome ; Disease Models, Animal ; Bacteria/genetics/classification ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}

Animals
*Ketamine/adverse effects
*Cystitis/chemically induced/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
Rats
Metabolomics/methods
Male
Rats, Sprague-Dawley
Urinary Bladder/metabolism
*Metabolome
Disease Models, Animal
Bacteria/genetics/classification

@article {pmid41382244,
year = {2025},
author = {Bae, IH and Kim, H and Kim, SM and Lee, YH},
title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {23},
pmid = {41382244},
issn = {2049-2618},
support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; },
mesh = {*Mycorrhizae/physiology/genetics ; *Symbiosis ; *Soil Microbiology ; *Microbiota ; *Tricholoma/physiology ; Soil/chemistry ; Nitrogen/metabolism ; Plant Roots/microbiology ; Ecosystem ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.

RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.

CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.},
}

*Mycorrhizae/physiology/genetics
*Symbiosis
*Soil Microbiology
*Microbiota
*Tricholoma/physiology
Soil/chemistry
Nitrogen/metabolism
Plant Roots/microbiology
Ecosystem
Bacteria/classification/genetics/metabolism

@article {pmid41372750,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {26},
pmid = {41372750},
issn = {1471-2180},
mesh = {*Wastewater/microbiology/chemistry ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Agricultural Irrigation ; Metals, Heavy/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Cities ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; },
abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.

METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.

RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37 µg/L), chromium (1.89 µg/L), and nickel (4.93 µg/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P < 0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P < 0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P < 0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.

CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.},
}

*Wastewater/microbiology/chemistry
*Metagenomics/methods
*Bacteria/genetics/drug effects/classification/isolation & purification
*Agricultural Irrigation
Metals, Heavy/analysis
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Cities
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Water Microbiology

@article {pmid39364864,
year = {2025},
author = {Dong, W and Hu, S and Yu, J and Liu, Y and Zeng, S and Duan, X and Deng, Y and Wang, Y and Yin, J and Xing, B and Shu, Z},
title = {Study on the Antidepressant Effect of Zhizichi Decoction by Regulating Metabolism and Intestinal Flora.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {28},
number = {16},
pages = {2826-2841},
pmid = {39364864},
issn = {1875-5402},
support = {82004245//National Natural Science Foundation of China/ ; 2018M641887//National Postdoctoral Science Foundation of China/ ; 822RC705//Natural Science Foundation of Hainan Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Antidepressive Agents/pharmacology/chemistry ; Rats ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Depression/drug therapy/metabolism ; Male ; Rats, Sprague-Dawley ; Disease Models, Animal ; Metabolomics ; Stress, Psychological/drug therapy ; },
abstract = {BACKGROUND: The incidence of depression is increasing year by year, and Zhizichi Decoction.ZZCD.has shown significant efficiency in the clinical treatment of mild depression, but its mechanism of action is still unclear. In this research, network pharmacology and metagenomics combined and metabolomics were used as research methods to explain the scientific connotation of the antidepressant effect of ZZCD from the aspects of the overall effect of organisms and microbial structure and function.

METHODS: The rat model of depression was established by chronic unpredictable mild stress (CUMS), and the improvement of depressive symptoms was evaluated by behavioral and histopathological methods. Network pharmacology predicted possible targets and important pathways of ZZCD. Metabolomics revealed its possible related biological pathways. Metagenomics showed the disturbance of ZZCD on intestinal microbial diversity structure and associated biological functions in depressed rats.

RESULTS: ZZCD can improve the behavioral performance of CUMS rats, and can significantly regulate the content of 5-HT, NE and other neurotransmitters in serum and brain tissue, and improve the damaged state of neurons in the hippocampus. Network pharmacology predicts that it mainly acts on biological processes such as inflammatory response and oxidative stress response. Metabolomics found that it affected metabolic pathways such as amino acid metabolism and lipid metabolism. The results of metagenomics showed that it significantly regulated the abundance of Firmicutes and Bacteroidetes. The above results predicted that it may affect signaling pathways such as the nervous system, inflammatory diseases and cell processing.

CONCLUSION: ZZCD may play an antidepressant role by regulating intestinal probiotics, energy metabolism, and inflammation reduction. This provides a scientific basis for the clinical application of ZZCD in traditional Chinese medicine and also makes it an optional alternative for the treatment of depression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Antidepressive Agents/pharmacology/chemistry
Rats
*Drugs, Chinese Herbal/pharmacology/chemistry
*Depression/drug therapy/metabolism
Male
Rats, Sprague-Dawley
Disease Models, Animal
Metabolomics
Stress, Psychological/drug therapy

@article {pmid41531093,
year = {2026},
author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W},
title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {650-662},
doi = {10.13227/j.hjkx.202411219},
pmid = {41531093},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Gossypium/growth & development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; },
abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.},
}

*Soil Microbiology
*Gossypium/growth & development
Metagenomics
Soil/chemistry
Biodegradation, Environmental
*Agriculture/methods
Microbiota

@article {pmid41530917,
year = {2026},
author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF},
title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611544},
doi = {10.1080/19490976.2025.2611544},
pmid = {41530917},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Big Data ; *Software ; Colorectal Neoplasms/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Reproducibility of Results ; },
abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.},
}

*Metagenomics/methods
Humans
*Metagenome
*Big Data
*Software
Colorectal Neoplasms/microbiology
*Bacteria/classification/genetics/isolation & purification
*Computational Biology/methods
Gastrointestinal Microbiome
Reproducibility of Results

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

*Intensive Care Units
*Bacteria/genetics/isolation & purification/classification/drug effects
Humans
Queensland
*Environmental Monitoring/methods
Drug Resistance, Bacterial/genetics
Microbiota/genetics
Metagenomics/methods
Cross Infection/microbiology

@article {pmid41406735,
year = {2026},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, MÁ and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
mesh = {Humans ; *Mouth/microbiology/metabolism/chemistry/enzymology ; *Esters/metabolism/chemistry ; Male ; Adult ; Female ; *Saliva/microbiology/enzymology/chemistry/metabolism ; *Bacteria/enzymology/genetics/isolation & purification/classification/metabolism ; Young Adult ; Microbiota ; *Bacterial Proteins/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; Middle Aged ; *Carboxylic Acids/metabolism/chemistry ; },
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}

Humans
*Mouth/microbiology/metabolism/chemistry/enzymology
*Esters/metabolism/chemistry
Male
Adult
Female
*Saliva/microbiology/enzymology/chemistry/metabolism
*Bacteria/enzymology/genetics/isolation & purification/classification/metabolism
Young Adult
Microbiota
*Bacterial Proteins/metabolism/genetics
Gas Chromatography-Mass Spectrometry
Middle Aged
*Carboxylic Acids/metabolism/chemistry

@article {pmid41372802,
year = {2025},
author = {Almas, S and Carpenter, RE and Tamrakar, VK and Singh, A and Sharma, A and Sharma, R},
title = {Precision metagenomics reveals microbial landscape in acute upper respiratory infections: a comprehensive dataset.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {18},
pmid = {41372802},
issn = {1756-0500},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Acute Disease ; Male ; Female ; Middle Aged ; Adult ; },
abstract = {OBJECTIVES: The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina[®]/IDbyDNA Respiratory Pathogen ID/AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance.

DATA DESCRIPTION: This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial resistance detection, and therapeutic interventions. Its potential for reuse and integration with other omics datasets enhances its significance. The comprehensive nature of the data facilitates research into relationships between the respiratory microbiota and host factors, including clinical outcomes, immune responses, or genetic predispositions. Moreover, the article underscores the interdisciplinary potential by advocating for the integration of this dataset with other relevant datasets such as transcriptomics or metabolomics, enabling a deeper understanding of the intricate interactions in acute upper respiratory infections. The presented dataset contributes to the expanding knowledge in precision metagenomics and holds the promise to propel research and clinical practices in the field of respiratory diseases.},
}

Humans
*Respiratory Tract Infections/microbiology
*Metagenomics/methods
*Microbiota/genetics
High-Throughput Nucleotide Sequencing
Acute Disease
Male
Female
Middle Aged
Adult

@article {pmid41365368,
year = {2026},
author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X},
title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.},
journal = {Bioresource technology},
volume = {442},
number = {},
pages = {133782},
doi = {10.1016/j.biortech.2025.133782},
pmid = {41365368},
issn = {1873-2976},
mesh = {*Phenanthrenes/metabolism ; *Cadmium/toxicity ; Biodegradation, Environmental/drug effects ; *Microbial Consortia/drug effects ; Arthrobacter/metabolism ; Klebsiella/metabolism ; Minerals/metabolism ; },
abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.},
}

*Phenanthrenes/metabolism
*Cadmium/toxicity
Biodegradation, Environmental/drug effects
*Microbial Consortia/drug effects
Arthrobacter/metabolism
Klebsiella/metabolism
Minerals/metabolism

@article {pmid41288100,
year = {2026},
author = {van Dam, F and Westmeijer, G and Rezaei Somee, M and Ketzer, M and Kietäväinen, R and Ono, S and Bertilsson, S and McIntosh, JC and Dopson, M and Drake, H},
title = {Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.},
journal = {mBio},
volume = {17},
number = {1},
pages = {e0301725},
doi = {10.1128/mbio.03017-25},
pmid = {41288100},
issn = {2150-7511},
mesh = {*Methane/metabolism/biosynthesis ; *Meteoroids ; Sweden ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics ; Metagenomics ; Phylogeny ; Archaea/metabolism/genetics ; },
abstract = {Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a δ[13]Cmethanol-methane isotope enrichment of up to 98.6‰. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.},
}

*Methane/metabolism/biosynthesis
*Meteoroids
Sweden
*Microbial Consortia
Bacteria/metabolism/classification/genetics
Metagenomics
Phylogeny
Archaea/metabolism/genetics

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

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

@article {pmid41381751,
year = {2025},
author = {Tabe, C and Motooka, D and Fujita, T and Makiguchi, T and Taima, K and Tanaka, H and Itoga, M and Ishioka, Y and Akita, T and Ishidoya, M and Chubachi, K and Fukushima, T and Tanaka, Y and Odagiri, H and Kameyama, Y and Kobori, Y and Tasaka, S and Fujii, H},
title = {The gut microbiota as a potential biomarker in patients with EGFR-mutant lung cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1672},
pmid = {41381751},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; ErbB Receptors/genetics/antagonists & inhibitors ; Female ; Male ; *Lung Neoplasms/drug therapy/genetics/microbiology ; Middle Aged ; Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics/microbiology ; *Mutation ; Protein Kinase Inhibitors/therapeutic use/adverse effects ; RNA, Ribosomal, 16S/genetics ; Diarrhea/microbiology/chemically induced ; Biomarkers, Tumor/genetics ; Feces/microbiology ; },
abstract = {Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are highly effective against EGFR-mutant non-small cell lung cancer (NSCLC); however, identifying biomarkers that predict prognosis and adverse events is necessary. Although the gut microbiota is considered to be a biomarker for NSCLC without mutations, no studies have examined its potential as a biomarker for EGFR-mutant NSCLC. Here, we investigated the association between gut microbiota composition and diarrhea, a common side effect caused by EGFR-TKIs. In addition, we examined the association between the efficacy of EGFR-TKIs and the gut microbiota. A total of 21 NSCLC patients with EGFR mutations were enrolled. Fecal samples were collected prior to EGFR-TKI treatment and 16S rRNA metagenome sequencing was performed to evaluate the microbiota profile. In addition, α-diversity, β-diversity, and Linear discriminant analysis Effect Size (LEfSe) analyses were performed. The α-diversity of the gut microbiota was higher in patients with grade 0-1 diarrhea than in those with grade 2-3 diarrhea (Shannon, p = 0.0367). In terms of β-diversity, there was a significant difference in the best overall response between patients with a partial response (PR) to EGFR-TKIs and those with stable disease (SD)/progressive disease (PD) (weighted p = 0.041). Analysis of microbial composition revealed an increased abundance of Ruminococcus in the PR group. In patients taking EGFR-TKIs, a higher α-diversity may be associated with less severe diarrhea. In addition, a high abundance of Ruminococcus may be a potential biomarker for predicting favorable efficacy of EGFR-TKIs.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
ErbB Receptors/genetics/antagonists & inhibitors
Female
Male
*Lung Neoplasms/drug therapy/genetics/microbiology
Middle Aged
Aged
*Carcinoma, Non-Small-Cell Lung/drug therapy/genetics/microbiology
*Mutation
Protein Kinase Inhibitors/therapeutic use/adverse effects
RNA, Ribosomal, 16S/genetics
Diarrhea/microbiology/chemically induced
Biomarkers, Tumor/genetics
Feces/microbiology

@article {pmid41354674,
year = {2025},
author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L},
title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {13},
pmid = {41354674},
issn = {2055-5008},
support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; },
mesh = {*Tryptophan/metabolism/biosynthesis ; Animals ; *Gastrointestinal Microbiome ; *Ursidae/microbiology ; Mice ; *Streptococcus/genetics/metabolism/isolation & purification/classification ; Feces/microbiology/chemistry ; Metagenomics ; Whole Genome Sequencing ; Humans ; Male ; },
abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.},
}

*Tryptophan/metabolism/biosynthesis
Animals
*Gastrointestinal Microbiome
*Ursidae/microbiology
Mice
*Streptococcus/genetics/metabolism/isolation & purification/classification
Feces/microbiology/chemistry
Metagenomics
Whole Genome Sequencing
Humans
Male

@article {pmid41353361,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {449},
pmid = {41353361},
issn = {2041-1723},
support = {UH2AI083264//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32AI162579//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; OPP1189217//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048956//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV048982//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
mesh = {Female ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Humans ; *Bacteria/genetics/classification ; Metagenome/genetics ; Metagenomics/methods ; Mycobiome/genetics ; Genome, Bacterial ; },
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}

Female
*Vagina/microbiology/virology
*Microbiota/genetics
Humans
*Bacteria/genetics/classification
Metagenome/genetics
Metagenomics/methods
Mycobiome/genetics
Genome, Bacterial

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

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

@article {pmid41524715,
year = {2026},
author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S},
title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.105948},
pmid = {41524715},
issn = {2050-084X},
support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; },
mesh = {*Dysbiosis/microbiology ; *Microbial Interactions ; Humans ; *Microbiota ; Metagenomics ; Models, Biological ; },
abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.},
}

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

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

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

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

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

Humans
*Gastrointestinal Microbiome/genetics
*Frailty/microbiology
Male
Female
Aged
*Aging
Comorbidity
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid41421776,
year = {2026},
author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES},
title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.},
journal = {Environmental research},
volume = {291},
number = {},
pages = {123595},
doi = {10.1016/j.envres.2025.123595},
pmid = {41421776},
issn = {1096-0953},
mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; Denitrification ; Bioreactors/microbiology ; *Atmospheric Pressure ; *Microbiota ; *Waste Disposal, Fluid/methods ; Nitrification ; Altitude ; Bacteria/metabolism ; },
abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.},
}

*Nitrogen/metabolism
*Carbon/metabolism
Denitrification
Bioreactors/microbiology
*Atmospheric Pressure
*Microbiota
*Waste Disposal, Fluid/methods
Nitrification
Altitude
Bacteria/metabolism

@article {pmid41418855,
year = {2026},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {291},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
mesh = {Humans ; *Arsenic/urine/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Infant ; Rural Population ; *Environmental Exposure ; Cross-Sectional Studies ; Feces/microbiology/chemistry ; Cohort Studies ; Longitudinal Studies ; *Environmental Pollutants/urine ; },
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.

METHODS: Participants provided urine and fecal samples at six weeks (6W; n = 219) or twelve months (12M; n = 219), a subset of whom provided samples at both (n = 167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/gene pathway relative abundance.

RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [β = 0.07 per doubling (95 %CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [β = -0.04 per doubling (95 %CI: 0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.

CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}

Humans
*Arsenic/urine/toxicity
Female
Male
*Gastrointestinal Microbiome/drug effects
Infant
Rural Population
*Environmental Exposure
Cross-Sectional Studies
Feces/microbiology/chemistry
Cohort Studies
Longitudinal Studies
*Environmental Pollutants/urine

@article {pmid41396034,
year = {2026},
author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y},
title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.},
journal = {Food & function},
volume = {17},
number = {1},
pages = {513-530},
doi = {10.1039/d5fo04527d},
pmid = {41396034},
issn = {2042-650X},
mesh = {Humans ; *Milk, Human/microbiology/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; *Gastrointestinal Microbiome ; Pregnancy ; *Diabetes, Gestational/metabolism/microbiology ; Infant, Newborn ; Adult ; Feces/microbiology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Tandem Mass Spectrometry ; Male ; },
abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.},
}

Humans
*Milk, Human/microbiology/chemistry/metabolism
Female
*Oligosaccharides/metabolism/analysis
*Gastrointestinal Microbiome
Pregnancy
*Diabetes, Gestational/metabolism/microbiology
Infant, Newborn
Adult
Feces/microbiology
Infant
Bacteria/classification/isolation & purification/genetics
Tandem Mass Spectrometry
Male

@article {pmid41392764,
year = {2026},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food & function},
volume = {17},
number = {1},
pages = {475-493},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Serotonin/metabolism ; Mice ; *gamma-Aminobutyric Acid/metabolism ; *Sleep Initiation and Maintenance Disorders/metabolism/microbiology/chemically induced ; Male ; *Probiotics ; *Bifidobacterium animalis/physiology ; Humans ; Signal Transduction ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Serotonin/metabolism
Mice
*gamma-Aminobutyric Acid/metabolism
*Sleep Initiation and Maintenance Disorders/metabolism/microbiology/chemically induced
Male
*Probiotics
*Bifidobacterium animalis/physiology
Humans
Signal Transduction
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid41351708,
year = {2025},
author = {Campbell, KL and Armitage, AR and Labonté, JM},
title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {21},
pmid = {41351708},
issn = {1432-184X},
mesh = {*Wetlands ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Geologic Sediments/microbiology/virology ; Nitrogen/metabolism ; Poaceae/microbiology ; Carbon/metabolism ; Viruses/classification/genetics/isolation & purification ; Metagenome ; Sulfur/metabolism ; Ecosystem ; },
abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.},
}

*Wetlands
*Microbiota
*Bacteria/genetics/classification/metabolism/isolation & purification
Geologic Sediments/microbiology/virology
Nitrogen/metabolism
Poaceae/microbiology
Carbon/metabolism
Viruses/classification/genetics/isolation & purification
Metagenome
Sulfur/metabolism
Ecosystem

@article {pmid40996449,
year = {2026},
author = {Mimpen, IL and Battaglia, TW and Parra-Martinez, M and Toner-Bartelds, C and Zeverijn, LJ and Geurts, BS and Verkerk, K and Hoes, LR and van Renterghem, AWJ and Noë, M and Hofland, I and Broeks, A and van der Noort, V and Stigter, ECA and Gulersonmez, CMC and Burgering, BMT and van Gogh, M and de Zoete, MR and Gelderblom, H and Dijkstra, KK and Wessels, LFA and Voest, EE},
title = {Microbial Metabolic Pathways Guide Response to Immune Checkpoint Blockade Therapy.},
journal = {Cancer discovery},
volume = {16},
number = {1},
pages = {95-113},
doi = {10.1158/2159-8290.CD-24-1669},
pmid = {40996449},
issn = {2159-8290},
support = {//Mrs. Anneke Hoogendijk/ ; //Foundation Weteringschans/ ; 09150162210100//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; //Oncode Institute/ ; },
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Metabolic Networks and Pathways ; *Neoplasms/drug therapy/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome ; Riboflavin/metabolism ; },
abstract = {UNLABELLED: Studies have identified a link between specific microbiome-derived bacteria and immune checkpoint blockade (ICB) efficacy. However, these species lack consistency across studies, and their immunomodulatory mechanisms remain elusive. To understand the influence of the microbiome on ICB response, we studied its functional capacity. Using pan-cancer metagenomics data from ICB-treated patients, we showed that community-level metabolic pathways are stable across individuals, making them suitable for predicting ICB response. We identified several microbial metabolic processes significantly associated with response, including the methylerythritol 4-phosphate (MEP) pathway, which was associated with response and induced Vδ2 T cell-mediated antitumor responses in patient-derived tumor organoids. In contrast, riboflavin synthesis was associated with ICB resistance, and its intermediates induced mucosal-associated invariant T (MAIT) cell-mediated immune suppression. Moreover, gut metabolomics revealed that high riboflavin levels were linked to worse survival in patients with abundant intratumoral MAIT cells. Collectively, our results highlight the relevance of metabolite-mediated microbiome-immune cell cross-talk.

SIGNIFICANCE: Microbial metabolic pathways are highly conserved across individuals and therefore offer an opportunity to link the microbiome to immunotherapy efficacy. We identified specific microbial metabolic pathways associated with response to ICB and provided mechanistic insights into the immunomodulatory influence of these pathways on antitumor immunity.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Metabolic Networks and Pathways
*Neoplasms/drug therapy/immunology/metabolism/microbiology
*Gastrointestinal Microbiome
Riboflavin/metabolism