@article {pmid41787302,
year = {2026},
author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W},
title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41787302},
issn = {1471-2164},
support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ecosystem ; China ; *Grasshoppers/microbiology/physiology ; *Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics ; Metagenome ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in insect adaptation, yet how habitat variation shapes microbial communities in pygmy grasshoppers remains unclear. We investigated this question using Tetrix japonica, which inhabits diverse ecosystems across China and provides an ideal model to study microbiome-environment interactions. Shotgun metagenomic sequencing was performed on gut samples from six populations representing coniferous forest, broadleaf forests in Shandong and Shaanxi, grassland, shrubland, and laboratory-reared populations. RESULTS: Microbial diversity and community composition varied significantly among habitats, with field populations exhibiting higher diversity than laboratory-reared ones. Despite environmental differences, a core microbiome comprising 1,162 shared species was consistently detected, suggesting stable symbiotic relationships. Habitat-specific microbial signatures were most evident between forest and grassland populations, with lignocellulose-degrading taxa enriched in forest habitats. Moreover, geographic separation between Shandong and Shaanxi broadleaf forests led to distinct microbial profiles despite similar vegetation. Functional analysis revealed differential enrichment of genes related to plant polymer degradation, nitrogen cycling, and secondary metabolite biosynthesis across habitats. CONCLUSION: These findings demonstrate that both habitat conditions and geography influence gut microbiome assembly in T. japonica, with microbiome plasticity facilitating adaptation. The reduced diversity observed in laboratory populations highlights the importance of natural habitats for maintaining functional microbiome integrity.},
}

Animals
*Ecosystem
China
*Grasshoppers/microbiology/physiology
*Gastrointestinal Microbiome
Metagenomics
Bacteria/classification/genetics
Metagenome
Biodiversity
Phylogeny

@article {pmid41796197,
year = {2026},
author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M},
title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41796197},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Wetlands ; *Salt-Tolerant Plants/microbiology ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenome ; India ; Avicennia/microbiology ; *Geologic Sediments/microbiology ; Archaea/genetics/classification ; },
abstract = {In this research, the rhizosphere soil microbiome diversity of mangrove trees such as Avicennia marina, Ceriops tagal & Rhizophora apiculata and salt marsh halophytes Suaeda maritima, Suaeda monoica and Sesuvium portulacastrum from Karankadu mangroves of Tamil Nadu, India was investigated. The collected sample was profiled by 16S rRNA Illumina NovaSeq 6000 platform sequencing of V3–V4 amplicon region by metagenomic approach to investigate the bacterial communities related with the different mangrove species. Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. Bacteria were the most abundant domain followed by Archaea and Eukaryota; Proteobacteria, Actinobacteria, Firmicutes, Fibrobacterota, Chlorobiota, and Bacteroidota were found to be predominant phyla present in all samples; Unculturable environmental microbes were also detected, particularly abundant in S. maritima and S. monoica samples. Staphylococcus aureus, Vibrio parahaemolyticus, Klebsiella pneumoniae, Salmonella enterica, Streptomyces griseocarneus were the most abundant species observed in this study. The variations in bacterial community structure across these ecosystems may be influenced by the distinct environmental conditions of each sampled mangrove habitat. For the first time, our findings highlight the richness of microbial diversity in the Karankadu mangroves, providing essential baseline data and revealing differences between mangrove trees and halophytes. This study offers valuable insights for further investigation into the mechanisms governing rhizosphere microbiome interactions with their host environment.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Wetlands
*Salt-Tolerant Plants/microbiology
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenome
India
Avicennia/microbiology
*Geologic Sediments/microbiology
Archaea/genetics/classification

@article {pmid41826827,
year = {2026},
author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E},
title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41826827},
issn = {1471-2180},
support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; },
mesh = {Animals ; *Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; *Hemiptera/microbiology ; *Plant Diseases/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Biodiversity ; },
abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'. RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts – three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774 kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host–pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11 Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions. CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.},
}

Animals
*Symbiosis
*Bacteria/classification/genetics/isolation & purification
Phylogeny
*Hemiptera/microbiology
*Plant Diseases/microbiology
Metagenomics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Biodiversity

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
mesh = {*Rhizosphere ; India ; *Soil Microbiology ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; *Piper/microbiology ; Phylogeny ; Soil/chemistry ; Plants, Medicinal/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Proteobacteria/genetics ; },
abstract = {The rhizosphere of medicinal plants harbors complex microbial communities that plays a key role in nutrient cycling, plant growth, and environmental adaptation. Piper longum L., an important medicinal plant, remains poorly explored with respect to its rhizospheric microbiome. In this study, rhizospheric soil samples of P. longum were collected at the spike stage from the Herbal Garden of Dayalbagh Educational Institute, Agra, India, and analyzed using metagenomic approach. Soil physicochemical analysis revealed a neutral to slightly alkaline pH with moderate nutrient availability, indicating favorable conditions for microbial activity. High-throughput Illumina sequencing generated ~ 19.94 million paired-end reads (~ 5.92 Gb), which were assembled into 97,432 scaffolds (52.26 Mb total length), and 45,876 protein-coding genes were predicted. Taxonomic profiling revealed dominance of Proteobacteria (42%), followed by Actinobacteria (13.9%), Thaumarchaeota (13.16%), Chloroflexi (8.21%), and Acidobacteria (7.28%). At the genus level, Nitrososphaera was the most abundant (23.58%), with Candidatus Nitrososphaera gargensis as the predominant species (11.21%), indicating an active microbial community of ammonia-oxidizing archaea involved in nitrogen fixation. Functional annotation using COG, KEGG, Pfam, GO, and FIGfams databases revealed enrichment of genes associated with amino acid transport and metabolism, carbohydrate metabolism, energy production, and environmental adaptation. Overall, this study provides the first metagenomic baseline of the P. longum rhizosphere microbiome and highlights its potential role in nutrient cycling and sustainable cultivation.},
}

*Rhizosphere
India
*Soil Microbiology
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
*Piper/microbiology
Phylogeny
Soil/chemistry
Plants, Medicinal/microbiology
High-Throughput Nucleotide Sequencing
Microbiota/genetics
Metagenome
RNA, Ribosomal, 16S/genetics
Proteobacteria/genetics

@article {pmid41882608,
year = {2026},
author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J},
title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41882608},
issn = {1472-6831},
mesh = {Humans ; Adolescent ; *Dental Caries/microbiology/etiology ; Risk Assessment/methods ; Female ; Male ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota ; Dental Plaque/microbiology ; },
abstract = {OBJECTIVE: This study aimed to develop and initially validate a caries risk assessment scale for adolescents undergoing fixed orthodontic treatment, and to exploratorily analyze the potential association between oral microbiota and caries risk levels. METHODS: Clinical examinations and questionnaires were conducted on 210 adolescent orthodontic patients before orthodontic treatment and at 1st, 3rd, and 6th month, and the caries risk assessment scale was constructed according to the correlation statistics. Six patients in low-risk group and middle-risk group were randomly selected. Dental plaque samples were collected before orthodontic treatment and 1st month, respectively. Bioinformatics analyses were performed to explore differences in microbial community composition and function. RESULTS: The caries risk assessment scale involves 7 factors, such as simplified debris index (DI-S), brushing time, and frequency of sugar intake. Differences in scale scores before and during orthodontic treatment at the 1st, 3rd, and 6th months correlated with the presence of caries at the corresponding orthodontic stages (P < 0.001). Differences in scores at 1st month correlated with the presence or absence of caries at 3rd and 6th month (P < 0.05). The differences in scores at 3rd month correlated with the caries status at 6th month (P < 0.001). The caries risk related Glycan biosynthesis and metabolism pathways were positively correlated with Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). The Carbohydrate Metabolism pathways were positively correlated with Prevotella_melaninogenica, Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). CONCLUSIONS: A practical caries risk assessment scale for orthodontic adolescents was established and shows promise for cross-sectional risk stratificationthroughout the orthodontic treatment cycle. Its longitudinal predictive efficacy requires further validation with appropriate statistical models. The microbial findings, particularly the involvement of Candidatus_Nanosynbacter_sp._HMT-352 in relevant metabolic pathways, are preliminary and hypothesis-generating. These results are constrained by the study's limited sample size and the lack of a high-risk comparator group, necessitating confirmation in larger, more comprehensive future studies.},
}

Humans
Adolescent
*Dental Caries/microbiology/etiology
Risk Assessment/methods
Female
Male
*Orthodontic Appliances, Fixed/adverse effects
*Microbiota
Dental Plaque/microbiology

@article {pmid41902972,
year = {2026},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S},
title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41902972},
issn = {1432-184X},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Altitude ; Biodegradation, Environmental ; Peru ; Soil Microbiology ; Metagenome ; *Microbiota ; Biodiversity ; Metagenomics ; },
abstract = {The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.},
}

*Phylogeny
*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism/isolation & purification
Altitude
Biodegradation, Environmental
Peru
Soil Microbiology
Metagenome
*Microbiota
Biodiversity
Metagenomics

@article {pmid41904207,
year = {2026},
author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W},
title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41904207},
issn = {2045-2322},
support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; Humans ; Animals ; Male ; *Lipid Metabolism ; *Glycemic Control ; Blood Glucose/metabolism ; Female ; *Lactobacillus johnsonii/physiology ; *Circadian Rhythm ; Mice ; Middle Aged ; Gastrointestinal Microbiome ; Feces/microbiology ; *Probiotics/administration & dosage ; },
abstract = {Although most patients with type 2 diabetes mellitus (T2DM) and circadian rhythm disruption have poor blood glucose control, a fraction of patients with T2DM and circadian rhythm disruption who still have good blood glucose control. Previous studies have shown that individuals with circadian rhythm disruption are more prone to developing T2DM, and the occurrence of T2DM is associated with the gut microbiota. However, the role of gut microbiota in patients with T2DM and circadian rhythm disruption remains unclear. Stool samples were collected from 6 patients with poorly controlled type 2 diabetes mellitus (T2DM) and circadian rhythm disruption, as well as from 6 patients with well-controlled T2DM and circadian rhythm disruption. Metagenomic sequencing was performed on the stool samples. Compared to the well-controlled group, the abundance of Lactobacillus johnsonii(L. johnsonii) was significantly decreased in the poorly controlled group. To investigate the effects of L. johnsonii supplementation on glucose and lipid metabolism, diabetic mice with circadian rhythm disruption were administered L. johnsonii and their metabolic indicators were measured. Metagenomic sequencing of the gut microbiota revealed a higher microbial diversity in the well blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (W-T2D-RD). Additionally, a significant decrease in the abundance of L. johnsonii was observed in patients with poor blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (P-T2D-RD) when compared to those with W-T2D-RD. Following supplementation of L. johnsonii to the mice in the type 2 diabetes mellitus rhythm disruption Lactobacillus johnsonii group (T2DM-RD-L), the fasting blood glucose levels and postprandial blood glucose levels were significantly reduced. Additionally, total cholesterol and low-density lipoprotein levels decreased, high-density lipoprotein levels increased in the T2DM-RD-L group. Lactobacillus johnsonii has a positive impact on both glucose and lipid metabolism in patients with type 2 diabetes mellitus and circadian rhythm disruption.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism/blood
Humans
Animals
Male
*Lipid Metabolism
*Glycemic Control
Blood Glucose/metabolism
Female
*Lactobacillus johnsonii/physiology
*Circadian Rhythm
Mice
Middle Aged
Gastrointestinal Microbiome
Feces/microbiology
*Probiotics/administration & dosage

@article {pmid41905975,
year = {2026},
author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC},
title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41905975},
issn = {2045-2322},
mesh = {Humans ; *Rubus ; *Gastrointestinal Microbiome ; Metagenomics ; Feces/microbiology ; C-Reactive Protein/metabolism ; Metagenome ; Triglycerides/blood ; },
abstract = {Red raspberries have been shown to exert beneficial effects on immunometabolic health in numerous studies; however, these effects are subject to interindividual variability. Building on a previous transcriptomic-based clustering analysis from an 8-week randomized controlled trial in which 24 individuals consumed 280 g of red raspberries daily, we investigated whether functional metagenomic profiling may enhance our understanding of the observed interindividual variability in metabolic responses. Participants were classified as responders (n = 13) or non-responders (n = 11) based on prior clustering approaches, which identified significant reductions in plasma levels of C-reactive protein (CRP), triglycerides, and total cholesterol in responders. Microbial DNA extracted from fecal samples collected before and after the intervention was sequenced, and carbohydrate-active enzyme (CAZyme) counts were generated using a bioinformatics pipeline. Differential analysis revealed distinct functional metagenomic profiles between responders and non-responders. Multiple linear regressions identified potential associations between baseline CAZyme levels and changes in CRP, with contrasting trends observed between responders and non-responders. CBM8 and CBM49 were among the highlighted CAZymes. GH5 and several GH5 subfamilies were also identified as candidate CAZymes associated with interindividual variability observed in metabolic responses. These findings support the integration of microbiome-derived functional data alongside other omics to improve precision nutrition strategies.},
}

Humans
*Rubus
*Gastrointestinal Microbiome
Metagenomics
Feces/microbiology
C-Reactive Protein/metabolism
Metagenome
Triglycerides/blood

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
mesh = {*Endophytes/genetics/physiology/classification ; *Symbiosis ; *Agroecology ; Genomics ; *Plants/microbiology ; Multiomics ; Agriculture ; Ecosystem ; Microbiota ; Metagenomics ; Bacteria/genetics/classification ; },
abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.},
}

*Endophytes/genetics/physiology/classification
*Symbiosis
*Agroecology
Genomics
*Plants/microbiology
Multiomics
Agriculture
Ecosystem
Microbiota
Metagenomics
Bacteria/genetics/classification

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41915167},
issn = {1432-184X},
mesh = {*Microbiota ; Large Language Models ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.},
}

*Microbiota
Large Language Models
*Bacteria/classification/genetics/isolation & purification

@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
mesh = {Animals ; *Virome/genetics ; Mice ; Liver/virology/parasitology ; Phylogeny ; *Echinococcosis/virology/parasitology ; Lung/virology/parasitology ; Metagenomics ; *Echinococcus/virology ; *Viruses/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; Female ; },
abstract = {The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.},
}

Animals
*Virome/genetics
Mice
Liver/virology/parasitology
Phylogeny
*Echinococcosis/virology/parasitology
Lung/virology/parasitology
Metagenomics
*Echinococcus/virology
*Viruses/classification/genetics/isolation & purification
Gastrointestinal Microbiome
Female

@article {pmid41942856,
year = {2026},
author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT},
title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41942856},
issn = {1471-2180},
support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; },
mesh = {Humans ; *Spondylitis, Ankylosing/microbiology ; Male ; Adult ; Female ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; },
abstract = {BACKGROUND: To explore the differences in intestinal microbiota between patients with ankylosing spondylitis (AS) and healthy individuals (HC) in terms of genetic, species composition, and functional levels, and to reveal the role of intestinal microorganisms in the pathogenesis of AS. METHODS: This study selected 17 AS patients (AS group) and 17 healthy subjects (HC group) from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine between August to October 2024. Basic clinical data, as well as the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Visual Analogue Scale (VAS) score, of the AS group, were collected. Fresh fecal samples were also collected for metagenomic sequencing. Differences in microbiota were analyzed using methods including Alpha diversity analysis, species abundance analysis, Principal Coordinates Analysis (PCoA), Non-metric Multidimensional Scaling (NMDS), DESeq2 analysis, Linear Discriminant Analysis Effect Size (LEfSe), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation. RESULTS: The number of unique genes in the AS group (566,526) was higher than that in the HC group (406,609). At the species level, there were no significant differences in Alpha diversity or the overall microbial structure (revealed by PCoA and NMDS) between the two groups (p > 0.05). However, significant differences in abundance were observed at the family, genus, and species levels. DESeq2 identified a total of 43 differential species, among which 22 species had increased abundance and 21 species had decreased abundance in the AS group. LEfSe analysis showed that the HC group had 16 dominant bacterial species, while the AS group had only Neoporus faecalis as the dominant species. There were differences in KEGG Level 3 functional pathways between the two groups, but no statistically significant difference was found in the overall functional structure (p = 0.698). Functional enrichment analysis revealed that AS-specific genes were primarily enriched in neurodegenerative disease pathways, protein processing in the endoplasmic reticulum, and autophagy-related pathways, with substantial contributions from genera including Bacteroides, Streptococcus, Eubacterium, and Faecalibacterium. However, neither individual differential species nor their functional pathways showed significant correlations with clinical disease activity scores (BASDAI and VAS)。. CONCLUSION: The studies indicated that although there was no significant difference in the overall diversity of intestinal microbiota between AS patients and healthy individuals, there were obvious distinctions in genetic composition, specific bacterial species, and functional pathways, suggesting that intestinal microorganisms may be involved in the pathogenesis of AS.},
}

Humans
*Spondylitis, Ankylosing/microbiology
Male
Adult
Female
*Gastrointestinal Microbiome/genetics
*Metagenomics
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Biodiversity

@article {pmid41961352,
year = {2026},
author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H},
title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.},
journal = {Neurochemical research},
volume = {51},
number = {2},
pages = {},
pmid = {41961352},
issn = {1573-6903},
mesh = {Animals ; *Toll-Like Receptor 4/metabolism ; Male ; *Depression/drug therapy/metabolism ; *Isoflavones/therapeutic use/pharmacology ; Signal Transduction/drug effects ; *Myeloid Differentiation Factor 88/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *NF-kappa B/metabolism ; Rats ; Rats, Sprague-Dawley ; *Antidepressive Agents/therapeutic use/pharmacology ; Hippocampus/metabolism/drug effects ; },
abstract = {Depression is a highly prevalent mental disorder in which dysfunction of the gut microbiota is implicated as a significant factor in its pathogenesis. Puerarin has been suggested to alleviate depression via the microbe-gut-brain axis (MGBA), although the precise mechanisms remain elusive. This study aimed to elucidate the association between the antidepressant effects of puerarin and its role in regulating intestinal flora imbalance and inhibiting subsequent activation of the LPS/TLR4 inflammatory pathway from metabolomics and metagenomics perspectives. A rat model of depression was established using a 6-week chronic unpredictable mild stress (CUMS) protocol. Depressive-like behaviors were assessed through the sucrose preference test (SPT), forced swim test (FST), and open field test (OFT). Inflammatory cytokines (TNF-α, IL-1β, IL-6), LPS, corticosterone, and 5-HT were measured via ELISA. Hippocampal and colonic protein expression of TLR4, MyD88, IκBα, and NF-κB was analyzed by western blot. Colon tissue integrity was evaluated using H&E staining, PAS staining, and transmission electron microscopy. Immunofluorescence was employed to detect Iba-1+ microglia, TLR4+ cells, and ZO-1 expression. Fecal metabolomics and metagenomics were conducted to identify differential metabolites and microbial composition, followed by KEGG and KO enrichment analyses to predict relevant pathways. Spearman correlation analysis was used to explore relationships among gut microbiota, metabolites, and behavioral indices. Puerarin markedly ameliorated depression-like behaviors in CUMS rats. Concurrently, puerarin inhibited the LPS/TLR4 signaling pathway and its downstream pro-inflammatory mediators in both the hippocampus and colon, resulting in a significant reduction in inflammatory responses across these regions, as well as in the serum. Metagenomic sequencing revealed that puerarin suppressed inflammation-associated bacteria, enhanced the abundance of Firmicutes, and induced alterations in the microbial community structure and composition. Metabolomic analysis demonstrated that puerarin could counteract dysregulated fecal metabolism, identifying 17 metabolites as potential key mediators in restoring metabolic homeostasis in CUMS rats. These biomarkers were implicated in several metabolic pathways, including Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, Alanine, Aspartate, and Glutamate metabolism. Puerarin may exert its antidepressant effects by modulating the gut microbial structure and metabolite profiles, thereby alleviating inflammatory stress in the colon, bloodstream, and hippocampus, potentially through inhibition of the LPS/TLR4 signaling pathway.},
}

Animals
*Toll-Like Receptor 4/metabolism
Male
*Depression/drug therapy/metabolism
*Isoflavones/therapeutic use/pharmacology
Signal Transduction/drug effects
*Myeloid Differentiation Factor 88/metabolism
*Gastrointestinal Microbiome/drug effects/physiology
*NF-kappa B/metabolism
Rats
Rats, Sprague-Dawley
*Antidepressive Agents/therapeutic use/pharmacology
Hippocampus/metabolism/drug effects

@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, Ş},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
mesh = {Animals ; *Aquaculture ; *Fishes/microbiology/physiology ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects/physiology ; *Minerals/metabolism/administration & dosage ; Diet/veterinary ; Animal Nutritional Physiological Phenomena ; Gastrointestinal Tract/microbiology ; },
abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.},
}

Animals
*Aquaculture
*Fishes/microbiology/physiology
Dietary Supplements/analysis
Animal Feed/analysis
*Gastrointestinal Microbiome/drug effects/physiology
*Minerals/metabolism/administration & dosage
Diet/veterinary
Animal Nutritional Physiological Phenomena
Gastrointestinal Tract/microbiology

@article {pmid41975427,
year = {2026},
author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P},
title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41975427},
issn = {1746-6148},
support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; },
mesh = {Animals ; *Transcriptome ; Sheep/blood/microbiology ; Female ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; *Milk ; *Milk Substitutes ; Animal Feed/analysis ; },
abstract = {Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.},
}

Animals
*Transcriptome
Sheep/blood/microbiology
Female
*Gastrointestinal Microbiome
*Metagenome
Feces/microbiology
*Milk
*Milk Substitutes
Animal Feed/analysis

@article {pmid41998362,
year = {2026},
author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R},
title = {Early microbial colonization study of daily-use plastics exposed to river water.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998362},
issn = {1573-0972},
mesh = {*Rivers/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Plastics/chemistry ; *Bacteria/classification/genetics/isolation & purification/growth & development ; Biofilms/growth & development ; Phylogeny ; Water Microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Polyethylene ; Polyethylene Terephthalates ; Microbiota ; },
abstract = {In rivers, microorganisms colonize plastic surfaces, initiating processes that can lead to their microbial decomposition. Our study investigates the bacterial community composition and diversity on the surfaces of plastics used daily, such as polyethylene terephthalate (PET) and low-density polyethylene (LDPE), which were exposed to river water from the Aller and Fusche rivers. Glass was used for comparison purposes. 16s rRNA sequencing revealed that the type of surface and the native microbial community in the river water, including the water quality, significantly influenced biofilm community assembly. River water samples, especially from the Fusche site, supported the highest microbial richness, while plastic exhibited moderate diversity, and glass beads hosted the lowest richness and diversity. Proteobacteria and Bacteroidetes dominated across all samples, with notable enrichment of functionally relevant families such as Rhodobacteraceae and Comamonadaceae. Ecologically relevant genera such as Flavobacterium, Hydrogenophaga, Rhodoferax, Sediminibacterium, and Rhodobacter dominated across samples. Alpha diversity reflected the richness of taxa within each sample, while beta diversity revealed distinct clustering based on both plastic type and site, indicating the influence of ecological pressure and niche partitioning. These findings highlight the capacity of plastic surfaces to harbour diverse and specialised bacterial assemblages, with implications for biogeochemical cycling, pollutant interactions, and potential microbial degradation pathways. This work contributes to deciphering the ecological roles of biofilms in freshwater plastisphere micro-environments and underscores the importance of material-specific microbial dynamics in assessing environmental risks.},
}

*Rivers/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Plastics/chemistry
*Bacteria/classification/genetics/isolation & purification/growth & development
Biofilms/growth & development
Phylogeny
Water Microbiology
Biodiversity
DNA, Bacterial/genetics
Polyethylene
Polyethylene Terephthalates
Microbiota

@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
mesh = {Humans ; Infant ; *Proctocolitis/microbiology/etiology ; *Food Hypersensitivity/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics/methods ; *Dietary Proteins/adverse effects ; Metagenome ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood. METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages. RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution. CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.},
}

Humans
Infant
*Proctocolitis/microbiology/etiology
*Food Hypersensitivity/microbiology
Female
Male
*Gastrointestinal Microbiome
Feces/microbiology
Metagenomics/methods
*Dietary Proteins/adverse effects
Metagenome

@article {pmid42012708,
year = {2026},
author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P},
title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42012708},
issn = {1436-6215},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Alcohol Drinking/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Aged ; Risk Factors ; *Carcinogenesis ; Feces/microbiology ; },
abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood. OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions. METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis. RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria. CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology
*Alcohol Drinking/adverse effects
*Gastrointestinal Microbiome
Male
Middle Aged
Female
Aged
Risk Factors
*Carcinogenesis
Feces/microbiology

@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42014993},
issn = {1471-2180},
mesh = {Animals ; Female ; Pregnancy ; Swine ; *Coronavirus Infections/veterinary/microbiology/virology ; Multiomics ; *Diarrhea/microbiology/veterinary/virology/metabolism ; *Swine Diseases/microbiology/virology/metabolism ; *Porcine epidemic diarrhea virus ; *Metabolome ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.},
}

Animals
Female
Pregnancy
Swine
*Coronavirus Infections/veterinary/microbiology/virology
Multiomics
*Diarrhea/microbiology/veterinary/virology/metabolism
*Swine Diseases/microbiology/virology/metabolism
*Porcine epidemic diarrhea virus
*Metabolome
Feces/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Gastrointestinal Microbiome
Metagenomics

@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42045813},
issn = {1471-2180},
mesh = {Humans ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/drug therapy ; Female ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; Mesalamine/therapeutic use ; Male ; Adrenal Cortex Hormones/therapeutic use ; Adult ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Middle Aged ; Crohn Disease/microbiology/drug therapy ; Colitis, Ulcerative/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome. METHODS: Fecal samples from 16 Crohn’s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy. RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the “pyrazinamide resistant rpsA” gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan). CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).},
}

Humans
Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/drug therapy
Female
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
Mesalamine/therapeutic use
Male
Adrenal Cortex Hormones/therapeutic use
Adult
Anti-Bacterial Agents/pharmacology
Metagenomics
Middle Aged
Crohn Disease/microbiology/drug therapy
Colitis, Ulcerative/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics

@article {pmid42080548,
year = {2026},
author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S},
title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0016326},
pmid = {42080548},
issn = {2379-5077},
support = {2021ZD0201900//Ministry of Science and Technology of the People's Republic of China/ ; 82071030//National Natural Science Foundation of China/ ; 82071029//National Natural Science Foundation of China/ ; 18DZ2260200//Science and Technology Commission of Shanghai Municipality/ ; },
mesh = {Animals ; *Hypoxia/complications/metabolism/microbiology ; Mice ; Male ; *Fatty Liver/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Disease Models, Animal ; Sleep Apnea, Obstructive/complications/metabolism ; Metabolomics ; },
abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.},
}

Animals
*Hypoxia/complications/metabolism/microbiology
Mice
Male
*Fatty Liver/metabolism/microbiology/etiology
*Gastrointestinal Microbiome
Humans
Liver/metabolism/pathology
Mice, Inbred C57BL
Disease Models, Animal
Sleep Apnea, Obstructive/complications/metabolism
Metabolomics

@article {pmid42148776,
year = {2026},
author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y},
title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0029226},
pmid = {42148776},
issn = {2379-5077},
support = {82373960, 81974513//National Natural Science Foundation of China/ ; 2025ZZTS0793//Fundamental Research Funds for Central Universities of the Central South University/ ; 2023JJ30891, 2025JJ50675, 2026JJ50342//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Bile Acids and Salts/metabolism ; Male ; *Fatty Liver/metabolism/microbiology ; Liver/metabolism/pathology ; Receptors, Cytoplasmic and Nuclear/metabolism ; Disease Models, Animal ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Receptor, Farnesoid X-Activated ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; Cholesterol 7-alpha-Hydroxylase/metabolism ; },
abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.

IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.},
}

Animals
Mice
Humans
*Gastrointestinal Microbiome
Bile Acids and Salts/metabolism
Male
*Fatty Liver/metabolism/microbiology
Liver/metabolism/pathology
Receptors, Cytoplasmic and Nuclear/metabolism
Disease Models, Animal
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Receptor, Farnesoid X-Activated
RNA, Ribosomal, 16S/genetics
Signal Transduction
Cholesterol 7-alpha-Hydroxylase/metabolism

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0030526},
pmid = {42171373},
issn = {2379-5077},
support = {K08AI159619//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/genetics/immunology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacterial Toxins/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Machine Learning ; Computational Biology/methods ; },
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

Humans
*Dysbiosis/microbiology/genetics/immunology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
*Bacterial Toxins/genetics
*Metagenome
*Bacteria/genetics/classification
*Microbiota/genetics
Machine Learning
Computational Biology/methods

@article {pmid42212786,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E},
title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0171425},
pmid = {42212786},
issn = {2379-5077},
support = {PUT 1371, PRG1414//Estonian Research Competency Council/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; MEiN/2023/DIR/3796//Ministerstwo Edukacji i Nauki/ ; PLG/2023/016234,PLG/2024/017180//Infrastruktura PL-Grid/ ; TT17//Estonian Center of Genomics/Roadmap II, funded by the Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; },
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.

IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
Sequence Analysis, DNA/methods

@article {pmid42212790,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T},
title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0014426},
pmid = {42212790},
issn = {2379-5077},
support = {PUT 1371, PRG1414//Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; 2025/56/C/NZ2/00481//NCN Sonatina/ ; 2020/38/E/NZ2/00598//NCN Sonata BIS/ ; MEiN/2023/DIR/3796//Minister of Science and Higher Education/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Humans ; },
abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.},
}

*Microbiota/genetics
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
Humans

@article {pmid42227741,
year = {2026},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0018826},
pmid = {42227741},
issn = {2379-5077},
support = {U54AG089323/NH/NIH HHS/United States ; P30AI045008/NH/NIH HHS/United States ; U19AI174998/NH/NIH HHS/United States ; },
mesh = {Humans ; *Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Feces/virology ; DNA, Viral/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Saliva/virology ; Bacteriophages/genetics ; },
abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.},
}

Humans
*Virome/genetics
Genome, Viral
High-Throughput Nucleotide Sequencing/methods
Feces/virology
DNA, Viral/genetics
*Metagenomics/methods
Sequence Analysis, DNA/methods
Saliva/virology
Bacteriophages/genetics

@article {pmid42233644,
year = {2026},
author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M},
title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0149825},
pmid = {42233644},
issn = {2379-5077},
support = {//March of Dimes Prematurity Research Center at UCSF/ ; },
mesh = {Female ; Humans ; *Microbiota/genetics ; *Vagina/microbiology ; *Lactobacillus crispatus/genetics ; *Uterine Cervical Dysplasia/microbiology ; Databases, Genetic ; Metagenomics/methods ; Genome, Bacterial ; },
abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.},
}

Female
Humans
*Microbiota/genetics
*Vagina/microbiology
*Lactobacillus crispatus/genetics
*Uterine Cervical Dysplasia/microbiology
Databases, Genetic
Metagenomics/methods
Genome, Bacterial

@article {pmid42348560,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0352336},
pmid = {42348560},
issn = {1932-6203},
mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; },
abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.},
}

Animals
*Dairying/methods
*Microbiota/genetics
Cattle
Milk/microbiology
Farms
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial/genetics
Metagenome
Metagenomics
Organic Agriculture

@article {pmid42350342,
year = {2026},
author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T},
title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {6},
pages = {499-510},
pmid = {42350342},
issn = {1007-8738},
mesh = {Animals ; *HLA-B27 Antigen/genetics/metabolism ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/genetics/metabolism ; Mice, Transgenic ; Humans ; Mice ; *Inflammation ; Female ; Dextran Sulfate ; },
abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.},
}

Animals
*HLA-B27 Antigen/genetics/metabolism
*Gastrointestinal Microbiome
*Colitis/microbiology/chemically induced/genetics/metabolism
Mice, Transgenic
Humans
Mice
*Inflammation
Female
Dextran Sulfate

@article {pmid40830751,
year = {2025},
author = {Ahmad, AA and Fletcher, K and Hesford, N and Glendinning, L},
title = {Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {520},
pmid = {40830751},
issn = {1471-2180},
support = {BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Chancellor's Fellowship//University of Edinburgh/ ; },
mesh = {Animals ; *Galliformes/microbiology ; *Metagenomics/methods ; *Dietary Fiber/metabolism ; Fermentation ; Cecum/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Scotland ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The avian caecal microbiota plays a vital role in host nutrition, enabling non-digestible, fibrous material to be converted into compounds that can be absorbed and used as an energy source by the host. The diet of adult red grouse (Lagopus scotica) is dominated by heather (Calluna vulgaris), which is particularly high in fibre. It is therefore likely that the caecal microbiota plays a key role in enabling grouse to thrive on this diet. In this study, we present the first characterisation of the caecal microbiota of red grouse using modern sequencing methods. RESULTS: We performed metagenomic sequencing on caecal content samples from fifteen red grouse from three upland estates in Scotland. From this data, we constructed and characterised twelve high-quality, species-level metagenome assembled genomes (MAGs). Eleven of these MAGs could not be assigned a taxonomic label at species level, indicating that they may be novel species. MAGs belonged to diverse taxa (5 phyla) and several encoded genes and pathways for the digestion of fibres, including cellulose, hemi-cellulose, xylooligosaccharides and pectin. Several MAGs also contained antimicrobial resistance genes, predominantly related to vancomycin resistance. CONCLUSIONS: This study is the first to reconstruct commensal microbial genomes from red grouse. The caeca contain diverse, often novel, microbial taxa capable of fermenting various fibres, potentially aiding in the digestion of the red grouse’s high-fibre diet. Further research is necessary to explore how these bacteria support red grouse nutrition and health.},
}

Animals
*Galliformes/microbiology
*Metagenomics/methods
*Dietary Fiber/metabolism
Fermentation
Cecum/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
Scotland
Metagenome
Phylogeny
*Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA

@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
mesh = {*Mycorrhizae/physiology ; *Rhizosphere ; *Nicotiana/growth & development/microbiology ; *Seedlings/growth & development/microbiology ; Soil Microbiology ; Plant Roots/microbiology/growth & development ; Microbiota ; },
abstract = {BACKGROUND: Numerous studies have demonstrated significant variations in the plant growth-promoting effects among different species of arbuscular mycorrhizal fungi (AMF). However, the underlying mechanisms remain incompletely understood, particularly regarding how distinct AMF species regulate the rhizosphere microbiome. RESULTS: Five AMF species (Funneliformis mosseae, Diversispora versiformis, Clariodeoglous etunicatum, Rhizophagus intraradices, and Acaulospora delicate) were inoculated to investigate their effects on tobacco seedling growth and rhizosphere microecological regulation. The results showed that all AMF inoculations significantly increased shoot and root biomass, N/P/K uptake, morphological traits (height, stem diameter, leaf area), chlorophyll content (SPAD), and root architecture (length, surface area, volume, diameter) of tobacco seedlings. Among them, the treatment inoculated with R. intraradices showed the most outstanding growth-promoting effect in all growth indicators. Metagenomic analysis indicated that AMF inoculation significantly altered the diversity and community structure of rhizosphere substrate microorganisms. Among them, R. intraradices inoculation yielded the highest microbial diversity, with an associated network exhibiting enhanced complexity. KEGG functional annotation revealed metabolic pathways (IAA biosynthesis, iron-siderophore transport regulation, exopolysaccharide production, and nutrient cycling) consistently associated with tobacco growth promotion in all AMF inoculations. However, species-specific mechanisms were observed: F. mosseae promotes tobacco seedling growth by enhancing IAA synthesis through the recruitment of beneficial microorganisms such as Nostoc, Flavisolibacter, Frateuria, and Sphingomonas. D. versiformis enhanced carbon fixation via the hydroxypropionate-hydroxybutyrate cycle, driven by the proliferation of Glaciecola, Pedococcus, Phycicoccus, and Hephaestia. C. etunicatum facilitated phosphorus/iron accumulation through organic phosphorus mineralization, phosphate transport, and iron acquisition accompanied by the recruitment of, Hartmannibacter, Lysobacter, Moheibacter, and Pseudolabrys. R. intraradices improved nitrogen assimilation through augmented nitrogen transport and assimilatory nitrate reduction (ANRA), correlated with the recruitment of Azospirillum, Sphingobium, Mesorhizobium, Paracoccus, and Parafilimonas. A. delicate stimulated plant growth via polyphosphate degradation and exopolysaccharide biosynthesis, associated with the enrichment of Segetibacter, Ferruginibacter, Hyphomicrobium and Pseudomonas. Notably, this study revealed that functional divergence in rhizosphere microbiomes associated with the five tested fungal species was primarily reflected in the abundance rather than the composition of functional genes. CONCLUSION: In summary, AMF inoculation significantly enhanced tobacco seedling biomass and agronomic traits by improving mineral nutrient assimilation efficiency and restructuring the rhizosphere microbial community. Different AMF species exhibited distinct microecological regulation patterns. This study elucidated the growth-promoting mechanisms of AMF from a microbial interaction perspective, providing a theoretical basis for establishing a sustainable tobacco cultivation system.},
}

*Mycorrhizae/physiology
*Rhizosphere
*Nicotiana/growth & development/microbiology
*Seedlings/growth & development/microbiology
Soil Microbiology
Plant Roots/microbiology/growth & development
Microbiota

@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1915},
pmid = {41345617},
issn = {1472-6831},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Mouth/microbiology ; Secondary Data Analysis ; *Microbiota ; },
abstract = {With an astounding global prevalence, both diabetes mellitus and gum disease pose significant health concerns. Gum disease has been identified as a risk factor for diabetes mellitus, and its treatment has shown improvements in markers of glucose management. We hypothesised that bacteria commonly associated with the oral microbiome could be disproportionately present in the gut of individuals with type 2 diabetes mellitus (T2DM) compared to healthy controls, suggesting a possible association between oral-associated bacteria and metabolic dysregulation. This hypothesis is supported by known interactions between the oral microbiome and systemic health, particularly the role of inflammation in both conditions. Therefore, we aimed to conduct a secondary analysis of whole-genomic sequencing data of studies published over the last twenty years (2004–2024) related to the gut microbiome of patients with T2DM to identify oral-associated bacteria in their gut compared to healthy individuals. We searched for studies related to the gut microbiome, whole metagenomics, and T2DM in Ovid Medline, EMBASE, and Web of Science databases. Studies that included whole metagenomic data from adult populations of all genders with T2DM were selected, resulting in the reanalysis of metagenomic sequencing data from a total of 9 studies (n = 1,224 metagenomes) for bacterial species data. From the 41,689 gut microbial species identified across the selected studies, 497 were classified as of oral-associated bacteria, corresponding with entries in the Human Oral Microbiome Database (HOMD). These oral bacteria comprised 1.19% of the gut microbiome. Notably, twenty oral-associated bacterial species were statistically significant in their presence among patients with diabetes compared to healthy individuals, irrespective of their abundance. Key oral pathogens included Corynebacterium striatum, Staphylococcus capitis, Kingella kingae, Corynebacterium propinquum, Prevotella sp. oral taxon 820, Prevotella scopos, Selenomonas artemidis, Bordetella pertussis, Selenomonas sp. oral taxon 137, and Staphylococcus hominis. Specifically, periodontal pathogens such as, Porphyromonas gingivalis, Tannerella forsythia, and Capnocytophaga sp. oral taxon 332 were found to be significantly higher in patients with T2DM. These bacteria are associated with conditions like endocarditis, bacteremia, and inflammatory responses, which are prevalent in both diabetes and periodontitis. Although causal relationships cannot be directly established, our findings suggest that bacteria typically originating from the oral cavity may be more prevalent in the gut microbiome of patients with T2DM, supporting the potential role of oral-gut microbial interactions in metabolic dysregulation.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology
*Gastrointestinal Microbiome
Metagenomics
*Mouth/microbiology
Secondary Data Analysis
*Microbiota

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {84},
pmid = {41390654},
issn = {1479-5876},
mesh = {*Breast Neoplasms/microbiology/genetics/metabolism ; Humans ; *Siderophores/metabolism ; Female ; *Escherichia coli/metabolism/genetics ; *Metagenomics/methods ; Multivariate Analysis ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Breast cancer remains a leading cause of cancer-related mortality in women. Recent evidence implicates the gut microbiome and metabolites in breast cancer pathogenesis. This study explores associations between gut microbial species, their predicted metabolites, and breast cancer to uncover potential mechanistic insights. METHODS: Comprehensive metagenomic analyses were conducted on the gut microbiome of pre- and postmenopausal breast cancer patients, where microbial species were profiled through AMPHORA2 and metabolites were predicted through antiSMASH. Multivariate association analysis was used to identify significant associations between specific microbial species, predicted metabolites, and breast cancer status. A custom ensemble machine learning classifier was developed to classify pre- and postmenopausal breast cancer cases and controls based on microbial and predicted metabolite features. Additionally, a synthetic microbiome dataset was generated through MIDASim to validate the reproducibility of the ML results. Using our results, we explored the underlying dynamics of identified taxa and metabolite in breast cancer through literature and statistical support. RESULTS: Our analysis identified 471 microbial species and predicted 40 key metabolites in the metagenomic data. Multivariate analysis identified significant positive associations (p-value < 0.05) of E. coli, siderophore, and thiopeptide with breast cancer. The custom ensemble model achieved accuracy and AUC as high as 78% and 90%, respectively, in classifying pre- and postmenopausal cases and controls. The high-ranking features i.e., E. coli, siderophore, and thiopeptide were consistent with the results of the multivariate association analysis, thereby substantiating their biological significance. Using these findings, we propose a mechanistic model in which E. coli secretes siderophores under iron-limited conditions in breast cancer patients, for iron sequestration from the host, which can potentially promote angiogenesis and tumor progression. CONCLUSION: Our findings suggest that microbial iron acquisition mechanisms may play a critical role in breast cancer pathophysiology. Functional validation of these mechanisms is needed to assess therapeutic potential. This study highlights gut microbiota and their metabolites as promising targets for breast cancer research and intervention.},
}

*Breast Neoplasms/microbiology/genetics/metabolism
Humans
*Siderophores/metabolism
Female
*Escherichia coli/metabolism/genetics
*Metagenomics/methods
Multivariate Analysis
Gastrointestinal Microbiome/genetics

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1211},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
mesh = {Animals ; Bees/microbiology/drug effects ; *Neonicotinoids/toxicity/adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; *Dysbiosis/chemically induced/microbiology ; *Insecticides/toxicity ; Guanidines/toxicity ; Thiamethoxam ; Metagenome ; Thiazoles/toxicity ; },
abstract = {The Western honey bee (Apis mellifera) plays an essential role in agriculture around the world. In Canada, honey bees contribute up to $7 billion in economic value annually by pollinating crops and producing honey. However, since 2006–2007 North American beekeepers have lost more than a quarter of their colonies each winter. In recent years, the losses have been up to 50% in some regions. The causes of losses are complex, including the interacting effects of nutrition, pathogens, and pesticides. Although the bee gut microbiome plays a crucial role in colony health and disease, studies on the effects of agricultural pesticides on the bee microbial community are sparse. We report the use of shotgun metagenomic sequencing to investigate bee gut microbiota changes, or dysbiosis, in response to two neonicotinoid insecticides, clothianidin and thiamethoxam. Common dysbiosis signatures included an increase in Bifidobacterium spp. after chronic sublethal exposure and an increase in Apibacter adventoris after short-term acute exposure. Other dysbiosis signatures were unique to each compound, such as an increase in Snodgrassella alvi for clothianidin and a decrease in Lactobacillus spp. for thiamethoxam. These findings enhance our understanding of how the honey bee gut microbiome responds to stressors and highlight identifiable microbial profile signatures which underscores the potential utility of gut microbiome profiling as a bee health diagnostic tool. Access to timely and accurate bee health diagnosis will inform regulatory actions to decrease and mitigate exposure to stressors and will facilitate managing and improving bee health.},
}

Animals
Bees/microbiology/drug effects
*Neonicotinoids/toxicity/adverse effects
*Gastrointestinal Microbiome/drug effects/genetics
Metagenomics/methods
*Dysbiosis/chemically induced/microbiology
*Insecticides/toxicity
Guanidines/toxicity
Thiamethoxam
Metagenome
Thiazoles/toxicity

@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {219},
pmid = {41469598},
issn = {1471-2334},
mesh = {Humans ; *Lung/microbiology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Tuberculosis/drug therapy/microbiology ; *Antitubercular Agents/therapeutic use ; *Microbiota/drug effects ; Metagenome ; },
abstract = {BACKGROUND: Tuberculosis (TB) remains the leading cause of bacterial disease-related mortality worldwide. While Koch’s single-agent model has long guided TB diagnostics and treatment, metagenomic studies reveal a resident lung microbiome disrupted by TB and its orally administered therapy, with downstream effects on the gut microbiome. Understanding these disruptions may uncover diagnostic and prognostic indicators. We systematically reviewed 38 studies involving 3394 individuals with TB and healthy controls across four continents to assess the impact of TB and its treatment on lung and gut microbiome diversity, structure, and composition. A meta-analysis of 29 studies and a patient-level amplicon metagenomic meta-analysis (AMMA) of 1617 individuals (1.3 billion reads) were conducted following PRISMA guidelines [PROSPERO: CRD42022329763]. RESULTS: No global consensus exists on TB's impact on lung microbial diversity. Pooled estimates suggest a reduction of ~0.14 in lung diversity and 0.41 in gut diversity. Patient-level analyses showed no overall significant difference in lung diversity (Shannon index), though reductions were evident in China but not South Africa. Conversely, gut diversity tended to be higher in TB cases. Disease status explained only 0.8–9% of variation in lung microbiota and 1.8–9% in gut communities. Composition-wise, TB was associated with depletion of anaerobic core lung genera (e.g. Prevotella, Neisseria, Veillonella, Haemophilus, Fusobacterium, Pseudomonas, Streptococcus, Porphyromonas, Treponema) and gut genera (e.g. Prevotella, Ruminococcus, Faecalibacterium, Clostridium, Roseburia, Rothia, Eubacterium, Escherichia). Treatment further reduced diversity at both sites, with additional loss of core taxa. CONCLUSION: TB is generally linked to reduced lung microbial diversity but increased gut diversity, with effects varying by country, suggesting context-specific rather than universal microbial signatures. Treatment consistently decreases diversity in both lung and gut. Although findings here primarily reflect the upper respiratory tract, they highlight potentially exploitable microbial dynamics. Future studies should integrate additional diversity metrics and broader metadata to refine these insights for advancing their clinical utility. CLINICAL TRIAL: Not applicable.},
}

Humans
*Lung/microbiology
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Tuberculosis/drug therapy/microbiology
*Antitubercular Agents/therapeutic use
*Microbiota/drug effects
Metagenome

@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
mesh = {*Vagina/microbiology ; Female ; *Specimen Handling/methods/standards ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; DNA Contamination ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy. RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes. CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.},
}

*Vagina/microbiology
Female
*Specimen Handling/methods/standards
*Microbiota/genetics
Humans
DNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
DNA Contamination

@article {pmid41498995,
year = {2026},
author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A},
title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {32},
pmid = {41498995},
issn = {1573-0972},
support = {42430404//National Natural Science Foundation of China/ ; },
mesh = {*Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Ice Cover/microbiology ; Altitude ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Metagenomics ; Phylogeny ; Ecosystem ; Nitrogen/metabolism ; Shotgun Sequencing ; },
abstract = {High-altitude rivers constitute ideal model systems for studying microbial roles in elemental cycling within complex ecosystems. Previous studies primarily addressed microbial community assembly, specific taxonomic groups, or antibiotic resistance gene risks, resulting in limited understanding of biogeochemical cycling profiles. Here, shotgun metagenomic sequencing was employed to profile the metabolic potential of planktonic and benthic microbiomes in the glacial-fed Rongbu River. We sequenced nine water and nine sediment samples along an altitudinal gradient, reconstructing 279 medium-to-high-quality metagenome-assembled genomes (MAGs), with 246 representing unclassified MAGs. Functional analyses revealed divergent niche specialization between habitats: (i) water MAGs encoded multifunctional carbohydrate-active enzymes (CAZymes), targeting labile polysaccharides while coupling nitrogen-sulfur metabolism to enhance nitrogen assimilation; and (ii) sediment MAGs specialized in complex polysaccharide degradation, exhibiting enriched denitrification and sulfide oxidation genes. Notably, a total of 13 plastic degradation genes (PDGs) were identified, which indicated altitudinal partitioning: high-elevation communities showed PBAT-degrading potential, while low-elevation MAGs harbored PVA-degrading genes. These findings indicated that altitude governed the spatial distribution of distinct biogeochemical potentials in high-altitude rivers. This study advances our understanding of elemental cycling processes in alpine river ecosystems.},
}

*Rivers/microbiology
*Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
*Ice Cover/microbiology
Altitude
*Microbiota/genetics
Geologic Sediments/microbiology
Metagenomics
Phylogeny
Ecosystem
Nitrogen/metabolism
Shotgun Sequencing

@article {pmid41514270,
year = {2026},
author = {González-Rovira, M and Sainz-Bueno, JA and García-Díaz, L and Martínez-Pancorbo, C and Sánchez, J and Gutiérrez, G and Magoutas, K and Mesías-Pérez, A and Mellado, E and Payne, M and Sousa, C and Moreno, ML},
title = {Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {273},
pmid = {41514270},
issn = {1479-5876},
support = {PID2024-157768OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; SUBN/2019/005//Federación de Asociaciones de Celíacos de España (FACE)/ ; US-15332/I+D+I//FEDER ANDALUCIA/ ; },
mesh = {Humans ; *Amniotic Fluid/microbiology ; Female ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/growth & development/isolation & purification ; *Sequence Analysis, DNA/methods ; Antimicrobial Peptides/metabolism ; Microbiota ; },
abstract = {BACKGROUND: The evidence of a low-biomass microbial community in the amniotic fluid (AF) is challenging the traditional concept of a sterile womb. To clarify microbial presence and host responses, a comprehensive, multi-methodological approach is required. METHODS: We designed an optimized culturing strategy that maximized microorganism recovery by implementing differential centrifugation and concentration of AF samples, followed by plating onto four distinct selective media types and incubation under both stringent aerobic (up to two weeks) and prolonged anaerobic (up to four weeks) conditions, including an initial pre-enrichment step in Brain Heart Infusion (BHI) broth for low-abundance organisms. These results were combined with PacBio 16S rRNA gene sequencing, Illumina shotgun metagenomics, and antimicrobial peptides (AMP) detection. Using this approach, we characterized microbial presence in 154 AF samples across gestational stages. Data normality was assessed with the Shapiro-Wilk test, guiding the selection of both parametric and non-parametric tests, and a p-value of < 0.05 was considered statistically significant. RESULTS: We detected culturable microorganisms in 33.1% of samples, with a higher proportion in elective caesarean Sect. (55.0%) compared to amniocentesis (29.5%), suggesting increased microbial load toward term. We applied stringent contamination controls, and repeatedly recovered viable microorganisms Bacillus, Cutibacterium, Micrococcus, and Staphylococcus, with Cutibacterium acnes and Staphylococcus epidermidis common. Both sequencing methods revealed a low-biomass, low-diversity microbial community with high inter-individual variability. Notably, striking microbial discordance in diamniotic twin pregnancies, challenged intrauterine homogeneity. Higher Human Beta Defensin (HBD) -1 levels correlated with absence of culturable bacteria or microbial DNA, while levels of HBD-1, HBD-3, and LL-37 were reduced in Staphylococcus-positive samples, suggesting a dynamic interplay between specific bacteria and host defences. CONCLUSIONS: Our findings indicate that viable bacteria and/or DNA can transiently access the prenatal environment microbial balance. We propose a novel perspective of a potential regulatory axis between microorganisms and AMP.},
}

Humans
*Amniotic Fluid/microbiology
Female
Pregnancy
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/growth & development/isolation & purification
*Sequence Analysis, DNA/methods
Antimicrobial Peptides/metabolism
Microbiota

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
mesh = {Animals ; *Fishes/microbiology ; Fresh Water/microbiology ; *Metagenomics/methods ; Seawater/microbiology ; *Microbiota ; Ecosystem ; Skin Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; Aquaculture ; },
abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.},
}

Animals
*Fishes/microbiology
Fresh Water/microbiology
*Metagenomics/methods
Seawater/microbiology
*Microbiota
Ecosystem
Skin Microbiome
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome
Aquaculture

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Antelopes/microbiology/parasitology/metabolism ; *Blastocystis/physiology ; Metagenome ; *Vitamin B Complex/biosynthesis ; Humans ; },
abstract = {The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Antelopes/microbiology/parasitology/metabolism
*Blastocystis/physiology
Metagenome
*Vitamin B Complex/biosynthesis
Humans

@article {pmid41549250,
year = {2026},
author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J},
title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {},
pmid = {41549250},
issn = {1471-230X},
support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; },
mesh = {Animals ; Female ; *Benzimidazoles/adverse effects ; *Diarrhea/chemically induced/microbiology/blood/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Metabolome ; *Aminopyridines/adverse effects ; Rats ; *Metagenome ; Rats, Sprague-Dawley ; Intestinal Mucosa/pathology ; },
abstract = {Abemaciclib-induced diarrhea is a common side effect of HR+/ HER2 − breast cancer treatment. The aim of this study was to explore changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea. Female rats were randomly divided into abemaciclib (orally administered abemaciclib, n = 12) and control (orally administered 0.9% saline, n = 6) groups. When the rats reached grade 3 diarrhea, the jejunum, ileum, and colon tissues were collected for histological analysis to assess intestinal mucosal damage. Rat feces were obtained for metagenomic analysis to analyze changes in the gut microbial composition. Rat plasma was used for untargeted metabolomic analysis to analyze plasma metabolic alterations. Pearson’s correlation analysis was conducted to examine the association between differential gut microbiota and differential plasma metabolites, and a microbiota-metabolite-pathway network was constructed. Rats in the abemaciclib group developed noticeable diarrhea and exhibited histopathological changes in the ileal epithelium and jejunum. In the abemaciclib group, α-diversity indices (Shannon, Simpson, and Invsimpsom) were significantly lower than in the control group, with reductions of 0.5, 0.01, and 52.77, respectively. Firmicutes, Bacteroidetes, and Proteobacteria were the most abundant phyla in all groups. Compared with the control group, the abundance of Firmicutes remarkably decreased in the abemaciclib group, whereas that of Proteobacteria and Verrucomicrobia dramatically increased. Differentially abundant species in the abemaciclib group included Escherichia coli, Butyricimonas virosa, Desulfovibrionaceae bacterium, and Helicobacter ganmani. Functional analysis showed that pathways related to carbohydrate metabolism were significantly altered. Additionally, 319 metabolites were differentially expressed between the two groups, including trimethylamine N-oxide, sarsasapogenin, tyrosol, brinzolamide, and cis-3-hexenyl acetate. Multiple pathways, including mTOR signaling pathway, were significantly enriched by differential metabolites. Furthermore, close associations between differential microbiota and metabolites were observed, and numerousmicrobiota-metabolite-pathway axes were identified, such as Pseudodesulfovibrio mercurii/Desulfovibrionaceae bacterium-cis-3-hexenyl acetate-alpha-linolenic acid metabolism. Our findings revealed that abemaciclib alters the gut microbiota composition, plasma metabolite profiles, and their related metabolic pathways in SD rats, and these changes are closely associated with the occurrence of diarrhea. However, this association does not establish a causal relationship, and further in-depth mechanistic studies are required for validation.},
}

Animals
Female
*Benzimidazoles/adverse effects
*Diarrhea/chemically induced/microbiology/blood/pathology/metabolism
*Gastrointestinal Microbiome/drug effects/genetics
*Feces/microbiology
*Metabolome
*Aminopyridines/adverse effects
Rats
*Metagenome
Rats, Sprague-Dawley
Intestinal Mucosa/pathology

@article {pmid41588320,
year = {2026},
author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X},
title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41588320},
issn = {1471-2180},
support = {32402705//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; *Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification ; Fatty Acids, Volatile/analysis/metabolism ; *Gastrointestinal Microbiome ; Archaea/classification/genetics/isolation & purification ; *Host Microbial Interactions ; *Viruses/classification/genetics/isolation & purification ; Rumen/microbiology ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing. RESULTS: The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups. CONCLUSIONS: These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.},
}

Animals
Cattle/growth & development/microbiology
*Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification
Fatty Acids, Volatile/analysis/metabolism
*Gastrointestinal Microbiome
Archaea/classification/genetics/isolation & purification
*Host Microbial Interactions
*Viruses/classification/genetics/isolation & purification
Rumen/microbiology
Metagenomics
Metagenome

@article {pmid41593136,
year = {2026},
author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S},
title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3724},
pmid = {41593136},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Deer/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Diet ; Seasons ; Bacteria/genetics/classification ; *Animal Feed/analysis ; },
abstract = {Plant secondary compounds (PSCs) impose physiological and nutritional constraints on herbivores, yet many species continue to rely on PSC-rich forage during critical periods of the year. Moose (Alces alces) on Isle Royale National Park depend heavily on balsam fir (Abies balsamea) during winter, exposing them to a chemically defended and nutritionally limited diet. To investigate how this foraging strategy shapes both physiological responses and gut microbial communities, we integrated fecal diet composition, urinary markers of detoxification and nutritional status, 16S rRNA gene sequencing, and shotgun metagenomic profiling from free ranging moose of two separated populations from the western and eastern region of the island. Balsam fir consumption varied strongly by region and was positively associated with glucuronic acid to creatinine (GA:C) and urea nitrogen to creatinine (UN:C) ratios, indicating increased detoxification activity and reduced nutritional condition. Microbial alpha diversity declined with higher fir intake in nutritionally limited individuals, while beta diversity differed by region, balsam fir consumption, and UN:C. Several bacterial genera responded to PSC exposure, including increases in the butyrate-producing genus Roseburia and shifts in network prominence of Phascolarctobacterium. Metagenomic data revealed pathways involved in the degradation of aromatic and terpenoid PSCs, although pathway abundances did not differ significantly with balsam fir consumption after multiple testing correction. These results show that winter foraging on balsam fir produces coordinated dietary, physiological, and microbial patterns, with both host and gut microbial detoxification capacities interacting to accommodate the chemical and nutritional challenges of a PSC-rich winter diet.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Deer/microbiology/physiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Diet
Seasons
Bacteria/genetics/classification
*Animal Feed/analysis

@article {pmid41604101,
year = {2026},
author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R},
title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {47},
pmid = {41604101},
issn = {1678-4405},
support = {952583//H2020 European Research Council/ ; },
mesh = {Humans ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.},
}

Humans
*Nanopore Sequencing/methods
*DNA, Bacterial/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Metagenomics/methods
High-Throughput Nucleotide Sequencing

@article {pmid41606550,
year = {2026},
author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X},
title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {41606550},
issn = {1471-2466},
support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; },
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Aspergillus fumigatus/isolation & purification ; *Respiration, Artificial/adverse effects ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Risk Factors ; China/epidemiology ; *Microbiota ; *Pneumonia/microbiology/mortality ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {AIM OF THE STUDY: Invasive aspergillosis is a life-threatening complication in mechanically ventilated patients with pneumonia, predominantly caused by Aspergillus fumigatus. However, its independent mortality risk and early-warning strategies in critically ill populations remain unclear. METHODS: In this multicenter retrospective cohort study, we enrolled 1567 mechanically ventilated patients with severe pneumonia who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) across 12 tertiary hospitals in China (January 2019–March 2023). Propensity score matching (1:1) balanced confounders, and Cox regression quantified the independent mortality risk of A. fumigatus infection. RESULTS: The A. fumigatus detection rate was 10.27% (161/1567). Post-matching, 28-day mortality was significantly higher in A. fumigatus-positive versus negative cohorts (66% vs 47%, p = 0.001). Multivariable analysis confirmed A. fumigatus as an independent mortality risk factor (HR = 1.79, 95%CI 1.49–2.17, p < 0.001), with significant associations to underlying renal disease (19% vs 12%, p = 0.005), connective tissue disease (7% vs 4%, p = 0.026), and multi-organ dysfunction (ep < 0.05). Microbial community analysis revealed co-colonization synergies with Enterococcus faecium, Enterococcus faecalis, Candida albicans, HSV-1, and EBV. CONCLUSIONS: A. fumigatus infection independently increases 28-day mortality risk in mechanically ventilated patients. Early intensified screening and intervention are warranted for individuals with ≥ 3 organ dysfunctions, underlying renal/connective tissue diseases, or respiratory co-colonization by synergistic microbes.},
}

Humans
Male
Female
Retrospective Studies
*Aspergillus fumigatus/isolation & purification
*Respiration, Artificial/adverse effects
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Aged
Risk Factors
China/epidemiology
*Microbiota
*Pneumonia/microbiology/mortality
High-Throughput Nucleotide Sequencing
Metagenomics

@article {pmid41612181,
year = {2026},
author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X},
title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41612181},
issn = {1471-2180},
support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; },
mesh = {Humans ; *Altitude ; China/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology ; *Adenoma/microbiology ; Male ; Female ; Archaea/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA). METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status. RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations. CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.},
}

Humans
*Altitude
China/epidemiology
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/epidemiology
*Adenoma/microbiology
Male
Female
Archaea/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid41618136,
year = {2026},
author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX},
title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41618136},
issn = {1471-2180},
support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Antelopes/microbiology ; *Gastrointestinal Microbiome/genetics ; Tibet ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; Metagenome ; Amidohydrolases/genetics ; Genome, Bacterial ; },
abstract = {BACKGROUND: The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations. RESULTS: This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience. CONCLUSIONS: In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.},
}

Animals
*Bile Acids and Salts/metabolism
*Antelopes/microbiology
*Gastrointestinal Microbiome/genetics
Tibet
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
Metagenome
Amidohydrolases/genetics
Genome, Bacterial

@article {pmid41629500,
year = {2026},
author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y},
title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6991},
pmid = {41629500},
issn = {2045-2322},
support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/metabolism ; *Feces/microbiology/chemistry ; *Metabolic Networks and Pathways ; Female ; Male ; Biomarkers ; Adult ; Metabolomics/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolome ; Dysbiosis/microbiology/metabolism ; Metagenomics ; },
abstract = {Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.},
}

Humans
*Crohn Disease/microbiology/metabolism
*Feces/microbiology/chemistry
*Metabolic Networks and Pathways
Female
Male
Biomarkers
Adult
Metabolomics/methods
*Gastrointestinal Microbiome
*Microbiota
Metabolome
Dysbiosis/microbiology/metabolism
Metagenomics

@article {pmid41629813,
year = {2026},
author = {Astudillo-Guerrero, C and Garrido, Á and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G},
title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).},
journal = {BMC geriatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41629813},
issn = {1471-2318},
mesh = {Humans ; Double-Blind Method ; *Fecal Microbiota Transplantation/methods ; Aged ; *Aging/physiology ; Male ; Female ; Aged, 80 and over ; *Sarcopenia/therapy ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; },
abstract = {BACKGROUND: Sarcopenia, characterized by the progressive loss of skeletal muscle mass and strength in older adults, is a key determinant of frailty and functional decline. Affecting up to 15% of individuals aged 65–80 years and more than 50% of those over 80, sarcopenia not only compromises physical autonomy but also increases the risk of metabolic dysfunction and cognitive decline. Emerging evidence suggests that age-related gut microbiota dysbiosis contributes to these impairments by reducing microbial diversity and altering host metabolic signaling, leading to chronic inflammation and mitochondrial dysfunction. The present study aims to evaluate the safety, tolerability, and preliminary efficacy of oral fecal microbiota transplantation derived from young, physically active donors administered to older adults, focusing on outcomes related to functional autonomy, muscle performance, metabolism and cognition. METHODS: This is a double-blind, randomized, placebo-controlled clinical trial involving community-dwelling adults aged 65–84 years. Participants will be randomized 1:1 to receive either FMT capsules or placebo following a short course of oral rifaximin (or placebo). Assessments will be performed at baseline and at 4, 8, and 20 weeks post-intervention. The primary outcomes are safety and tolerability, as well as changes in the Global Index of Functional Autonomy (GDLAM battery) and muscle strength. Secondary outcomes include gait speed, body composition (DXA), metabolic biomarkers, gut microbiota composition (shotgun metagenomics), cognitive performance, and psychological well-being. EXPECTED IMPACT: By restoring microbial diversity and function, FMT from young, active donors may enhance muscle quality, cognitive resilience, and metabolic health in older adults. This study introduces a novel, non-invasive therapeutic approach based on lyophilized and encapsulated microbiota, offering a feasible and scalable strategy to promote healthy aging. TRIAL REGISTRATION: ClinicalTrials.gov NCT06649981. Date of registration October 21, 2024.},
}

Humans
Double-Blind Method
*Fecal Microbiota Transplantation/methods
Aged
*Aging/physiology
Male
Female
Aged, 80 and over
*Sarcopenia/therapy
Randomized Controlled Trials as Topic
Gastrointestinal Microbiome/physiology
*Exercise/physiology

@article {pmid41629888,
year = {2026},
author = {Luo, M and Xiao, X and Wu, Y},
title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41629888},
issn = {1471-2431},
support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; },
mesh = {Humans ; *Phototherapy ; *Hyperbilirubinemia, Neonatal/therapy/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Metagenomics ; Male ; Feces/microbiology ; Female ; },
abstract = {BACKGROUND: Phototherapy serves as the primary treatment for neonatal hyperbilirubinemia (NH). This research aims to investigate the impact of phototherapy on the gut microbiota of NH, and to provide reliable theoretical evidence for the clinical application of phototherapy in such cases. METHODS: In this self-controlled longitudinal study, 26 newborns diagnosed with NH were enrolled. Fecal samples were collected before (pre-treatment) and 48 h after (post-treatment) initiating phototherapy. The gut microbiota was profiled using high-throughput 16 S ribosomal RNA (rRNA) gene sequencing. Gut microbiota composition and diversity were analyzed using standard bioinformatics pipelines. Data were processed with standard bioinformatics tools for taxonomic annotation, diversity analysis, and functional prediction based on the COG, KEGG, and MetaCyc databases. Statistical significance was assessed using the Wilcoxon signed-rank test (P < 0.05). RESULTS: While no significant differences were observed at the species level, analysis at the genus level revealed significant alterations in the gut microbiota. The genera Clostridium and Megamonas were identified as significantly increased post-phototherapy. Linear discriminant analysis effect size (LEfSe) analysis further confirmed distinct microbial signatures between the two groups: pre-treatment samples were enriched with families such as Porphyromonadaceae, Lachnospiraceae, Alcaligenaceae, Ruminococcaceae, Moraxellaceae, and the order Pseudomonadales. In contrast, post-treatment samples were predominantly characterized by the class Erysipelotrichi and its associated taxa (Erysipelotrichales and Erysipelotrichaceae). α-diversity indices (Sobs, Chao, Shannon, Simpson) showed no significant differences between the two groups, whereas β-diversity analysis indicated significant microbial community separation (P < 0.05). Predicted functional profiles (based on 16 S rRNA gene data using PICRUSt2) suggested predominant roles in metabolism, genetic information processing, and biosynthesis. However, no significant differences were observed between the pre- and post-treatment groups. CONCLUSIONS: Phototherapy significantly modulated the gut microbial composition of neonates with NH, notably increasing the abundance of Clostridium and Megamonas, and shifting the community towards Erysipelotrichi, while overall microbial functional capacity remained stable. These findings highlight the dynamic yet resilient nature of the neonatal gut microbiota under phototherapy and provide a foundation for microbiome-informed management strategies in neonatal hyperbilirubinemia.},
}

Humans
*Phototherapy
*Hyperbilirubinemia, Neonatal/therapy/microbiology
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Metagenomics
Male
Feces/microbiology
Female

@article {pmid41634410,
year = {2026},
author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY},
title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.},
journal = {Inflammation},
volume = {49},
number = {1},
pages = {78},
pmid = {41634410},
issn = {1573-2576},
support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology/prevention & control ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects/physiology ; *Imiquimod/toxicity ; *Metagenome ; *Skin/pathology/drug effects ; Akkermansia ; Male ; *Verrucomicrobia ; Feces/microbiology ; },
abstract = {A decreased abundance of fecal Akkermansia muciniphila (Akk) has been observed in patients with psoriasis and psoriatic arthritis. The potential beneficial effects of Akk in managing psoriasis have been proposed, yet results remain inconsistent and mechanisms unclear. Using imiquimod (IMQ)-treated C57BL/6 mice, we conducted a metagenomic association study of pasteurized Akk (pAkk) in the IMQ mice through whole-genome shotgun sequencing. We also performed a dextran sodium sulfate (DSS)-induced colitis experiment and an intestinal permeability test. The association among pAkk supplements, skin thickness, inflammatory profiles, fecal microbiota alterations, functional genetic predictions, intestinal epithelium inflammation, and barrier integrity was investigated. The study demonstrated that pAkk supplementation ameliorated IMQ-induced skin thickening, weight loss, spleen weight gain, serum IL-17A, TNF-α levels, and DSS-induced colitis. pAkk supplementation was linked to greater fecal microbial diversity and alterations in fecal microbiota composition, with increased prevalence of Muribaculaceae, Bifidobacterium pseudolongum, Desulfovirionaceae, Erysipelotrichaceae, and Alistipes ihumi, which have been implicated in the Gamma-Aminobutyric Acid (GABA) shunt, cholinergic synapse, cell cycle, and Mitogen-Activated Protein Kinase (MAPK) pathways. In conclusion, pAkk may mitigate IMQ-induced skin thickening and DSS-induced colitis, associated with reduced levels of TNF-α and IL-17A. pAkk supplementation alters fecal microbiota and metabolic pathways in IMQ-treated mice.},
}

Animals
*Colitis/chemically induced/microbiology/prevention & control
Mice
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects/physiology
*Imiquimod/toxicity
*Metagenome
*Skin/pathology/drug effects
Akkermansia
Male
*Verrucomicrobia
Feces/microbiology

@article {pmid41634542,
year = {2026},
author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y},
title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41634542},
issn = {1471-2180},
support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; },
mesh = {*Zea mays/microbiology/metabolism/chemistry ; Fermentation ; *Probiotics/metabolism ; Metabolomics ; *Microbiota ; Laccase/metabolism ; *Enzymes/metabolism ; Lactobacillus/metabolism ; Peroxidases/metabolism ; Bacillus subtilis/metabolism ; Cellulose/metabolism ; Bacteria/metabolism/classification/genetics ; Cellulase/metabolism ; },
abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear. METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10[8] CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process. RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties. CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.},
}

*Zea mays/microbiology/metabolism/chemistry
Fermentation
*Probiotics/metabolism
Metabolomics
*Microbiota
Laccase/metabolism
*Enzymes/metabolism
Lactobacillus/metabolism
Peroxidases/metabolism
Bacillus subtilis/metabolism
Cellulose/metabolism
Bacteria/metabolism/classification/genetics
Cellulase/metabolism

@article {pmid41654923,
year = {2026},
author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY},
title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41654923},
issn = {1479-5876},
support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Cytokines/blood ; Pregnancy ; *Virome ; Infant, Newborn ; Infant ; *Syphilis/blood/virology ; Adult ; Infectious Disease Transmission, Vertical ; *Mothers ; Phylogeny ; Longitudinal Studies ; },
abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.},
}

Humans
Female
*Cytokines/blood
Pregnancy
*Virome
Infant, Newborn
Infant
*Syphilis/blood/virology
Adult
Infectious Disease Transmission, Vertical
*Mothers
Phylogeny
Longitudinal Studies

@article {pmid41661326,
year = {2026},
author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H},
title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.},
journal = {Surgery today},
volume = {56},
number = {7},
pages = {1351-1359},
pmid = {41661326},
issn = {1436-2813},
mesh = {Humans ; *Weight Loss ; *Gastrectomy/methods ; Female ; *Laparoscopy/methods ; Male ; Treatment Outcome ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Obesity, Morbid/surgery/microbiology/metabolism ; *Bariatric Surgery/methods ; *Mouth/microbiology ; },
abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.},
}

Humans
*Weight Loss
*Gastrectomy/methods
Female
*Laparoscopy/methods
Male
Treatment Outcome
*Gastrointestinal Microbiome
Adult
Middle Aged
*Obesity, Morbid/surgery/microbiology/metabolism
*Bariatric Surgery/methods
*Mouth/microbiology

@article {pmid41663924,
year = {2026},
author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y},
title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41663924},
issn = {1471-2180},
support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; Sheep/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Metabolomics ; *Eating ; Metabolome ; Metagenomics ; Digestion ; },
abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling. RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI. CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.},
}

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

@article {pmid41663943,
year = {2026},
author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W},
title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41663943},
issn = {1471-2180},
support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; },
mesh = {*Triticum/microbiology/growth & development/physiology ; Drought Resistance ; *Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; *Microbiota ; *Streptomyces/physiology ; Droughts ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; },
abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance. RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings. CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.},
}

*Triticum/microbiology/growth & development/physiology
Drought Resistance
*Plant Roots/microbiology
Soil Microbiology
Rhizosphere
*Microbiota
*Streptomyces/physiology
Droughts
Bacteria/classification/genetics/isolation & purification
Metagenomics

@article {pmid41691172,
year = {2026},
author = {Motta, H and Perin, APA and Rosin, GF and Reuwsaat, JCV and Mocelin, I and Lopes, FC and Mayer, FQ and de Medeiros, VP and Brum, IS and Baethgen, LF and Gregianini, TS and Staats, CC and Vainstein, MH and Kmetzsch, L},
title = {SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41691172},
issn = {1471-2180},
support = {405934/2022-0//Instituto Nacional de Ciência e Tecnologia (INCT FUNVIR)/ ; 408717/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/2551-0000396-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *COVID-19/microbiology ; SARS-CoV-2 ; *Bacteria/classification/genetics/isolation & purification ; Nasopharynx/microbiology ; *Respiratory System/microbiology ; Female ; Retrospective Studies ; Brazil ; Male ; Middle Aged ; *Respiratory Tract Infections/microbiology ; Adult ; Metagenomics ; },
abstract = {BACKGROUND: The respiratory microbiome plays a critical role in host defense mechanisms and influences disease outcomes. However, the impact of SARS-CoV-2 infection on microbial community composition, function, and resistance potential across different respiratory tract compartments remains incompletely understood. To address this, we analyzed 127 retrospective respiratory samples from SARS-CoV-2-positive and negative patients from Southern Brazil. The dataset included nasopharyngeal swabs from the upper respiratory tract (URT) and samples from the lower respiratory tract (LRT) of patients with Severe Acute Respiratory Infection (SARI). Microbial taxonomic profiles, diversity, co-occurrence networks, functional pathways, and antibiotic resistance genes (ARGs) were assessed through shotgun metagenomic sequencing. RESULTS: SARS-CoV-2 infection did not affect diversity in the URT, but was associated with altered bacterial beta diversity in the LRT. The LRT microbial composition was markedly altered in SARS-CoV-2-positive cases, with reduced abundance of pathogens such as Stenotrophomonas and Pseudomonas and an increased prevalence of Prevotella and Alloprevotella. Co-occurrence network analysis uncovered a loss of complexity in SARS-CoV-2-positive URT samples and the emergence of novel interactions associated with infection in the LRT. Functional profiling demonstrated that SARS-CoV-2-positive LRT samples were enriched in metabolic pathways, whereas SARS-CoV-2-negative LRT samples were enriched in virulence pathways. Resistome profiling indicated minimal differences in ARG diversity and mechanism distribution, although SARS-CoV-2-negative LRT samples exhibited higher ARG abundance. CONCLUSION: SARS-CoV-2 infection reshapes the composition, interactions, and functional potential of the LRT microbiome, while the URT remains relatively stable. These findings underscore the compartment-specific impact of SARS-CoV-2 infection on the respiratory microbiome.},
}

Humans
*Microbiota/genetics
*COVID-19/microbiology
SARS-CoV-2
*Bacteria/classification/genetics/isolation & purification
Nasopharynx/microbiology
*Respiratory System/microbiology
Female
Retrospective Studies
Brazil
Male
Middle Aged
*Respiratory Tract Infections/microbiology
Adult
Metagenomics

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {263},
number = {3},
pages = {1031-1045},
pmid = {41697296},
issn = {1615-6102},
mesh = {Animals ; *Goats/microbiology ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Dairying ; *Farms ; *Microbiota/genetics ; Female ; },
abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.},
}

Animals
*Goats/microbiology
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Dairying
*Farms
*Microbiota/genetics
Female

@article {pmid41699578,
year = {2026},
author = {Wu, H and Li, N and Yang, S and Qiu, J and Zhang, M and Wang, L and Gao, R and Wu, L and Yu, Q and Cheng, X},
title = {Prevotella denticola promotes caries by inducing oral microbial dysbiosis.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41699578},
issn = {1472-6831},
support = {82170937//the National Nature Science Foundation of China/ ; 81800955//the National Nature Science Foundation of China/ ; (No. 2025GH-YBXM-033)//External Cooperation Areas of the Key Research and Development (R&D) Program of Shaanxi Province/ ; LCB202408//the Special Project of the National Clinical Research Center for Oral Diseases/ ; },
mesh = {Humans ; *Dental Caries/microbiology ; *Dysbiosis/microbiology ; Biofilms/growth & development ; *Dental Plaque/microbiology ; Adult ; *Prevotella ; Microbiota ; Female ; Male ; Metagenomics ; },
abstract = {BACKGROUND: While the role of oral microbial dysbiosis in cariogenicity is widely appreciated, it remains unclear whether some resident microorganisms are active contributors in this process. Recently, increasing evidence showed that Prevotella spp. are associated with caries whereas the identified roles at species level remain undefined. This study aimed to analyze the effects of Prevotella denticola on microbial ecosystems and pathogenic mechanisms associated with caries. METHODS: Here, we applied metagenomics to supragingival microbiota (dental plaque) samples from 62 adults to identify disease-relevant species. P. denticola was highly enriched in caries-affected individuals (P < 0.001). The dynamic biofilm formation, spatial arrangement, and cariogenic activity of oral biofilms with or without P. denticola were examined via multiscale/computational imaging and virulence assays. RESULTS: P. denticola, exerting a previously unidentified mechanism in supragingival biofilms, promoted oral biofilm cariogenicity through altering the microbial ecosystem and biofilm structure. In vivo studies demonstrated that P. denticola induced the formation of a more cariogenic biofilm on supragingival tooth surfaces. CONCLUSIONS: Collectively, P. denticola has an ecological impact on the mixed oral microbiota and disrupts microbial equilibrium. These findings indicated that P. denticola infection plays a critical role in caries occurrence.},
}

Humans
*Dental Caries/microbiology
*Dysbiosis/microbiology
Biofilms/growth & development
*Dental Plaque/microbiology
Adult
*Prevotella
Microbiota
Female
Male
Metagenomics

@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
mesh = {Animals ; *Physical Conditioning, Animal ; Male ; *Inflammation/microbiology/pathology/blood ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/genetics ; *Metabolomics ; Mice, Obese ; Insulin Resistance ; *Metagenomics ; Diet, High-Fat ; *Obesity/microbiology ; Body Weight ; Cytokines/metabolism ; Mice ; Lipids/blood ; },
abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored. METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N = 8) and high-fat diet group (HFD group, N = 18). Successfully modeled mice were further assigned to model group (group B, N = 8) and exercise group (group C, N = 8). Group C underwent a 6-week treadmill exercise program (12 m/min, 60 min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics. RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P < 0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-α, NLRP3, IL-1β, and IL-18 significantly increased (P < 0.05 or P < 0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-α and other indicators in obese mice (P < 0.05 or P < 0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise. CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.},
}

Animals
*Physical Conditioning, Animal
Male
*Inflammation/microbiology/pathology/blood
Mice, Inbred C57BL
*Gastrointestinal Microbiome/genetics
*Metabolomics
Mice, Obese
Insulin Resistance
*Metagenomics
Diet, High-Fat
*Obesity/microbiology
Body Weight
Cytokines/metabolism
Mice
Lipids/blood

@article {pmid41706260,
year = {2026},
author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T},
title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {29},
number = {2},
pages = {338-346},
pmid = {41706260},
issn = {1436-3305},
support = {Research Project Grant//Kawasaki Medical School/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Helicobacter pylori/isolation & purification ; *Helicobacter Infections/drug therapy/microbiology/complications ; Female ; Male ; *Microbiota/genetics ; Middle Aged ; Metagenomics/methods ; Aged ; Case-Control Studies ; Saliva/microbiology ; Carcinogenesis ; Gastric Mucosa/microbiology ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Few reports have investigated bacterial microbiome in relation to gastric cancer after eradication of Helicobacter pylori (H. pylori). We aimed to conduct a genetic analysis of the gastric and oral microbiome, to identify its association with development of gastric cancer after H. pylori eradication. METHODS: The patients with prior endoscopic submucosal dissection (ESD) history after eradication (cancer patients) and control patients after eradication who underwent upper gastrointestinal endoscopy at Kawasaki Medical School Hospital from May 2021 to March 2023 were enrolled. Saliva and gastric mucus samples were collected and profiled by 16S rRNA gene amplicon sequencing. RESULTS: The subjects consisted of 24 cancer patients and 27 controls. The abundance of the genus Rothia in gastric mucus of the cancer patients was significantly higher compared to the controls. Conversely, the genus Parvimonas was significantly less abundant in the cancer patients. These differences in salivary samples between the two groups were not observed. The abundance of the genus Parvimonas in the gastric mucous was associated with the gastric atrophy, but genus Rothia was not. CONCLUSIONS: Genus Rothia may have some influence on carcinogenesis following H. pylori eradication.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Helicobacter pylori/isolation & purification
*Helicobacter Infections/drug therapy/microbiology/complications
Female
Male
*Microbiota/genetics
Middle Aged
Metagenomics/methods
Aged
Case-Control Studies
Saliva/microbiology
Carcinogenesis
Gastric Mucosa/microbiology
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41709052,
year = {2026},
author = {Idris, H and Hairi, HH and Ahmad, A and Danish-Daniel, M and Zin, NM and Sanderson, RA and Raja Yahya, MFZ and Majhool, AA and Hassan, MY and Azman, MAZ},
title = {Revealing actinobacterial diversity inhabiting Malaysian Beach Ridges Interspersed with Swales (BRIS) soil : insights from culture-dependent and metagenomic approaches.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {3},
pages = {301-313},
pmid = {41709052},
issn = {1618-1905},
mesh = {*Actinobacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Malaysia ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/chemistry ; *Biodiversity ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {The discovery of novel antibiotics remains a pressing global challenge as many known microorganisms continue to yield compounds already present in existing drugs. To overcome this limitation, bioprospecting in underexplored and extreme environments using both culture-dependent and culture-independent strategies has become essential. In this study, we investigated the microbial diversity of Beach Ridges Interspersed with Swales (BRIS) soil from Setiu, Terengganu, Malaysia—an environment characterized by poor nutrient retention, low water-holding capacity, and acidic conditions with lack information available on their microbial community composition. Therefore, this study was conducted with the main objectives to investigate actinomycetes community composition in BRIS soil using metagenomics and culture-dependent approaches. To address these objectives, a dual approach was employed: (i) culture-dependent isolation of actinomycetes using selective media, followed by morphological and 16S rRNA gene-based phylogenetic analysis, and (ii) culture-independent high-throughput sequencing of the 16S rRNA gene (Illumina MiSeq) to characterize the broader microbial community. Results from the selective isolation yielded 180 actinomycete isolates grouped into 69 colour-based categories, with 15 representatives identified by 16S rRNA sequencing as belonging predominantly to Streptomyces, alongside the rare genus Dermacoccus. In contrast, metagenomic analysis revealed a far richer microbial landscape comprising 4719 OTUs, 32 bacterial phyla, and 380 genera, including a high proportion of uncultured taxa. Notably, actinobacterial diversity was dominated by Acidothermus, whereas Streptomyces predominated in culture-dependent isolation, highlighting the complementary nature of both approaches. These findings confirm that BRIS soil harbours unique microbial communities shaped by its physicochemical conditions, with potential as a reservoir for rare actinomycetes and novel bioactive compounds. The study provides the first combined culture-dependent and metagenomic insight into BRIS soil microbiota and underscores its promise for future pharmaceutical and biotechnological exploration.},
}

*Actinobacteria/classification/genetics/isolation & purification
*Soil Microbiology
Malaysia
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics/chemistry
*Biodiversity
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry

@article {pmid41711914,
year = {2026},
author = {Demin, K and Onasenko, K and Beletskaya, A and Tsoy, A and Boyko, M and Kulikov, M and Kulikova, D and Prazdnova, E},
title = {Studying organosulfonate metabolism in southern Russia chernozem soil microbial community: ubiquity of the desulfonation pathways and possible mixotrophy in common soil heterotrophs.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {201},
pmid = {41711914},
issn = {1432-072X},
support = {SP-12-23-04//Priority 2030/ ; },
mesh = {*Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Russia ; *Microbiota ; Alkanesulfonates/metabolism ; Taurine/metabolism ; Metagenomics ; Sulfites/metabolism ; Phylogeny ; Soil/chemistry ; Oxidation-Reduction ; },
abstract = {Microbial metabolism of organosulfonates (OS) have been researched for at least three decades. However, the studies conducted so far were heavily focused on marine ecosystems, while in terrestrial ecosystems microbial desulfonation pathways are poorly characterized. Here we describe culturable microbial community of chernozem soil from the perspective of OS-based metabolism. Using the metagenomic and culture-dependent approaches, we compare microbial isolates grown on OS to the isolates enriched using common media for soil bacteria and show that there is no substantial difference in terms of taxonomy and OS metabolism genes representation. Alkanesulfonates and taurine are the primary OS compounds metabolized by soil bacteria through ssuDE and tauD enzymatic systems, while other OS desulfonation pathways are rare or absent. Actinobacterial and alphaproteobacterial representatives were the dominant part of OS-utilization community. We show in vitro taurine desulfonation and subsequent re-utilization of produced sulfite by soil actinobacterial isolates of Streptomyces anulatus and Arthrobacter siccitolerans. We hypothesize that microbial desulfonation coupled to sulfite oxidation may be a strategy to generate energy from both organic and inorganic molecules oxidation in heterotrophs (that is, mixotrophy). Finally, it is that OS-metabolism represents a ubiquitous metabolic capability rather than a niche trait, interlinking key biogeochemical cycles, particularly sulfur, nitrogen, and carbon.},
}

*Soil Microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Russia
*Microbiota
Alkanesulfonates/metabolism
Taurine/metabolism
Metagenomics
Sulfites/metabolism
Phylogeny
Soil/chemistry
Oxidation-Reduction

@article {pmid41714980,
year = {2026},
author = {Ceylani, T and Teker, HT and Önlü, H and Ünver, T and Allahverdi, H and Şahin, E and Atalan, E},
title = {Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41714980},
issn = {1471-2164},
support = {FOA-2024-3587//Inönü University Scientific Research Projects Coordination Unit (BAP)/ ; },
mesh = {Animals ; *Probiotics/pharmacology ; Male ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Diet ; Rats, Wistar ; Fatty Acids, Volatile/metabolism ; Metagenomics ; Metabolomics ; Indoles/metabolism ; },
abstract = {BACKGROUND: The developmental phase is a pivotal biological period for the maturation of the gut microbiota and the establishment of lifelong metabolic health. During these period, dietary patterns that induce dysbiosis, such as the high-fat, low-fiber “cafeteria diet,” disrupt the production of key metabolites in the gut-metabolite axis, including short chain fatty acids (SCFAs) and indole-3-propionic acid (IPA). This study employs a multi-omics approach to examine the impact of cafeteria diet exposure during the developmental period (days 21–56) in 21-day-old male Wistar rats on microbiota composition, SCFA, and IPA levels, and to assess the extent to which concurrent probiotic administration can mitigate these disruptions. RESULTS: The cafeteria diet led to a marked reduction in alpha diversity indices (Shannon p = 0.021; Simpson p = 0.034) and altered the Firmicutes/Bacteroidetes ratio (p = 0.015). Beta diversity analysis indicated a distinct separation between groups (PERMANOVA p = 0.002). Metabolite analysis revealed significant reductions in acetic acid (p = 0.004), isobutyric acid (p = 0.094), butyric acid (p = 0.0014), valeric acid (p = 0.0001), heptanoic acid (p = 0.0125), and IPA (p = 0.002), whereas probiotic administration largely restored these levels. At the species level, cafeteria diet markedly increased Segatella copri, while probiotic intervention partially restored beneficial taxa such as Faecalibacterium prausnitzii and butyrate-producing genera (Anaerostipes hadrus, Intestinimonas butyriciproducens, Blautia wexlerae, and Flintibacter sp. KGMB00164), as evidenced primarily by shotgun metagenomics. Correlation analysis further revealed strong positive associations between butyrate and F. prausnitzii (ρ = 0.65, p = 0.003) and between IPA and B. longum (ρ = 0.68, p = 0.002). Collectively, these results highlight the protective role of probiotic intervention against diet-induced dysbiosis by reinforcing microbiota metabolite interactions. CONCLUSIONS: By integrating metagenomic and metabolomic analyses, this multi-omics study demonstrates that exposure to a high-fat cafeteria diet during the developmental period disrupts microbiota composition and metabolite production, whereas concurrent probiotic administration largely prevent these effects, serving a protective role in the gut-metabolite axis. The study underscores the potential of early-life probiotic intervention, supports SCFA and IPA production, as a critical strategy to optimize microbiota-metabolite interactions and promote long-term gut and systemic health.},
}

Animals
*Probiotics/pharmacology
Male
Multiomics
*Gastrointestinal Microbiome/drug effects
Rats
*Diet
Rats, Wistar
Fatty Acids, Volatile/metabolism
Metagenomics
Metabolomics
Indoles/metabolism

@article {pmid41731364,
year = {2026},
author = {Liu, Y and Sun, H and Tan, X and Li, K and He, Z and Hu, S},
title = {Ultra-deep metagenomic sequencing enables reconstruction of diverse, high quality microbial genomes from human urine samples.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41731364},
issn = {1471-2180},
support = {2021YFF0703805//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Urinary Tract Infections/microbiology/diagnosis/urine ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Genome, Microbial/genetics ; Escherichia coli/genetics/isolation & purification ; Microbiota/genetics ; Fungi/genetics/isolation & purification/classification ; },
abstract = {BACKGROUND: Urinary tract infections (UTIs) represent a major global health challenge, necessitating the precise identification of causative pathogens for effective diagnosis and treatment. While metagenomic next-generation sequencing (mNGS) has emerged as a powerful diagnostic tool, its clinical application has been limited by the lack of high-quality microbial genomes from urine samples. RESULTS: We reconstructed 223 reliable quality MAGs spanning bacterial, fungal, mycoplasmal, and viral, including the first demonstration of multiple Escherichia coli subpopulations within individual urine samples. The collection comprised six fungal genomes, ten mycoplasma genomes, and eight completed viral genomes. Comparative analysis showed 72% concordance with culture while detecting additional pathogens in 30% of cases, including fastidious organisms missed by conventional methods. CONCLUSIONS: This study establishes an optimized mNGS framework that overcomes current diagnostic limitations in UTIs through high-depth sequencing and minimal host contamination, enabling unprecedented resolution of the urinary microbiota, including the first identification of intra-sample E. coli subpopulations. The comprehensive MAG collection provides a valuable resource for advancing UTI diagnostics, mechanistic research, and personalized treatment strategies.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Urinary Tract Infections/microbiology/diagnosis/urine
*Urine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Genome, Microbial/genetics
Escherichia coli/genetics/isolation & purification
Microbiota/genetics
Fungi/genetics/isolation & purification/classification

@article {pmid41731377,
year = {2026},
author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M},
title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41731377},
issn = {1471-2180},
mesh = {*Bacteria/classification/genetics/isolation & purification ; Morocco ; *Fungi/genetics/classification/isolation & purification ; *Plant Diseases/microbiology ; Fusarium/pathogenicity ; *Phoeniceae/microbiology ; Soil Microbiology ; *Metagenomics/methods ; Plant Roots/microbiology ; Disease Resistance ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots. RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma. CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.},
}

*Bacteria/classification/genetics/isolation & purification
Morocco
*Fungi/genetics/classification/isolation & purification
*Plant Diseases/microbiology
Fusarium/pathogenicity
*Phoeniceae/microbiology
Soil Microbiology
*Metagenomics/methods
Plant Roots/microbiology
Disease Resistance
*Microbiota/genetics

@article {pmid41735826,
year = {2026},
author = {Qian, Q and Li, N and Cha, S and Zheng, S and Li, W and Yin, G and Sun, M and Ye, P and Hu, M and Shi, R and Zhang, Y and Shen, W},
title = {Identification and functional characterization of Pseudomonas fluorescens as a novel intratumoral bacterium in colorectal cancer.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41735826},
issn = {1471-2180},
support = {82303959//The National Natural Science Foundation of China/ ; 81302162//National Natural Science Foundation of China Youth Foundation/ ; SSPW2022-KF06//Open Project of Zhenjiang Traditional Chinese Medicine Spleen and Stomach Disease Clinical Medicine Research Center/ ; GSP-ZXY20//Zhongda Hospital Affiliated to Southeast University, Jiangsu Province High-Level Hospital Construction Funds/ ; },
mesh = {Humans ; *Pseudomonas fluorescens/isolation & purification/genetics/classification/physiology ; *Colorectal Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome ; Cell Proliferation ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Phylogeny ; Middle Aged ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden as one of the leading causes of cancer-related mortality. Recent research has highlighted the crucial role of gut microbiota in CRC development. Through high-throughput full-length 16 S rDNA sequencing of tumor and adjacent non-tumor tissues from 14 CRC patients, significant microbial differences were identified. At the phylum level, Firmicutes (52.59%), Bacteroidetes (18.51%), and Proteobacteria (14.89%) dominated both tissue types, while at the genus level, Bacteroides (8.02%) and Escherichia (4.50%) showed the highest abundance. Notably, 17 bacterial species exhibited differential abundance between tumor and normal tissues, with Anaerotignum faecicola and Pseudomonas fluorescens being significantly enriched in tumor tissues. Functional prediction analysis revealed the microbiota’s predominant involvement in carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways. Subsequent validation in 20 additional patient samples confirmed P. fluorescens enrichment in tumor tissues, and in vitro experiments demonstrated its ability to promote CRC cell viability and proliferation. These findings provide valuable insights into CRC-associated microbial signatures and suggest P. fluorescens as a potential contributor to tumor progression, offering new directions for developing diagnostic markers and therapeutic interventions in CRC management.},
}

Humans
*Pseudomonas fluorescens/isolation & purification/genetics/classification/physiology
*Colorectal Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
Gastrointestinal Microbiome
Cell Proliferation
Bacteria/classification/genetics/isolation & purification
Male
Female
Phylogeny
Middle Aged
Sequence Analysis, DNA
DNA, Bacterial/genetics

@article {pmid41735848,
year = {2026},
author = {Van Uffelen, A and Gobbo, A and Fraiture, MA and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K},
title = {Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41735848},
issn = {1471-2164},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Nanopore Sequencing/methods ; Nanopores ; Shotgun Sequencing ; *Software ; Bacteria/classification/genetics ; Microbiota ; },
abstract = {BACKGROUND: Shotgun metagenomics enables to study microbial communities without biases from culturing and isolation, but taxonomic classification to the species level remains challenging due to high false positive rates. Oxford Nanopore Technologies offers new opportunities to address these challenges by producing longer reads. However, different pipelines and tools use different methods to reduce false positives, resulting in variable outcomes with limited exploration of what works best in practice. Relative abundance filtering is often used to improve precision by removing false positives but reduces also recall by removing true positives. In this study, we optimized a broadly applicable taxonomic classification pipeline for long-read nanopore sequencing data that improves precision. The pipeline uses the tool KMA as the underlying classifier, followed by specific post-processing and optimization of filtering thresholds. Based on ten defined mock communities, different filter thresholds were evaluated, alongside the effect of the sequencing yield and the limit of detection (LOD). RESULTS: Our optimized pipeline substantially outperformed default classifier settings, and the conventionally used relative abundance filtering. Classification accuracy improved with higher sequencing yields, requiring at least a post-filtering yield of 500M bases, and ideally 1000M bases, for reliable results. At yields above 1000M bases, median precision could be improved up to 95% while maintaining median recall at 91.62%. Further increasing median precision to 99% reduced recall to 79.08%. Similarly, higher sequencing yields lowered LOD. For yields above 1000 M bases, the limit of detection remained stable at 0.1% up to a median precision of 95%, while yields below 1000M showed an LOD of 1%. Validation on ten probiotic-derived mock communities confirmed the pipeline’s performance and general applicability. CONCLUSION: Our optimized classification pipeline for nanopore sequencing data provides substantially higher precision compared to default approaches and is suitable for diverse metagenomic applications. We provide specific guidance on expected recall and precision values for minimum sequencing yields and their associated LODs. Our optimized pipeline, called KAPTAIN (KMA-bAsed Pipeline for meTAgenomic specIes ideNtification), is publicly available on GitHub (https://github.com/BioinformaticsPlatformWIV-ISP/KAPTAIN) and also the Galaxy instance of our institute (https://galaxy.sciensano.be) to be used by other scientists.},
}

*Metagenomics/methods
*Computational Biology/methods
*Nanopore Sequencing/methods
Nanopores
Shotgun Sequencing
*Software
Bacteria/classification/genetics
Microbiota

@article {pmid41749306,
year = {2026},
author = {Liu, Z and Liu, M and Chen, H and Li, S and Zheng, N and Xing, G and Zhang, Y and Xu, J and Li, M and Xiao, C and Lu, T and Yan, Q and Lei, Z and Feng, M and Li, Y},
title = {Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41749306},
issn = {1479-5876},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/virology ; *Lung Neoplasms/drug therapy/virology ; *Virome ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; Female ; Male ; Feces/virology ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiota is a key modulator of immune checkpoint inhibitor (ICI) efficacy, yet the contribution of the gut virome remains poorly defined, particularly in advanced non–small cell lung cancer (NSCLC). Here, we characterized the gut virome and explored its potential role in shaping response to PD-1 blockade. METHODS: We performed metagenomic virome profiling of fecal samples from 338 advanced NSCLC patients treated with PD-1 inhibitors and evaluated model generalizability in an independent external cohort (n = 30). Viral diversity, taxonomic composition, and functional potential were analyzed. Virus–bacteria co-occurrence networks were constructed, and random forest classifiers were developed to predict treatment response. RESULTS: Viral Shannon diversity decreased progressively with poorer clinical response, and β-diversity analyses revealed distinct virome community structures between responders (R) and non-responders (NR). Differential abundance analysis identified 194 NR-enriched vOTUs, predominantly assigned to Peduoviridae and Inoviridae, and 594 R-enriched vOTUs, mainly from Herelleviridae and Microviridae. Host prediction indicated that NR-enriched vOTUs frequently targeted bacterial genera such as Clostridium_M, Bacteroides, and Escherichia, whereas R-enriched vOTUs targeted beneficial genera such as Faecalibacterium and Roseburia. Network analyses further revealed response-specific virus–bacteria interaction modules. Functional profiling showed that NR-enriched vOTUs were associated with metabolic functions, including K01689 (eno; enolase). A virus-only random forest model outperformed a bacterium-only model in predicting response (area under the curve [AUC] = 0.768 vs. 0.664) and maintained superior performance in the external cohort (AUC = 0.742). In addition, Akkermansia muciniphila positivity was associated with a higher-diversity, responder-favorable virome configuration. CONCLUSIONS: The gut virome undergoes marked remodeling during anti–PD-1 therapy in advanced NSCLC and displays distinct taxonomic, ecological, and functional signatures associated with clinical outcome. These findings support the gut virome as a strong predictor of ICI response and highlight its potential as both a biomarker and a therapeutic target.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/drug therapy/virology
*Lung Neoplasms/drug therapy/virology
*Virome
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism
Female
Male
Feces/virology
Treatment Outcome

@article {pmid41761072,
year = {2026},
author = {Costa, J and Pascoal, F and Baptista, MS and Hop, H and Assmy, P and Wold, A and Magalhães, C and Duarte, P},
title = {Comparative analysis of prokaryotic communities, hydrography, and biogeochemistry in Atlantic vs non-Atlantic influenced Svalbard fjords.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41761072},
issn = {1471-2180},
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Seawater/microbiology/chemistry ; Svalbard ; *Archaea/classification/genetics/isolation & purification ; *Estuaries ; Phylogeny ; Arctic Regions ; DNA, Bacterial/genetics ; Atlantic Ocean ; *Microbiota ; Sequence Analysis, DNA ; Metagenomics ; },
abstract = {BACKGROUND: Fjords in Svalbard are undergoing significant changes due to climate warming. Those along the west coast of Spitsbergen are particularly affected by the increasing influence of “warm” Atlantic Water (AW), a process known as Atlantification. We compared Kongsfjorden, a relatively “warm” fjord on the west coast, with Rijpfjorden, a typical cold Arctic fjord on the north coast of Nordaustlandet, combining physical and biogeochemical data with 16S rRNA gene amplicon and shotgun metagenomic sequencing. We hypothesize that differences in fjords’ water masses and prokaryotic communities provide insight into the effects of Atlantification as it expands eastwards along the shelf north of Svalbard. RESULTS: We found that warm AW dominated in Kongsfjorden, whereas Rijpfjorden was dominated by cold Arctic Water and Winter Cooled Water. Our results suggest that the Atlantic-influenced Kongsfjorden is a nutrient sink, whereas Rijpfjorden showed similar behavior only in 2016, a particularly warm year, otherwise no clear sink/source role could be identified. Analysis of 16S rRNA gene sequences revealed that Proteobacteria had higher relative abundances in Kongsfjorden while Bacteroidota dominated in Rijpfjorden. Ammonium and nitrite-oxidizing prokaryotes were most prevalent in deeper water masses of both fjords. The archaeal taxa of the ammonia-oxidizing community, mainly Nitrosopumilus and Nitrosopelagicus, were consistently more dominant than ammonium and nitrite-oxidizing bacteria. Denitrification and nitrogen fixation genes differed between the fjords, with Kongsfjorden having a higher coverage of diazotroph genes. CONCLUSIONS: Kongsfjorden and Rijpfjorden displayed distinct hydrographic conditions, with Kongsfjorden being under a stronger influence of Atlantification. Our results suggest that warmer water masses are linked to higher nutrient uptake. The clear association between microbial communities and water masses offers insight into changes driven by Atlantification.},
}

RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Seawater/microbiology/chemistry
Svalbard
*Archaea/classification/genetics/isolation & purification
*Estuaries
Phylogeny
Arctic Regions
DNA, Bacterial/genetics
Atlantic Ocean
*Microbiota
Sequence Analysis, DNA
Metagenomics

@article {pmid41761093,
year = {2026},
author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA},
title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41761093},
issn = {1471-2105},
mesh = {*Unsupervised Machine Learning ; *Dysbiosis/microbiology/diagnosis ; Humans ; *Gastrointestinal Microbiome ; Autoencoder ; *Deep Learning ; Long Short Term Memory ; Ensemble Learning ; },
abstract = {PURPOSE: Gut microbiome dysbiosis is a critical determinant for autologous fecal microbiota transplantation (Auto-FMT) eligibility, yet current classification approaches rely predominantly on supervised learning with manually annotated sequencing labels, which are often scarce. This study proposes DynaBiome, a framework designed to predict gut dysbiosis by leveraging unsupervised learning and clinical phenotypic proxies as a scalable alternative to ground-truth genomic labeling. METHODS: Our framework employs an LSTM autoencoder architecture to capture temporal microbiome dynamics within 14-day windows. The model reconstructs normal microbiome patterns, where high reconstruction errors signal potential dysbiosis. To ensure rigorous evaluation and prevent data leakage, the dataset was partitioned via a strict patient-level split. Unsupervised anomaly signals were refined via phenotypic proxy labels (e.g., fever, neutropenia) via weak supervision, and ensemble learning methods were applied to optimize classification performance. RESULTS: The initial LSTM autoencoder successfully flagged dysbiotic sequences but required refinement to reduce false positives. Ensemble learning significantly enhanced predictive accuracy. The stacked ensemble (with Logistic Regression meta-learner) demonstrated optimal performance with an ROC AUC of 0.8908 and a Weighted F1-score of 0.7909. This approach significantly outperformed the standard One-Class SVM baseline (ROC AUC 0.6033), confirming the superiority of deep temporal modeling over static anomaly detection. Critically, the model achieved performance levels comparable to fully supervised baselines, confirming the efficacy of the proxy-label framework. CONCLUSION: Integrating unsupervised temporal feature extraction with stacked ensemble methods provides a viable framework for dysbiosis prediction. These results demonstrate that leveraging phenotypic via weak supervision can effectively approximate supervised baselines, thereby reducing the reliance on comprehensive metagenomic annotations for longitudinal patient monitoring.},
}

*Unsupervised Machine Learning
*Dysbiosis/microbiology/diagnosis
Humans
*Gastrointestinal Microbiome
Autoencoder
*Deep Learning
Long Short Term Memory
Ensemble Learning

@article {pmid41762333,
year = {2026},
author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S},
title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41762333},
issn = {1573-0972},
mesh = {Animals ; *Nitrogen/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Coleoptera/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenomics ; Nitrogen Fixation/genetics ; Ammonia/metabolism ; Larva/microbiology ; Phylogeny ; },
abstract = {White grubs, Holotrichia longipennis, are major agricultural pests that cause extensive crop damage. The gut microbiota plays a critical role in nitrogen metabolism, enabling larvae to thrive on nitrogen-poor diets. Shotgun metagenomic sequencing revealed a diverse gut microbiota dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with Enterobacter (32%), Bacillus (20%), and Rhizobium showing clear spatial variation across gut compartments. Functional annotation (FOAM, FAPROTAX) identified bacterial genes involved in uric acid degradation (puuE, allC), urea hydrolysis (ureA, ureB, ureC), and ammonia assimilation via the GS–GOGAT/GDH pathways (gdhA, glnA, glnK, gltB, gltD), whereas nitrogen fixation genes (nifH, nifK, nifD) were absent. KEGG-based quantification (FeatureCounts, HTSeq) showed significantly higher nitrogen metabolism gene abundance in the hindgut, especially gdhA, glnA, and urease genes, which was validated by qPCR with 86-fold, 108-fold, and 34-fold upregulation, respectively. Uricolytic and ammonia-tolerant bacteria (Sporosarcina, Ureaplasma, Corynebacterium, Klebsiella) were isolated and functionally characterized, confirming their active role in nitrogen recycling, with urease assays showing higher ammonia production in the hindgut (0.155 µmol NH3/min/mg protein). Importantly, antibiotic treatment caused a dose-dependent reduction in gut bacterial abundance and larval survival, demonstrating the essential role of symbionts in host physiology. This study provides the first comprehensive evidence that H. longipennis larvae depend on gut microbes for nitrogenous waste recycling and identifies gut nitrogen-cycling bacteria and their key metabolic pathways (urease and ammonia-assimilation systems) as actionable targets for microbiome-based pest control strategies.},
}

Animals
*Nitrogen/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
*Coleoptera/microbiology/metabolism
*Gastrointestinal Microbiome/genetics/physiology
Metagenomics
Nitrogen Fixation/genetics
Ammonia/metabolism
Larva/microbiology
Phylogeny

@article {pmid41764137,
year = {2026},
author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J},
title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.},
journal = {Obesity surgery},
volume = {36},
number = {4},
pages = {1607-1620},
pmid = {41764137},
issn = {1708-0428},
mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/surgery/metabolism/complications/blood ; *Bile Acids and Salts/metabolism/blood ; *Gastrointestinal Microbiome/physiology ; *Gastrectomy/methods ; Adult ; Biomarkers/metabolism/blood ; *Obesity, Morbid/surgery/complications/microbiology ; Remission Induction ; Follow-Up Studies ; },
abstract = {OBJECTIVE: To identify predictive biomarkers from the perspectives of gut microbiota and bile acid metabolites for polycystic ovary syndrome (PCOS) remission following metabolic bariatric surgery in patients with PCOS and obesity. METHODS: We conducted a one-year follow-up of patients with obesity and PCOS who underwent sleeve gastrectomy (SG) to assess their PCOS remission status. Metagenomics and bile acid metabolomics were performed and compared between the remission and non-remission groups to identify differential microbial species and bile acid metabolites. The associations between these biomarkers and PCOS remission was then evaluated using Generalized Estimating Equations (GEE) models and Receiver Operating Characteristic (ROC) analysis. RESULTS: SG led to marked improvements in metabolic parameters and hyperandrogenemia. These changes were accompanied by substantial shifts in the gut microbiome, which correlated with alterations in gonadal hormone levels. Based on PCOS outcomes, patients were categorized into remission and non-remission groups. The remission group showed a higher abundance of A. equolifaciens and Clostridium sp CAG 299, along with lower baseline circulating levels of ursodeoxycholic acid (UDCA). These factors were positively associated with PCOS remission. ROC analysis demonstrated that the combination of A. equolifaciens, Clostridium sp CAG 299, UDCA, and average follicle number yielded an AUC of 0.93 for predicting remission. CONCLUSION: A composite biomarker signature incorporating specific gut microbiota profiles, circulating UDCA levels, and ovarian follicle count shows strong potential as an effective predictor of PCOS remission after SG.},
}

Humans
Female
*Polycystic Ovary Syndrome/microbiology/surgery/metabolism/complications/blood
*Bile Acids and Salts/metabolism/blood
*Gastrointestinal Microbiome/physiology
*Gastrectomy/methods
Adult
Biomarkers/metabolism/blood
*Obesity, Morbid/surgery/complications/microbiology
Remission Induction
Follow-Up Studies

@article {pmid41771971,
year = {2026},
author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J},
title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41771971},
issn = {2045-2322},
support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; },
mesh = {Animals ; Mice ; *Reishi/chemistry ; *Spores, Fungal/chemistry ; *Proteome ; *Metabolome/drug effects ; *Immunocompromised Host/drug effects ; Phagocytosis/drug effects ; Proteomics ; Metabolomics ; Male ; *Gastrointestinal Microbiome/drug effects ; Killer Cells, Natural/immunology/drug effects ; Multiomics ; Hemolysin Proteins/blood ; Macrophages/immunology/drug effects ; },
abstract = {Ganoderma lucidum has a long-standing history of use as a medicinal mushroom, with its spore oil (GLSO) extracted from broken cell walls using CO2 supercritical extraction. However, there is a notable scarcity of experimental studies on the protective effects and underlying mechanisms of GLSO on immune function impairment. The present study aims to explore the characteristics that GLSO contributes to protecting immune functions in cyclophosphamide-induced immunocompromised mice through a multi-omics analysis approach. GLSO administration significantly improved serum hemolysin levels, macrophage phagocytosis, and NK cell activity in immunosuppressed mice. Metagenomics, metabolomic, and proteomic analyses revealed that the immune protection mediated by GLSO was associated with structural rearrangements within gut microflora and shifts in microbial diversity. Specifically, there was an increase in beneficial microorganisms and a decrease in pathogenic organisms, accompanied by various alterations in metabolites and protein expressions. The identified 5 metabolites (propionic acid, beta-glycyrrhetinic acid, 3-aminosalicylic acid, creatine, and 2-phenylacetamide) and 5 proteins (Slc9a9, Blm, Hk3, AP1M2, and J chain) might serve as potential mediators of GLSO to alleviate immune dysfunction collectively caused by CYP in immunosuppressed mice.},
}

Animals
Mice
*Reishi/chemistry
*Spores, Fungal/chemistry
*Proteome
*Metabolome/drug effects
*Immunocompromised Host/drug effects
Phagocytosis/drug effects
Proteomics
Metabolomics
Male
*Gastrointestinal Microbiome/drug effects
Killer Cells, Natural/immunology/drug effects
Multiomics
Hemolysin Proteins/blood
Macrophages/immunology/drug effects

@article {pmid41781852,
year = {2026},
author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC},
title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41781852},
issn = {1471-2180},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
mesh = {Humans ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Eye/microbiology ; Female ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: The human body harbors diverse microbial communities that play essential roles in health and disease. While the gut microbiome (GM) has been extensively studied and linked to numerous systemic conditions, the ocular surface microbiome (OSM) remains less well understood due to its low microbial biomass and technical challenges in sequencing. Previous work has suggested possible connections between gut dysbiosis and ocular disease, but whether the OSM and GM are directly related remains unclear. RESULTS: This study investigated the relationship between the ocular surface microbiome (OSM) and the gut microbiome (GM) by analysing matched samples from both niches in the same individuals. Using high-throughput sequencing, we characterised microbial composition and diversity at each niche, followed by statistical analysis to show common taxa. A Mantel test was applied to assess potential correlations between the two microbial communities. Our results revealed no significant correlation between the composition of the OSM and GM, neither in structure nor in diversity. CONCLUSION: This study suggests that the two niches are shaped independently, likely due to their distinct environmental conditions and microbial densities. These findings highlight the uniqueness of each microbiome and underscore the need for niche specific approaches when investigating host microbiome interactions. TRIAL REGISTRATION: ClinicalTrials.gov, TRN: NCT02438111, Registration date: 28 April 2015, and TRN: NCT 04658238, Registration date: 01 December 2020.},
}

Humans
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
*Eye/microbiology
Female
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
Male
Adult
Dysbiosis/microbiology
Middle Aged

@article {pmid41781883,
year = {2026},
author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J},
title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41781883},
issn = {1471-2180},
support = {32171607//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metagenome ; Macaca/microbiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Genome, Bacterial ; },
abstract = {BACKGROUND: Gut microbiota plays a crucial role in type 2 diabetes mellitus (T2DM) pathogenesis. Spontaneous T2DM macaques offer a valuable model for investigating contributions of gut microbiota to T2DM pathogenesis due to physiological similarities to humans and the absence of glucose-lowering drug interference. RESULTS: We performed de novo assembly of metagenome-assembled genomes (MAGs) to explore the diversity and function of the gut microbiome at the genome level. We obtained 317 non-redundant MAGs from fecal metagenomes of macaques and 325 MAGs from humans, 168 of which were potential novel species. Most members of Lachnospiraceae, the main carriers of carbohydrate-active enzymes (CAZymes) and virulence genes, significantly increased in the guts of T2DM macaques and unmedicated T2DM patients. Further analysis on the MAGs of Lachnospiraceae identified concordant enrichment of potential microbial signatures of T2DM, including the macaque-derived Eubacterium_Q sp900314445 (Mm_bin23) and human-derived Eubacterium_F sp003491505 (Hs_bin20) and Eubacterium ramulus (Hs_bin147). They all carried intestinal barrier-associated virulence genes and diabetes-associated hypervirulence genes, which might be associated with barrier dysfunction, inflammation, and disrupt glucose homeostasis, thereby potentially contributing to the pathogenesis of T2DM. CONCLUSIONS: This study assembled extensive MAGs from the gut microbiome of spontaneous T2DM macaques and asymptomatic controls. Furthermore, we identified three Eubacterium genomes harboring virulence genes and diabetes-associated genes, which were significantly enriched in both T2DM macaques and T2DM humans, highlighting the potential roles of these microbes in T2DM pathogenesis. Overall, this study provides a critical foundation for elucidating gut microbiome-mediated mechanisms and developing targeted therapeutic strategies for T2DM.},
}

Animals
*Diabetes Mellitus, Type 2/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Metagenome
Macaca/microbiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Genome, Bacterial

@article {pmid41784805,
year = {2026},
author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J},
title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41784805},
issn = {1420-9071},
support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; },
mesh = {Animals ; *Melatonin/pharmacology/therapeutic use ; *Tryptophan/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Autistic Disorder/drug therapy/metabolism/microbiology ; Rats ; Valproic Acid ; Female ; Pregnancy ; Rats, Sprague-Dawley ; *Behavior, Animal/drug effects ; Disease Models, Animal ; Metabolomics ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.},
}

Animals
*Melatonin/pharmacology/therapeutic use
*Tryptophan/metabolism
Male
*Gastrointestinal Microbiome/drug effects
*Autistic Disorder/drug therapy/metabolism/microbiology
Rats
Valproic Acid
Female
Pregnancy
Rats, Sprague-Dawley
*Behavior, Animal/drug effects
Disease Models, Animal
Metabolomics

@article {pmid41786830,
year = {2026},
author = {Nowak, RG and Gough, E and Holm, JH and Hu, F and Akinyombo, K and Okudo, C and Ozumba, PJ and Jonathan, EC and Tiamiyu, AB and Kokogho, A and Adebajo, SB and Shoyemi, E and Baral, SD and Lombardi, K and Peel, S and Lim, JN and Gaydos, CA and Manabe, YC and Sears, CL and Shardell, M and Ravel, J and Crowell, TA and Tuddenham, S},
title = {Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41786830},
issn = {2045-2322},
support = {R21 AI156765/AI/NIAID NIH HHS/United States ; U54 EB007958/EB/NIBIB NIH HHS/United States ; R01MH099001/MH/NIMH NIH HHS/United States ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; Male ; *Homosexuality, Male ; *HIV Infections/microbiology/virology/epidemiology ; *Metagenomics/methods ; Nigeria/epidemiology ; Adult ; *Rectum/microbiology ; *Gastrointestinal Microbiome/genetics ; Viral Load ; Sexual Behavior ; },
abstract = {Emerging data suggest unique features characterize the rectal microbiota of men who have sex with men (MSM) and people living with HIV (PLWH). The microbiota may have important health implications in these groups, but most studies have been conducted in the United States or Europe. This study leveraged metagenomic sequencing to evaluate relationships between rectal microbiota composition and clinical, behavioral and demographic characteristics in a cohort of Nigerian MSM. PLWH with suppressed viral load had lower α-diversity (richness) compared to people without HIV (PWoH), with similar trends for PLWH with an unsuppressed viral load. Lower α-diversity (Shannon) was associated with use of petroleum jelly lubricant for anal sex. Lower relative abundance of the genus Prevotella was seen in PLWH with a suppressed viral load versus PWoH. There were differences in abundance of the top 20 taxa associated with age, HIV status (enhanced in virally suppressed PLWH versus PWoH), lubricant use, receptive anal intercourse, and condom use, suggesting multiple clinical and behavioral factors impact the rectal microbiota. Future characterization of health outcomes associated with the rectal or gut microbiota in MSM and PLWH as well as potential interventional insights will necessitate larger, dedicated studies across diverse geographic locations.},
}

Humans
Male
*Homosexuality, Male
*HIV Infections/microbiology/virology/epidemiology
*Metagenomics/methods
Nigeria/epidemiology
Adult
*Rectum/microbiology
*Gastrointestinal Microbiome/genetics
Viral Load
Sexual Behavior

@article {pmid41787261,
year = {2026},
author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N},
title = {Lifestyle associates with unique resistome and microbiome signatures in children.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41787261},
issn = {1471-2180},
mesh = {Humans ; *Life Style ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Child, Preschool ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Child ; Sweden ; Female ; Male ; *Drug Resistance, Bacterial/genetics ; Infant ; Breast Feeding ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Feces/microbiology ; },
abstract = {BACKGROUND: Antibiotic resistance is a global health crisis that is not solely explained by antibiotics usage. However, environmental and lifestyle contributions to antimicrobial resistance (AMR) in children are not well understood, especially compared to adults. As the gut functions as a reservoir for antibiotic resistance genes (ARGs), the aim of this study was to better understand the influence of lifestyle on the gut microbiome and resistome using shotgun-metagenomic sequencing data of Swedish children from the PARSIFAL (Prevention of Allergy Risk factors for Sensitization In children related to Farming and Anthroposophic Lifestyle) study. RESULTS: Farm children exhibited high proportions of unique bacterial species and differentially abundant ARGs linked to the farm environment, and similar differences were found in anthroposophic children. Age, breastfeeding duration, and obesity significantly influenced the overall resistance load, independently of lifestyle. Despite limited statistical power, our findings suggest that lifestyle and environment both shape the microbiome and resistome of children. CONCLUSIONS: This study corroborates the possible influence of the farm environment on the gut microbiome and resistome, revealing a highly individualized repertoire of low-abundance microbes and ARGs in farm children. Additionally, associations of age, obesity and the duration of exclusive breastfeeding with ARG load were found in a currently understudied age range. Overall, this study raises the need for further research on rare species and ARGs as well as their transmission dynamics in relation to the environment.},
}

Humans
*Life Style
*Bacteria/genetics/classification/drug effects/isolation & purification
Child, Preschool
Anti-Bacterial Agents/pharmacology
*Gastrointestinal Microbiome/genetics
Child
Sweden
Female
Male
*Drug Resistance, Bacterial/genetics
Infant
Breast Feeding
*Drug Resistance, Microbial/genetics
Metagenomics
Feces/microbiology

@article {pmid41796297,
year = {2026},
author = {Shi, K and He, Q and Wang, S and Guo, J},
title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41796297},
issn = {1471-2180},
support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; },
mesh = {Humans ; *Deep Learning ; *Gastrointestinal Microbiome/genetics ; Phenotype ; Long Short Term Memory ; Convolutional Neural Networks ; Metagenomics/methods ; Longitudinal Studies ; Predictive Learning Models ; },
abstract = {BACKGROUND: The gut microbiota plays a vital role in maintaining human health. In recent years, extensive researches has focused on phenotype prediction in relation to various diseases, with the gut microbiota as a key predictor. Nevertheless, most existing studies rely on single-time-point analyses, which are insufficient to capture the dynamic patterns of host states and temporal variations inherent in longitudinal data. RESULTS: In this study, we propose a deep learning framework, AWSD-CNN-LSTM, designed to classify host phenotypes using longitudinal metagenomic data. Unlike conventional approaches that treat each time point as an independent sample, our method models the sequential samples of each individual as a whole, integrating convolutional neural network (CNN) and long short-term memory network (LSTM) to effectively capture temporal dependencies in longitudinal microbiome sequencing data. In addition, the model incorporates an adaptive point-wise self-distillation mechanism to more accurately characterize host-specific patterns. Compared with state-of-the-art methods, AWSD-CNN-LSTM demonstrates superior performance on the PROTECT, DIABIMMUNE, and Infants datasets, achieving area under the receiver operating characteristic curve (AUC) values of 0.896, 0.813, and 0.894, respectively. CONCLUSIONS: For the task of disease phenotype classification based on temporal data, we propose a novel framework that effectively captures the characteristics of time-series data and achieves high accuracy across multiple datasets. Our approach holds promise as a potential new tool for microbial knowledge discovery.},
}

Humans
*Deep Learning
*Gastrointestinal Microbiome/genetics
Phenotype
Long Short Term Memory
Convolutional Neural Networks
Metagenomics/methods
Longitudinal Studies
Predictive Learning Models

@article {pmid41803433,
year = {2026},
author = {Jalal, RS and Alshehrei, FM},
title = {Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803433},
issn = {2045-2322},
support = {UJ-25-DR-1837//University of Jeddah/ ; },
mesh = {*Glycosyltransferases/metabolism/genetics ; *Rhizosphere ; Soil Microbiology ; Phylogeny ; Microbiota ; Plant Roots/microbiology ; Biocatalysis ; },
abstract = {The rhizospheric microbiomes associated with wild plant species Moringa oleifera and Abutilon fruticosum, endemic to the arid northwestern Mecca region of Saudi Arabia, represent untapped reservoirs of genetic capability with significant implications for agriculture, biotechnology, medicine, and environmental sustainability. Leveraging high-throughput metagenomic sequencing and advanced bioinformatics, this study systematically cataloged carbohydrate-active enzymes (CAZymes), with a particular focus on glycosyltransferase (GT) families, within these root-associated microbial consortia. The analysis revealed pronounced compositional divergence between rhizospheric and bulk soil microbiomes, underscoring the influence of plant species and edaphic factors in shaping niche-specific microbial assemblages and functional repertoires. The two rhizospheric microbiomes were consistently enriched in all six CAZy classes, with lineage-specific CAZymes of GT families (GT2 and GT84 in M. oleifera and GT31, GT39, and GT66 in A. fruticosum). These lineage-specific CAZymes catalyze the synthesis of structurally diverse polysaccharides, including cellulose, chitin, β-glucans, mannans, and chondroitin, thereby positioning the rhizospheric microbiomes of Moringa oleifera and Abutilon fruticosum as promising reservoirs of biocatalysts for possible future applications in industrial applications, biomedical engineering, and environmentally sustainable technologies. The evolutionary history of these enzymes in hot, oligohydric soils suggests adaptation to thermal and water-limited conditions, which may render them particularly suitable for deployment in industrial and biotechnological bioreactors. These CAZymes are predicted to be positioned as pivotal assets for sustainable bioeconomy initiatives and possible therapeutic glycoengineering.},
}

*Glycosyltransferases/metabolism/genetics
*Rhizosphere
Soil Microbiology
Phylogeny
Microbiota
Plant Roots/microbiology
Biocatalysis

@article {pmid41805951,
year = {2026},
author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM},
title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41805951},
issn = {1432-184X},
mesh = {*Cacao/microbiology/virology ; Colombia ; Fermentation ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; *Fungi/genetics/classification/isolation & purification/metabolism ; Viruses/genetics/classification/isolation & purification ; *Microbiota ; Desiccation ; *Metagenome ; Food, Processed ; Food Microbiology ; },
abstract = {Shotgun metagenomics is an approach increasingly applied to investigate microbial succession and functional potential in complex fermented food systems, including cocoa bean fermentation. In this study, we used Illumina-based shotgun metagenomic sequencing to characterize microbial community dynamics and metabolic potential across two post-harvest cocoa processing routes (R1 and R2) in Boyacá, Colombia, encompassing both fermentation and drying stages. Cocoa beans were sampled at defined time points during fermentation and subsequent natural drying, and non-host metagenomic reads were subjected to taxonomic classification and functional annotation to assess fungi, bacteria, and viruses. A clear multi-ecological succession was observed throughout post-harvest processing. Fungal communities shifted from a yeast-dominated profile, mainly Saccharomyces and Pichia during fermentation, to the emergence of the filamentous fungus Aspergillus during drying. Bacterial populations transitioned from diverse Enterobacteriaceae in early fermentation to a near-complete dominance of Acetobacter, which persisted throughout the drying phase. Viral communities also displayed structured successional patterns, with Lambdavirus and Punavirus prevalent in early fermentation, followed by Spbetavirus, Lafunavirus, and Pemunavirus during later stages and drying. Functional analyses revealed high metabolic potential for carbohydrate, energy, and amino acid metabolism during early fermentation, followed by a marked reduction in later stages, indicating a metabolic slowdown. Core metabolic functions were retained during drying at substantially lower activity levels. This integrated metagenomic analysis links microbial structure to functional potential and provides a scientific basis for optimizing starter cultures and post-harvest processing strategies to enhance cocoa quality and safety.},
}

*Cacao/microbiology/virology
Colombia
Fermentation
*Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics
*Fungi/genetics/classification/isolation & purification/metabolism
Viruses/genetics/classification/isolation & purification
*Microbiota
Desiccation
*Metagenome
Food, Processed
Food Microbiology

@article {pmid41807604,
year = {2026},
author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L},
title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807604},
issn = {2045-2322},
mesh = {*Bacillus/genetics/isolation & purification/classification ; Italy ; Phylogeny ; Microbiota ; Humans ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.},
}

*Bacillus/genetics/isolation & purification/classification
Italy
Phylogeny
Microbiota
Humans
RNA, Ribosomal, 16S/genetics

@article {pmid41808169,
year = {2026},
author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J},
title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {41808169},
issn = {1475-2859},
support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; },
mesh = {Humans ; *Metabolome ; Multiomics ; Recurrence ; *Calcium Oxalate/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; *Kidney Calculi/microbiology/metabolism ; *Nephrolithiasis/microbiology/metabolism ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Caffeine/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {BACKGROUND: The incidence and recurrence rate of nephrolithiasis have been increasing annually. Recent evidence highlights a close association between the composition and function of the gut microbiome and the occurrence and recurrence of kidney stones. We performed a multi-omic study to investigate changes in gut microbiota and their metabolites during nephrolithiasis development and recurrence, and to explore the underlying molecular mechanisms. Stool samples from 37 recurrent stone patients, 38 first-episode stone patients, and 39 healthy controls were collected for 16S rDNA amplicon sequencing and liquid chromatography-mass spectrometry. Ten samples from each group were randomly selected for metagenomic sequencing. RESULTS: Compared to incident cases, recurrent stone patients exhibited further reduced gut microbial richness and diversity, with enrichment of Enterobacterales, Pseudomonadota, Gammaproteobacteria, Enterobacteraceae, Escherichia-Shigella, and Bacillia. In the recurrent kidney stone group, 9 metabolites were upregulated and 86 downregulated, with enrichment of genes in purine and caffeine metabolism pathways. We identified 10 metabolites as recurrence biomarkers and significant correlations between Escherichia-Shigella and Asn-Tyr, Leu-Ala-Ile, Tyrosyl-Alanine, or 3'-hydroxyhexobarbital. Additionally, gender-specific gut microbiota signatures were observed. Oxalate decarboxylase and short-chain fatty acid-related enzymes decreased during stone formation but rebounded with recurrence. Caffeine and its metabolites were significantly downregulated in recurrent patients, suggesting a potential association with stone formation and recurrence that merits further investigation. CONCLUSIONS: Our study comprehensively characterizes gut microbiome and metabolome signatures associated with nephrolithiasis recurrence. The findings reveal that recurrent nephrolithiasis is characterized by impaired gut microbial evenness, enrichment of specific taxa including Escherichia-Shigella, and dysregulated metabolic pathways such as purine metabolism and caffeine metabolism. The 10 identified metabolites show promise as potential recurrence biomarkers, with notable correlations between Escherichia-Shigella and key metabolites. These results highlight the critical association of the gut microbiome-metabolome axis with renal stone recurrence, providing novel microbial and metabolic targets for early prediction, with potential implications for prevention and personalized treatment that require further validation.},
}

Humans
*Metabolome
Multiomics
Recurrence
*Calcium Oxalate/metabolism
*Gastrointestinal Microbiome
Male
Female
*Kidney Calculi/microbiology/metabolism
*Nephrolithiasis/microbiology/metabolism
Adult
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Middle Aged
Caffeine/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid41824271,
year = {2026},
author = {Singh, K and Sambyal, D and Julka, JM},
title = {Metagenomic exploration of bacterial community shifts before, during, and after passage through earthworm Eutyphoeus waltoni.},
journal = {Biologia futura},
volume = {77},
number = {2},
pages = {387-399},
pmid = {41824271},
issn = {2676-8607},
mesh = {Animals ; *Oligochaeta/microbiology ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; },
abstract = {Understanding the transformation of soil microbial communities during their passage through the earthworm gut provides essential insights into soil health and ecosystem functioning. In this study, we employed 16S rRNA gene sequencing to investigate the bacterial community dynamics in the surrounding soil, gut, and casts of anecic earthworm Eutyphoeus waltoni, an important ecosystem engineer. This research aims to elucidate the microbial selection and transformation processes that occur as microorganisms pass through the earthworm’s alimentary canal. E. waltoni was selected for its significant role in organic matter decomposition and nutrient cycling within Indian soils. While species like Eisenia fetida and Lumbricus terrestris are well-studied, E. waltoni remains understudied despite its ecological importance. We observed notable shifts in microbial communities across the three microhabitats, primarily composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria. The gut environment selectively enriched Firmicutes, particularly Clostridioides, and reduced Proteobacteria. In the cast, microbial recovery was partial, with the presence of genera such as Azospira and Nitrospira, which are linked to nutrient turnover. These findings demonstrate that E. waltoni selectively restructures microbial assemblages, promoting taxa that enhance nutrient cycling and biogeochemical processes.},
}

Animals
*Oligochaeta/microbiology
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Soil Microbiology
*Metagenomics/methods
*Microbiota/genetics

@article {pmid41826874,
year = {2026},
author = {Wang, H and Fu, Y and Xu, H and Song, X 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 = {Viromic profiling of amniotic fluid reveals distinct viral communities associated with maternal health status.},
journal = {BMC pregnancy and childbirth},
volume = {26},
number = {1},
pages = {},
pmid = {41826874},
issn = {1471-2393},
support = {No. 2023YFD1801300//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; JSYGY-1-2023-03(03)//Hospital Management Innovation Research Project of Jiangsu Provincial Hospital Association/ ; Nos. SH2023058, SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; },
mesh = {Humans ; Female ; *Amniotic Fluid/virology ; Pregnancy ; *Virome/genetics ; Phylogeny ; Adult ; China ; Metagenomics ; *Maternal Health ; Case-Control Studies ; Health Status ; },
abstract = {BACKGROUND: Amniotic fluid is a critical compartment in pregnancy; however, its virome remains poorly characterized, and potential associations with maternal–fetal health are largely unexplored. This study aimed to comprehensively profile the human amniotic fluid virome and explore its association with maternal health status during pregnancy. METHODS: We performed viral metagenomic sequencing of 515 amniotic fluid samples from 515 pregnant women in Changzhou, China, including healthy pregnancies (n = 275) and pregnancies with complications (n = 240). Viral sequences were identified using a bioinformatics pipeline, and phylogenetic analyses were used to assess genetic relationships. RESULTS: We identified diverse viral sequences, including members of viral families such as Anelloviridae and Paramyxoviridae. BLAST-based nucleotide comparisons showed high nucleotide identity to previously reported viruses, indicating that many detected sequences are closely related to known viruses. Phylogenetic analyses further supported their placement within established viral taxa. Community-level analyses indicated differences in virome composition profiles between the healthy control and disease groups. CONCLUSIONS: Our findings describe a previously undercharacterized virome in human amniotic fluid. This study establishes a basis for future investigations into the origins and potential associations of these viral signatures with pregnancy health, highlighting the importance of assessing their clinical relevance for both maternal and neonatal outcomes. Because metagenomic sequencing detects viral nucleic acids, these findings do not establish viral infectivity or causality.},
}

Humans
Female
*Amniotic Fluid/virology
Pregnancy
*Virome/genetics
Phylogeny
Adult
China
Metagenomics
*Maternal Health
Case-Control Studies
Health Status

@article {pmid41840154,
year = {2026},
author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A},
title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41840154},
issn = {1678-4405},
support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
mesh = {Animals ; Bees/microbiology/classification ; *Gastrointestinal Microbiome ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; Sympatry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.},
}

Animals
Bees/microbiology/classification
*Gastrointestinal Microbiome
Phylogeny
*Bacteria/classification/genetics/isolation & purification
Sympatry
RNA, Ribosomal, 16S/genetics

@article {pmid41862737,
year = {2026},
author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY},
title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41862737},
issn = {1420-9071},
support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Humans ; *Tryptophan/metabolism ; *Wnt Signaling Pathway ; Rats ; Fibrosis/metabolism ; Male ; Mice ; beta Catenin/metabolism ; *Kidney/pathology/metabolism ; Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; *Kidney Diseases/metabolism/pathology ; Female ; Middle Aged ; },
abstract = {Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism/genetics
Humans
*Tryptophan/metabolism
*Wnt Signaling Pathway
Rats
Fibrosis/metabolism
Male
Mice
beta Catenin/metabolism
*Kidney/pathology/metabolism
Gastrointestinal Microbiome
Rats, Sprague-Dawley
*Kidney Diseases/metabolism/pathology
Female
Middle Aged

@article {pmid41862790,
year = {2026},
author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H},
title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41862790},
issn = {1471-2180},
support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; },
mesh = {Animals ; *Ursidae/microbiology ; Seasons ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification/drug effects ; Feces/microbiology ; *Diet/veterinary ; Plant Leaves ; Metagenomics ; },
abstract = {The nutritional changes of giant pandas (Ailuropoda melanoleuca) in response to the seasonal variations from bamboo shoots (rich in proteins) to fibrous leaves trigger significant alterations in the structure and functions of the gut microbiome. However, the effect these dietary changes have on the gut resistome, especially in older adults, is not well characterized. In this study, shotgun metagenomic sequencing and quantitative PCR (qPCR) were used to investigate the microbial composition, functional potential, and profiles of antibiotic- and metal-resistance genes (ARG and MRG) in feces of adult (n = 11) and geriatric captive pandas (n = 11) that were fed on bamboo shoots or leaves. The microbes varied considerably among diet and age groups, with diet becoming the main source of taxonomic and functional disparity (P < 0.05). Shoot-fed pandas exhibited higher alpha diversity at the genus level and distinct clustering in principal coordinate analyses, whereas leaf-fed groups showed enrichment of taxa associated with fiber degradation and stress tolerance (P < 0.05). Functional annotation of bacterial responses to diet showed changes in carbohydrate processing pathway, carbohydrate transport, and cellular process pathways by changes in the KEGG pathway (P < 0.05). Changes depending on diet were also identified with significant changes in carbohydrate-active enzyme (CAZy) family during changes in the composition of the bamboo parts. Metagenomics and qPCR revealed that several antibiotic resistance genes, such as aac(3)-Xa, bcrA, tet44, sul2 and macB, were highly interacting between diet and age and the most diverse resistome was found in geriatric pandas (P < 0.05). Correlation analysis demonstrated that there is a positive co-occurrence pattern of Enterobacteriaceae and several ARGs. Collectively, our findings demonstrate that seasonal dietary shifts and host aging jointly restructure the gut microbiome and resistome of giant pandas, suggesting diet-mediated modulation of microbial adaptation, resistance dissemination, and ecological resilience in captivity.},
}

Animals
*Ursidae/microbiology
Seasons
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification/drug effects
Feces/microbiology
*Diet/veterinary
Plant Leaves
Metagenomics

@article {pmid41866358,
year = {2026},
author = {Deepthi, M and Vadakkadath Meethal, K},
title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41866358},
issn = {2045-2322},
mesh = {Animals ; *Aedes/microbiology/drug effects ; Larva/microbiology/drug effects ; Recombinant Proteins/pharmacology/genetics ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; Insecticides/pharmacology ; *Antimicrobial Peptides/genetics/pharmacology ; Mosquito Control/methods ; Oligopeptides ; },
abstract = {Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).},
}

Animals
*Aedes/microbiology/drug effects
Larva/microbiology/drug effects
Recombinant Proteins/pharmacology/genetics
Escherichia coli/genetics/metabolism
*Gastrointestinal Microbiome/drug effects
Insecticides/pharmacology
*Antimicrobial Peptides/genetics/pharmacology
Mosquito Control/methods
Oligopeptides

@article {pmid41874663,
year = {2026},
author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C},
title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41874663},
issn = {1432-184X},
support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; },
mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Nitrogen/metabolism ; *Aquaculture ; RNA, Ribosomal, 16S/genetics ; Denitrification ; Nitrification ; Biofilms ; Metagenomics ; *Microbiota ; },
abstract = {The composition and function of bacterial communities in recirculating aquaculture systems (RAS) vary significantly across operational phases and treatment units. Yet the causal links between these bacterial dynamics and nitrogen removal mechanisms remain obscure. In this study, we demonstrated dynamic shifts in bacterial community composition and nitrogen removal function within RAS throughout cultivation and in each unit, by water quality monitoring, 16 S rRNA gene sequencing, metagenomics, 15N isotope tracing and kinetic modeling. Bacterial community composition shifted temporally, marked by a decline in r-strategists and increases in both α- and β-diversity from the start-up to the culture phase, a succession primarily driven by salinity, total dissolved solids, and conductivity. Ecologically, this transition is indicative of a shift in dominant life-history strategies, from an r-selected pioneer community to a K-selected, more stable and resilient community. Denitrification, anammox, and nitrification dominated nitrogen removal pathways, collectively representing 45.2% of the nitrogen-cycling functional genes. In addition, there was significant spatiotemporal heterogeneity in bacterial nitrogen removal. Spatially, aquatic bacteria exhibited higher denitrification activity, while biofilm-attached anammox bacteria of K-strategist demonstrated disproportionately high metabolic activity relative to their low abundance; this was probably regulated by biofilm-associated quorum sensing. Temporally, the ammonia-oxidizing bacteria (AOB) enabled an initial rapid ammonia degradation, whereas nitrite-oxidizing bacteria (NOB) and denitrifiers dominated later-stage decreases in nitrite and nitrate, indicating that the bacterial nitrogen removal function responded to nutrient dynamics. This study demonstrated the coupling mechanisms between ecological adaptation strategies of bacterial communities and nitrogen removal function in RAS, thereby establishing a basis for precision management technologies targeting functional bacteria.},
}

*Bacteria/metabolism/genetics/classification/isolation & purification
*Nitrogen/metabolism
*Aquaculture
RNA, Ribosomal, 16S/genetics
Denitrification
Nitrification
Biofilms
Metagenomics
*Microbiota

@article {pmid41874734,
year = {2026},
author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM},
title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41874734},
issn = {1573-0972},
mesh = {Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Plant Roots/microbiology ; *Calotropis/microbiology ; Archaea/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Brazil ; *Extremophiles ; Soil/chemistry ; Phylogeny ; Ecosystem ; DNA, Bacterial/genetics ; },
abstract = {This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.},
}

Soil Microbiology
*Rhizosphere
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics
Plant Roots/microbiology
*Calotropis/microbiology
Archaea/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Brazil
*Extremophiles
Soil/chemistry
Phylogeny
Ecosystem
DNA, Bacterial/genetics

@article {pmid41888360,
year = {2026},
author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ},
title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41888360},
issn = {1573-0972},
mesh = {*Wastewater/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Mining ; Cyanides/metabolism ; Metagenome ; Gold ; Phylogeny ; Bioreactors/microbiology ; *Microbial Consortia/genetics ; Lakes/microbiology ; Metagenomics ; Aerobiosis ; Whole Genome Sequencing ; Water Purification/methods ; Denitrification ; Sequence Analysis, DNA ; },
abstract = {Biological treatment of cyanide-contaminated wastewater is mediated by microbial consortia in which different organisms perform distinct, functionally specialized roles. This study investigated microbial communities involved in gold mine wastewater treatment with integrated aerobic-anoxic reactors seeded with consortia from an alkaline soda lake, Lake Chitu. Whole-genome sequencing of isolates (WGS) and metagenomic sequencing of the bioreactor were performed to characterize the consortia, resulting in the identification of 23 non-redundant genomes, comprising 14 whole-genome sequencing isolates and 19 metagenome-assembled genomes (MAGs). Most isolated genomes were similar to the recovered metagenomes of MAGs. Except for Alkalibacterium, all isolates possessed one or more genes potentially involved in cyanide or cyanate transformation, along with at least one type of terminal oxygenase; however, the gene encoding cynD, which is required for the direct hydrolysis of free cyanide (CN[-]), was not detected. Three representative Halomonas isolates harboured the nitrate reductase narGHI, nitrite reductase nirS, nitric oxide reductase norB/norC, and nitrous-oxide reductase nosZ genes for full denitrification. All of the isolates possessed several gene clusters associated with different heavy metal resistances. This study suggests that the microbial inoculum sourced from Lake Chitu harbors diverse microorganisms possessing genes potentially involved in cyanide-related metabolic pathways. The findings of this study add to our understanding of the alkaliphilic microbial population that degrades cyanide and cyanide intermediates and provide insight into how these organisms break down cyanide and resist cyanide and heavy metal inhibitory effects.},
}

*Wastewater/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
Mining
Cyanides/metabolism
Metagenome
Gold
Phylogeny
Bioreactors/microbiology
*Microbial Consortia/genetics
Lakes/microbiology
Metagenomics
Aerobiosis
Whole Genome Sequencing
Water Purification/methods
Denitrification
Sequence Analysis, DNA

@article {pmid41894043,
year = {2026},
author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J},
title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41894043},
issn = {1573-7446},
support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology/blood/growth & development/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; Metabolome ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; },
abstract = {The rumen microbial community is influenced by various factors such as diet, age, genetics, and breed. This study employs metagenomics and untargeted metabolomics to investigate the characteristics of rumen microbiota and plasma metabolite changes in crossbred beef cattle (Simmental♀× Belgian Blue♂) as they age, as well as their regulatory effects on growth performance. The LEfse analysis results indicated that the dominant microorganisms in the 12-month-old crossbred beef cattle group were Stomatobaculum sp., Succiniclasticum ruminis, and uncultured Succiniclasticum sp., etc., while the dominant microorganisms in the 18-month-old crossbred beef cattle group were Succinivibrio sp., Oceanobacillus sp., and uncultured Holdemanella sp., etc. The differentially expressed metabolites in the rumen and plasma were significantly enriched in the Pyrimidine metabolism pathway and the Valine, leucine and isoleucine biosynthesis pathway. Through GSEA analysis, it was found that the rumen metabolites Thymidine, 4,5-Dihydroorotic acid, Uracil, and Uridine were more abundant at 12 months of age (P < 0.05), while the plasma metabolite 2s-Amino-3s-methylpentanoic acid was more abundant at 18 months of age (P < 0.05). As the age increases, the rumen microbiota of crossbred beef cattle tends to mature and stabilize, and the ability of rumen metabolites and plasma metabolites to provide protein for the host gradually enhances. In summary, our research results aim to provide basic information on the regulatory role of microorganisms and metabolites in the growth performance of crossbred beef cattle, and also offer targets for precise nutritional regulation of beef cattle.},
}

Animals
*Rumen/microbiology
Cattle/microbiology/blood/growth & development/metabolism
*Gastrointestinal Microbiome
Female
Male
Metabolome
*Microbiota
Bacteria/classification/genetics/isolation & purification
Metagenomics

@article {pmid41903008,
year = {2026},
author = {Heyse, J and Props, R and Defoirdt, T and Boon, N},
title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41903008},
issn = {1573-0972},
support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Penaeidae/microbiology/growth & development ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Aquaculture ; *Microbiota/genetics ; *Water Microbiology ; Metagenome ; Larva/microbiology/growth & development ; Phylogeny ; },
abstract = {Enhancing our understanding of the role of microbial life strategies and their trade-offs in the functioning of microbial communities is essential for improving the management of microbial communities. In aquaculture microbiomes, management aimed at increasing the dominance of K-strategists has experimentally been shown to influence cultivation performance. To understand the mechanisms behind such observations, we need to improve our understanding of the typical properties and behaviour of r- and K-strategists. Several studies have advanced our understanding of theoretical trade-offs that may shape these life strategies, but our understanding of which trade-offs are relevant under natural conditions is still limited. In this study, we investigated the in situ growth strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture by reconstructing 67 high quality metagenome assembled genomes (MAGs), which covered between 31 and 85% of the sampled communities. We found evidence for niche separation between r- and K-biased strategists residing in these communities, with r-biased strategists typically encoding more and more versatile transport and metabolism pathways, and having a higher fitness for exploitation of spatially structured nutrient hotspots. We further increased the knowledge regarding the influence of r- and K-biased strategistson aquaculture cultivation performance by showing that the in situ growth activity of r-biased strategists could be linked better with cultivation performance than the relative abundance of r- and K-biased strategists.},
}

Animals
*Penaeidae/microbiology/growth & development
*Bacteria/classification/genetics/growth & development/isolation & purification
Aquaculture
*Microbiota/genetics
*Water Microbiology
Metagenome
Larva/microbiology/growth & development
Phylogeny

@article {pmid41904418,
year = {2026},
author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S},
title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {41904418},
issn = {2730-6844},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; Adult ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVE: Microbiome being a potential biomarker holds the future hope for insight into GD pathogenesis, diagnosis and cure. Many factors such as diet, lifestyle, environment, host genetics shape the diversity and composition of human microbiome. Although recent studies have indicated that gut microbiome dysbiosis was significantly associated with the onset of gestational diabetes mellitus (GDM). Information on the alteration of gut microbiota composition in Pakistani women is limited. Therefore, present study was designed to elucidate gut microbiota taxonomic composition and relative abundance of taxa in local GD women. DATA DESCRIPTION: 16S Metagenomics data revealed variation in bacterial community structure in gestational diabetic (GD), pregnant non-diabetic (PND), non-pregnant diabetic (NPD) and non-pregnant non-diabetic (NPND) women. Predominant bacterial phyla residing faecal sample of GD, NPD, PND included Firmicutes, Bacteriodota, Proteobacteria accounting for 95.07%, 97.1% and 97.04%, of relative abundance respectively. While Predominant phyla inhabiting faecal sample of NPND included firmicutes, Bacteriodota, and Actinobacteriodota accounting for 98.4%. Simpson’s Reciprocal Index showed great variability, the value ranged between 11.655 and 16.17. The distance matrix depicted dissimilarity between samples with dissimilarity coefficient values ranging between 0.381 and 0.588. These findings would pave the way for future studies, which will aid in early diagnosis, management and treatment. CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Female
*Diabetes, Gestational/microbiology
Pregnancy
*RNA, Ribosomal, 16S/genetics
*Metagenomics
Pilot Projects
*Gastrointestinal Microbiome/genetics
Adult
Feces/microbiology
Bacteria/genetics/classification

@article {pmid41910796,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D},
title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41910796},
issn = {1573-7446},
mesh = {Animals ; *Ponds/microbiology ; *Aquaculture/methods ; Egypt ; *Penaeidae/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; *Water Microbiology ; },
abstract = {Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.},
}

Animals
*Ponds/microbiology
*Aquaculture/methods
Egypt
*Penaeidae/microbiology
*Bacteria/classification/isolation & purification/genetics
*Gastrointestinal Microbiome
*Microbiota
*Water Microbiology

@article {pmid41918091,
year = {2026},
author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J},
title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41918091},
issn = {1471-2180},
support = {2022YFC26023002//National Key Research and Development Program of China/ ; },
mesh = {*Hot Springs/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics/metabolism/isolation & purification ; China ; Metagenomics/methods ; Hot Temperature ; Temperature ; *Microbiota/genetics/physiology ; Phylogeny ; Metagenome ; },
abstract = {BACKGROUND: Understanding microbial adaptation to extreme environments remains a key challenge in microbial ecology. Geothermal hot springs, characterized by temperature gradients and varying geochemical conditions, represent valuable natural laboratories for studying microbial diversity, adaptive strategies, and evolutionary mechanisms. However, despite many studies of hot spring communities, how temperature gradients shape key microbial adaptation strategies remains insufficiently understood, limiting our ability to explain survival and function in extreme environments. RESULTS: Our study investigated microbial community composition and functional profiles across a natural thermal gradient (50–93 °C) in six hot springs on the Western Sichuan Plateau using optimized contig- and MAG-based metagenomic strategies. Enhanced annotation approaches significantly improved taxonomic resolution in these extreme environments. Metagenomic analyses revealed distinct shifts in microbial communities along the thermal gradient: moderate-temperature springs (50–70 °C) were dominated by Pseudomonadota and Bacteroidota, exhibiting heterotrophic flexibility and utilizing the Calvin–Benson–Bassham cycle and diverse nitrogen reduction pathways; high-temperature springs (70–90 °C) were enriched in Chloroflexota, which primarily employed the Wood–Ljungdahl pathway coupled with enhanced sulfur metabolism; and extreme-temperature springs (≥ 90 °C) were characterized by Aquificota and Thermoproteota, relying on specialized autotrophic pathways (rTCA, DH/HH cycles), streamlined nitrogen assimilation, and sulfur oxidation pathways. These thermophilic lineages showed genome streamlining, reduced regulatory complexity, and specialized metabolic strategies, reflecting narrower ecological niches and deeper phylogenetic branches. CONCLUSIONS: This metagenomic investigation across a temperature gradient in western Sichuan hot springs highlights temperature as an essential driver of microbial community structure, genome evolution, and adaptive specialization. Thermophilic lineages in extreme-temperature environments exhibited streamlined genomes, specialized metabolic functions, and narrower ecological niches, consistent with adaptation to persistent thermal stress. The findings enhance understanding of microbial evolutionary strategies and underscore the ecological significance of temperature-driven adaptation in extreme environments.},
}

*Hot Springs/microbiology
*Adaptation, Physiological
*Bacteria/classification/genetics/metabolism/isolation & purification
China
Metagenomics/methods
Hot Temperature
Temperature
*Microbiota/genetics/physiology
Phylogeny
Metagenome