@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Glycine max/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; *Metagenomics ; Animals ; *Metagenome ; Microbiota ; },
abstract = {OBJECTIVES: The metagenomic dataset of 16S rRNA and ITS gene amplicons of DNA were obtained from the cultivated soybean rhizosphere of organic and inorganic treatments. The organic treatments consisted of poultry waste, and cow dung treatments while the inorganic consisted of samples from untreated soybean plots and the bulk. Amplicon sequencing was performed on the Illumina platform, and the raw sequence data were processed and analyzed using Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.). DATA DESCRIPTION: The analysis revealed a metagenomic library from soybean rhizospheric soils, providing insights into diversity and distribution of the bacterial and fungal community diversities. The most predominant bacteria phylum taxa across the treatments were Proteobacteria, Firmicutes, Actinobacteriota and Bacteriodota, while those for fungi were Ascomycota, Basidiomycota and Glomeromycota. The dataset provides insights into how different organic fertilization sources affect the structure, composition, and diversity of the microbiome in the soybean rhizosphere. The sequences have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) with assigned bioproject accession numbers; 16S rRNA (SRP540791) and ITS (SRP541849).},
}

*Rhizosphere
*Soil Microbiology
*Glycine max/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
*Metagenomics
Animals
*Metagenome
Microbiota

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
mesh = {Animals ; *Gene Transfer, Horizontal ; Humans ; Chickens/microbiology ; China ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics ; One Health ; Feces/microbiology ; *Genes, Bacterial ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Interspersed Repetitive Sequences ; East Asian People ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited. RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market. CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.},
}

Animals
*Gene Transfer, Horizontal
Humans
Chickens/microbiology
China
*Bacteria/genetics/drug effects/classification/isolation & purification
*Microbiota/genetics
One Health
Feces/microbiology
*Genes, Bacterial
Metagenomics
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Metagenome
Interspersed Repetitive Sequences
East Asian People

@article {pmid40605035,
year = {2025},
author = {Liu, J and Zhang, Y and Xu, L and Gu, G and Dong, Z},
title = {Parabacteroides johnsonii inhibits the onset and progression of colorectal cancer by modulating the gut microbiota.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {734},
pmid = {40605035},
issn = {1479-5876},
support = {School Science [2022] No.7//Clinical Program of Air Force Medical University/ ; 22BJQN004//Fourth Military Medical University/ ; },
mesh = {Animals ; *Colorectal Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; Humans ; *Disease Progression ; Feces/microbiology ; Male ; Mice ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most prevalent malignant tumor and the second leading cause of cancer-related deaths globally. The genus Parabacteroides is an important component of the gut microbiota. P. distasonis and P. goldsteinii are reported probiotics, and their roles in CRC have been investigated in related studies. However, the association between P. johnsonii and CRC remains unknown. METHODS: P. johnsonii (10–42) and Lactococcus formosensis (22–2) were isolated from healthy human feces. 29 mice that demonstrated normal feeding and activity were randomly assigned to four groups: normal control (NC group), CRC model (IC group), P. johnsonii (PJ group), and L. formosensis (LO group). Colonic tumor tissues from the IC, PJ, and LO groups and normal colon tissues from the NC group were then collected for HE staining and immunohistochemical staining. Fecal samples from mice during the hyperproliferative and adenoma phases were collected for Metagenomic sequencing and metabolite analysis. RESULTS: P. johnsonii intervention reduced the number and slowed the growth of colonic tumors, improved tumor histological scores, and decreased microenvironmental inflammation levels. P. johnsonii improved the composition of intestinal flora in mice with colon cancer, increased gut microbial species diversity, and maintained gut microbiota stability. Furthermore, P. johnsonii intervention increased the abundance of Bifidobacterium pseudolongum and Lactobacillus, which play a role in ameliorating AOM/DSS-induced gut microbiota dysbiosis. P. johnsonii intervention affected the metabolic pathways, including amino sugar degradation and galactose metabolism, sphingolipid synthesis, amino acid synthesis, and polyphenol synthesis pathways, with the tryptophan metabolism pathway as the primary pathway being affected. CONCLUSION: Our study profiled the P. johnsonii administration reduces the number of tumors and lower tumor staging in AOM/DSS-induced colon cancer mice by modulating gut microbiota and its metabolites at early stages.},
}

Animals
*Colorectal Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
Humans
*Disease Progression
Feces/microbiology
Male
Mice

@article {pmid40608175,
year = {2025},
author = {Ye, Z and Yu, Y and Cao, Z and Ye, Z and Gu, X and Shen, X and Cai, B and Lin, B and Ji, C and Qiao, N and Wu, Z and Chen, Z and Ma, Z and Chen, L and Liang, B and Liao, Y and He, W and Shen, Q and Han, J and Cao, X and Zhou, X and Shou, X and Shen, M and Wang, Y and Zhang, Z and Ye, H and Zhang, Q and Gao, R and Zhang, Y},
title = {Microbiome and metabolic disorder in prolactinoma: intrinsic gender differences and extrinsic therapy effects.},
journal = {Pituitary},
volume = {28},
number = {4},
pages = {83},
pmid = {40608175},
issn = {1573-7403},
support = {24ZR1408900//Natural Science Foundation of Shanghai Municipality/ ; 320.6750.2023-13-11//Wu Jieping Medical Foundation/ ; 2023ZD0506800//National Major Science and Technology Projects of China/ ; 82202906//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Prolactinoma/microbiology/drug therapy/metabolism ; Male ; Female ; Adult ; Dopamine Agonists/therapeutic use ; *Pituitary Neoplasms/microbiology/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *Metabolic Diseases/microbiology/drug therapy/metabolism ; Middle Aged ; },
abstract = {PURPOSE: Prolactinoma is the most common functional pituitary adenoma. As for gender disparity in the metabolic state, males tended to have higher rates of metabolic disorders, while treatment with dopamine agonists enabled partial improvement in metabolic disorders. Oral medication used to be the first-line treatment option; thus, the efficacy of dopamine receptor agonists is linked to the intestinal microenvironment. The gut microbiome is known to interact with host physiology and metabolic profile. Therefore, it is necessary to uncover the linkages between the alteration of gut microbiota and prolactinoma. METHODS: 28 Patients diagnosed with prolactinoma and 31 healthy controls were included. Fecal samples were collected for 16 S rRNA gene sequencing and metagenomic sequencing to identify featured intestinal microflora between patients and healthy individuals, as well as to examine how gender and dopamine agonists affect the gut microbiome’s structure. RESULTS: Agathobacter, Blautia, Dorea, Fusicatenibacter, and Mediterraneibacter were prominent in the PRLoma group. Bilophila wadsworthia, Clostridium sp. CAG:7, Megasphaera elsdenii, and Mycoplasma sp. CAG:472 were independently associated with metabolic disorders in male patients. This metabolic regulatory effect may result from the levels of Xylose, the glycine to serine ratio, N2-acetyl, N6, N6-dimethyllysine levels, and the cholesterol to oleoyl-linoleoyl-glycerol (18:1 to 18:2) ratio in plasma. Furthermore, administering dopamine agonists reduced harmful species such as Fusobacterium mortiferum, Bacteroides fragilis, and Ruminococcus biciculans, potentially contributing to an improved metabolic status. CONCLUSIONS: Patients with prolactinoma have different intestinal flora than healthy individuals. In addition to the occurrence of prolactinoma and concomitant serum prolactin excess, the gender effect and administration of dopamine agonists are also involved in regulating intestinal microbiota and the metabolic status of the host.},
}

Humans
*Prolactinoma/microbiology/drug therapy/metabolism
Male
Female
Adult
Dopamine Agonists/therapeutic use
*Pituitary Neoplasms/microbiology/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects/physiology
*Metabolic Diseases/microbiology/drug therapy/metabolism
Middle Aged

@article {pmid40629292,
year = {2025},
author = {Ying, L and Yuhao, W and Yafang, H and Jiao, L and Lina, D and Qinze, S and Chenghai, Y and Shaoxiong, Z and Yuexi, G and Mingwang, S and Zelin, C and Chuangchuang, W and Zihan, G and Xin, L and Lu, M and Lei, Z},
title = {Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {423},
pmid = {40629292},
issn = {1471-2180},
support = {82103868//National Natural Science Foundation of China/ ; 8191101420//National Natural Science Foundation of China/ ; 20220301//Young Talent Fund of Association for Science and Technology in Shaanxi/ ; 2023BSHTBZZ03//Shaanxi Province Postdoctoral Research Project/ ; 2023P098//Shaanxi Provincial Social Science Project/ ; 3111500001//Outstanding Young Scholars Funding/ ; xtr022019003//Xi'an Jiaotong University Basic Research and Profession Grant/ ; YX6J004//Xi'an Jiaotong University Young Talent Support Grant/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Adolescent ; Cross-Sectional Studies ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Male ; Child ; Metabolomics ; Metabolome ; *Stress, Physiological ; Metagenomics ; *Stress, Psychological/microbiology ; },
abstract = {BACKGROUND: Gut microbiota and microbiota-derived metabolites have been implicated in the regulation of stress-related diseases, yet their associations with chronic stress in adolescents remain unclear. Multi-omics studies on this topic in adolescents are still limited. This study aimed to characterize gut microbiota and metabolites in adolescents under chronic stress. METHODS: In this cross-sectional study, we assessed chronic stress in 124 adolescents aged 12–16 years using the Adolescent Life Events Scale and the Study Stress Scale. Participants were stratified by stress level into low (n = 42), medium (n = 41), and high stress (n = 41) groups. Fecal samples were collected from all participants for 16S rRNA gene sequencing. Subsequently, a subset of 30 adolescents with high stress and 29 low stress adolescents underwent metagenomic sequencing and untargeted metabolomics. RESULTS: Adolescents experiencing high-chronic stress showed lower alpha diversity, differential beta diversity, and a more complicated microbial network compared to those experiencing lower stress. Spearman’s rank correlation and Kruskal-Wallis test identified five genera with decreased abundances in high stress adolescents, including Faecalibacterium, Bacteroides, Akkermansia, Lachnospiraceae unclassified, and Ruminococcus (Pfdr<0.05). Additionally, 12 species showed decreased abundances and 5 increased abundances, and logistic regression analysis further revealed that the relative abundances of Bifidobacterium catenulatum, Streptococcus suis, Ruminococcus sp. CAG 108, and Phascolarctobacterium faecium were associated with chronic stress (Pfdr<0.05), after adjusting for sex, age, fruit consumption, and body mass index. We identified 21 differential metabolites, predominantly enriched in metabolic pathways based on KEGG analysis. Moreover, 19 out of these metabolites were significantly correlated with at least one of the four species significantly associated with chronic stress. These metabolites may explain health effects of species associated with chronic stress. CONCLUSIONS: Chronic stress in adolescents is associated with altered gut microbiota composition and metabolite profiles, providing insights into possible mechanisms underlying stress-related diseases and highlighting the importance of longitudinal studies to clarify temporal and causal relationships.},
}

Humans
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Adolescent
Cross-Sectional Studies
*Bacteria/classification/genetics/isolation & purification/metabolism
Female
Male
Child
Metabolomics
Metabolome
*Stress, Physiological
Metagenomics
*Stress, Psychological/microbiology

@article {pmid40790469,
year = {2025},
author = {Qin, M and Ding, W and Qin, L and Liang, R and Guo, Y and Zhao, Y and Xu, H and Wen, Y and Pang, Y and Li, L},
title = {Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {499},
pmid = {40790469},
issn = {1471-2180},
support = {2022TFC2304803//National Key Research and Development Program of China,China/ ; },
mesh = {Humans ; *Tuberculosis, Pulmonary/microbiology ; *Dysbiosis/microbiology ; *Microbiota/genetics ; Female ; *Respiratory System/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Lung/microbiology ; Mouth/microbiology ; Metagenomics/methods ; },
abstract = {BACKGROUND: The microbiota is actively engaged in interaction networks both with the host and among its own constituent members. However, comprehensive studies examining the microbiome profiles across various respiratory sites in pulmonary tuberculosis (PTB) are lacking. Here, we explored the diversity of the microbiome in PTB patients across multiple respiratory sites and investigated potential interactions between the microbiomes of these sites. METHODS: A total of 130 respiratory tract samples were collected from multiple sites of 22 patients with PTB and 14 healthy individuals, including the oral cavity, trachea, and both the healthy and affected sides of the lungs. These samples were subjected to metagenomic sequencing to analyze the characteristics and diversity of the respiratory microbiome. RESULTS: We found that the respiratory tract of PTB patients had higher microbial diversity than seen in the healthy individuals (8,182 vs 6,465). Among them, Rothia, Prevotella and Actinomyces exhibited higher proportions in PTB. The characteristics of high diversity features in the oral site were more prominent with PTB, especially the notable difference of Rothia mucilaginosa. Additionally, Streptococcus, Neisseria, Prevotella and Fusobacterium have strong interactions with other species at present at various sites of PTB patients, as well as frequent communication between these species during migration in the upper and lower respiratory tract. CONCLUSIONS: The diversity and translocation of microbiota across the respiratory tract in PTB patients are associated with increased susceptibility of microbiome. The predominance of Rothia, Prevotella, and Actinomyces may represent progression-associated microbial signatures, warranting mechanistic studies on their pathogenic potential through host-microbe interactions to guide therapeutic targeting.},
}

Humans
*Tuberculosis, Pulmonary/microbiology
*Dysbiosis/microbiology
*Microbiota/genetics
Female
*Respiratory System/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Lung/microbiology
Mouth/microbiology
Metagenomics/methods

@article {pmid40847308,
year = {2025},
author = {Wan, S and Li, M and Li, W and Ren, Y and Wu, Y and Luo, Q and Gong, W},
title = {Development and validation of a multimodal model integrating gut microbiota and metabolite for identifying sarcopenia in patients with MASLD: a study from two centers in China.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {129},
pmid = {40847308},
issn = {1475-2891},
support = {82401448//National Natural Science Foundation of China/ ; 2021A1515110799//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20240813145414019//Shenzhen Science and Technology Program/ ; NSZD2024015//Shenzhen Nanshan District Science and Technology Plan Funding Program/ ; },
mesh = {Humans ; *Sarcopenia/diagnosis/microbiology/metabolism/complications ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; China ; Middle Aged ; Aged ; Feces/microbiology ; Metabolomics/methods ; *Non-alcoholic Fatty Liver Disease/complications/microbiology/metabolism ; *Metabolome ; },
abstract = {BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease worldwide, and identifying sarcopenia is critical since it is correlated with poor prognosis. Little is known about mechanistic alterations in the pathogenesis of this condition. This study aimed to explore the alterations in the gut microbiome and metabolome in patients with sarcopenia and develop a predictive model. METHODS: We performed shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of fecal samples from the discovery cohort (70 patients without sarcopenia, 30 with sarcopenia). A microbiota-metabolite score (MM score) was developed using LASSO regression to identify key microbiome and metabolite features associated with sarcopenia. A multimodal prediction model incorporating the MM score and clinical parameters was then developed and validated in an independent cohort of 50 patients. RESULTS: Patients with sarcopenia exhibited altered gut microbiota and metabolomic profiles, with significantly elevated Enterococcus faecium and Bacteroides vulgatus species, and elevated bile acids. Integration of the MM score with clinical variables (age, BMI, AST, presence of diabetes) resulted in a multimodal model with an AUC of 0.911, outperforming existing models including FIB-4 (AUC 0.765), NFS (AUC 0.724), and using only MM score alone (AUC 0.818). In a prospective validation cohort, the multimodal model demonstrated superior diagnostic performance (AUC 0.897), with significant improvements in clinical utility as evidenced by calibration curves and decision curve analysis. CONCLUSIONS: This study developed a novel multimodal model combining gut microbiome, metabolomics, and clinical data for accurate prediction of sarcopenia, offering a promising approach for early identification of high-risk MASLD patients with sarcopenia.},
}

Humans
*Sarcopenia/diagnosis/microbiology/metabolism/complications
Male
Female
*Gastrointestinal Microbiome/physiology
China
Middle Aged
Aged
Feces/microbiology
Metabolomics/methods
*Non-alcoholic Fatty Liver Disease/complications/microbiology/metabolism
*Metabolome

@article {pmid40859157,
year = {2025},
author = {Gao, ZQ and Su, JW and Qin, Y and Ye, T and Cao, H and Yang, LH and Elsheikha, HM},
title = {Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {553},
pmid = {40859157},
issn = {1471-2180},
mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Vitamin K 2 ; *Vitamin B Complex/biosynthesis ; Metagenome ; },
abstract = {BACKGROUND: The gut microbiota are crucial for synthesizing vitamins vital for chicken health and production, including vitamins B and K2. However, the microbial pathways and temporal dynamics of these vitamins during different laying periods are not well understood, limiting targeted strategies to support poultry health and production. Clarifying these processes is essential for optimizing nutrition and enhancing poultry productivity. RESULTS: This study investigated the metagenomic landscape of microbe-driven vitamin biosynthesis with the aim of elucidating the chicken gut microbiome’s potential to produce vitamins B and K2 across various laying periods. We collected and analyzed 26,053 chicken gut genomes from diverse sources, yielding 14,121 medium-quality, non-redundant genomes for downstream analysis. Genome clustering analysis identified 2,920 species-level genome bins, predominantly from Baccetota. The gene catalog contained approximately 15.09 million non-redundant genes, of which 1.90 million were associated with the biosynthesis of vitamins B and K2. These genes were predominantly distributed among the phyla Bacillota, Bacteroidota, Pseudomonadota and Actinomycetota. Among the 14,121 non-redundant genomes, 3,453 high-quality genomes were identified as capable of de novo synthesizing at least one vitamin. Importantly, 7.67% of these genomes were capable of synthesizing five or more vitamins, while 33.85% could synthesize only one. The comparative genomic analysis of cobalamin biosynthesis underscores the dominance of the anaerobic pathway, with Bacillota emerging as a key contributor. CONCLUSIONS: The findings highlight the microbiome’s crucial role in vitamin biosynthesis, showing substantial taxonomic and temporal variations. This study suggests that microbial involvement plays a pivotal role in vitamin synthesis, which could inform microbiota-based nutritional strategies to support poultry health and productivity.},
}

Animals
*Chickens/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Vitamin K 2
*Vitamin B Complex/biosynthesis
Metagenome

@article {pmid41029837,
year = {2025},
author = {Cabrera, C and Carrión, N and Mateo, D and Vicens, P and Pinzón, A and Heredia, L and Forcadell-Ferreres, E and Pino, M and Yerga, B and Zaragoza, J and Vicente-Pascual, M and Moral, A and Arco, T and Arjó, M and Martínez, E and Galvez, S and Lozano, MJ and Torrente, M},
title = {Gut microbiota characterization in ageing, mild cognitive impairment, and Alzheimer's disease in the context of mediterranean lifestyle in a Spanish population.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {211},
pmid = {41029837},
issn = {1758-9193},
support = {PID2019-103888RB-I00//Ministerio de Ciencia e Innovación/ ; PID2019-103888RB-I00//Agencia Estatal de Investigación/ ; },
mesh = {Humans ; *Alzheimer Disease/microbiology/epidemiology ; Spain/epidemiology ; Female ; Aged ; Male ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology ; Cross-Sectional Studies ; *Aging ; Aged, 80 and over ; Middle Aged ; Case-Control Studies ; Feces/microbiology ; *Diet, Mediterranean ; Life Style ; },
abstract = {BACKGROUND: Alzheimer’s disease (AD) is a neurodegenerative disorder often preceded by a prodromal stage of Mild Cognitive Impairment (MCI). Previous research suggests that gut microbiota (GMB) dysbiosis may contribute to cognitive decline via the microbiota-gut-brain axis (MGBA). Notably, GMB composition patterns can vary across populations and stages of dementia. This study aimed to characterize the GMB in a cohort of older adults from Tarragona (Spain) diagnosed with AD or MCI, or presenting a healthy cognitive status (HC), all of whom follow a Mediterranean lifestyle (ML). METHODS: The present cross-sectional, multicenter case–control study analyzed fecal samples from 99 individuals,including 31 with AD, 30 with MCI, and 38 HC,aged 60–85 years, recruited from seven hospitals and specialized cognitive centers in the province of Tarragona, Spain. Shotgun metagenomic sequencing was conducted with taxonomic profiling using Kraken2. APOE genotyping was performed from fecal DNA using TaqMan assays. Richness, alpha and beta diversity, differential abundance, multivariate linear modeling, and Jonckheere–Terpstra trend tests were conducted to identify GMB species signatures associated with MCI and AD. RESULTS: Richness, alpha and beta diversity did not differ across groups. Differential abundance analysis identified 109 taxa, of which ten microbial species were shared across comparisons. Notably, several species, including Coprococcus comes and Odoribacter splanchnicus, emerged as replicable candidates, showing both discriminatory value and severity-related declines, alongside taxa with context-dependent or adverse associations. CONCLUSIONS: Overall GMB diversity did not differ across cognitive groups, but specific taxa, particularly short-chain fatty acid producers, showed consistent associations with cognitive decline in this ML cohort. These findings support a role for the GMB in AD pathology and suggest that targeting key microbial species may provide novel avenues for prevention and intervention.},
}

Humans
*Alzheimer Disease/microbiology/epidemiology
Spain/epidemiology
Female
Aged
Male
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology
Cross-Sectional Studies
*Aging
Aged, 80 and over
Middle Aged
Case-Control Studies
Feces/microbiology
*Diet, Mediterranean
Life Style

@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Altitude ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; Animals ; Male ; Adult ; Mice ; Female ; Metagenome ; Feces/microbiology ; Amino Acids/blood ; *Bacteria/classification/genetics/isolation & purification ; Phenotype ; Blood Glucose ; Bacteroides ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure. RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-α (TNF-α)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype. CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.},
}

Humans
*Altitude
*Gastrointestinal Microbiome/physiology
*Metabolome
Animals
Male
Adult
Mice
Female
Metagenome
Feces/microbiology
Amino Acids/blood
*Bacteria/classification/genetics/isolation & purification
Phenotype
Blood Glucose
Bacteroides

@article {pmid41060580,
year = {2025},
author = {Vega-Carranza, AS and Escamilla-Montes, R and Luna-González, A and Diarte-Plata, G and Fierro-Coronado, JA and García-Gutiérrez, C and Ceseña, CE},
title = {Investigating the effects of synbiotics, postbiotics and bacilli in the modulation of gut microbiota and the survival of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {4},
pages = {2845-2854},
pmid = {41060580},
issn = {1678-4405},
mesh = {Animals ; *Penaeidae/microbiology/growth & development ; *Synbiotics/analysis/administration & dosage ; *Vibrio parahaemolyticus/physiology ; *Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; *Bacillus/physiology ; },
abstract = {The effect of feed and water additives was evaluated on the gut microbiota and survival of white shrimp challenged with V. parahaemolyticus. Bacillus licheniformis BCR 4 − 3 and vibrio cultures were spray dried. Inulin, probiotics, and postbiotics of bacilli (SPB) and postbiotics of vibrios (PVp) were added to commercial feed. Viable bacilli cells were added to water. An experiment with four treatments in triplicate was performed to determine the effect of diet on survival and the intestinal microbiota by sequencing the V3 region of the bacterial 16S ribosomal gene. Metagenomic analysis was performed on the Shaman, MicrobiomeAnalyst, and Ivikodak platforms. The growth was not affected by the additives but survival of animals in treatments was significantly higher as compared to control group. The phyla and genera that predominated in the white shrimp intestine were Proteobacteria, Bacteroidetes, Firmicutes, Vibrio, Agarivorans, Tropicibacter, and Roseovarius. The Vibrio genus increased in treatments with bacilli in feed and water and decreased in PVp in feed. The control and treatments shared 219 Operational Taxonomic Units. No changes were observed in the bacterial diversity (richness and relative abundance of species). In the bacterial community of the shrimp intestine (species replacement) changes were observed. Bacterial functional profile (Lipid, amino acid, and energy metabolism and digestive and immune systems) was modulated in treatments. Synbiotics, postbiotics, and bacilli in water enhance survival rates and modulated the gut microbiota of L. vannamei.},
}

Animals
*Penaeidae/microbiology/growth & development
*Synbiotics/analysis/administration & dosage
*Vibrio parahaemolyticus/physiology
*Gastrointestinal Microbiome
*Probiotics/administration & dosage
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
*Bacillus/physiology

@article {pmid41073888,
year = {2025},
author = {Michel, A and Leoz, M and Nesi, N and Petat, H and Ar Gouilh, M and Charbonnier Le Clezio, C and Marguet, C and Hassel, C and Plantier, JC},
title = {Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {908},
pmid = {41073888},
issn = {1471-2164},
mesh = {*Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Fungi/genetics/isolation & purification/classification ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; *Respiratory System/microbiology ; *RNA/isolation & purification ; },
abstract = {BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits—one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)—to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p < 0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.},
}

*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
Humans
Fungi/genetics/isolation & purification/classification
Metagenomics/methods
Bacteria/genetics/classification/isolation & purification
*Respiratory System/microbiology
*RNA/isolation & purification

@article {pmid41085588,
year = {2025},
author = {Purohit, HV and Chakraborty, J},
title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {383},
pmid = {41085588},
issn = {1573-0972},
mesh = {*Metagenomics/methods ; *DNA-Binding Proteins/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Microbiota/genetics ; Gene Expression Regulation, Bacterial ; },
abstract = {Nucleoid-associated proteins (NAPs) are small, abundant DNA-binding proteins that play critical roles in bacterial chromosome organization and global gene regulation. In microbial communities, NAPs such as H-NS, HU, IHF, Lrp, Fis, and Dps shape nucleoid architecture and dynamically influence gene expression in response to environmental cues. Culture-dependent investigations in model organisms such as Escherichia coli helped to first identify and functionally characterize important NAPs, hence establishing the basis for knowledge of their structural and regulatory roles. The advent of metagenomics has brought a shift in how we study NAPs, especially within the complex and often uncultivable world of microbial communities. Freed from the constraints of traditional cultivation-based techniques, researchers can now access the collective genetic material of entire ecosystems. High-throughput shotgun sequencing, coupled with advances in single-cell genomics, may allow us to pinpoint NAP-encoding genes directly from environmental DNA. In doing so, we begin to see how these architectural proteins not only shape genomes but also help define the ecological structure, resilience, and adaptability of the communities they inhabit. This review showcases recent progress in the application of metagenomic strategies to NAP research. We also examine the computational hurdles with identification of NAPs within complex datasets, where sequence similarity alone may not be enough to confidently distinguish NAPs from the broader family of DNA-binding proteins. The integration of multi-omics approaches, and high-resolution spatial techniques promises to deepen our understanding of how NAPs function in their native habitats. By capturing the genomic signatures of NAPs across microbial ecosystems, metagenomics is helping to illuminate the central roles these proteins play in genome organization, regulatory control, and environmental adaptation.},
}

*Metagenomics/methods
*DNA-Binding Proteins/genetics/metabolism
*Bacterial Proteins/genetics/metabolism
*Bacteria/genetics/metabolism
*Microbiota/genetics
Gene Expression Regulation, Bacterial

@article {pmid41174528,
year = {2025},
author = {Sharma, D and Valmiki, H and Chayal, P and Kumar, S and Chhotaray, S},
title = {Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {703},
pmid = {41174528},
issn = {1471-2180},
mesh = {Animals ; *Buffaloes/microbiology ; *Milk/microbiology ; Female ; *Microbiota/genetics ; *Mastitis/microbiology/veterinary ; *Acinetobacter/genetics/isolation & purification/classification ; DNA, Bacterial/genetics ; Phylogeny ; Bacteria/classification/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification/classification ; Metagenome ; },
abstract = {Mastitis has been a major challenge in dairy industry incurring heavy loss to dairy farmers. Although targeted antibiotic regime is successful for culturable microbes, the non-culturable and novel microbes are often overlooked. Hence, the present study employed a whole-metagenome profiling to investigate and compare the microbial diversity among the milk samples of healthy and affected buffaloes. 16 Milk samples were collected from Murrah buffaloes and classified into three groups based on the somatic cell count and California Mastitis Test score, i.e., Clinical (3), Sub-clinical (6), and Healthy (7). DNA extraction from milk was followed by Whole Meta-Genome Shotgun (WGS) sequencing to study microbial diversity. The study revealed that Proteobacteria as the most abundant phylum in the clinical mastitis cases, which could be related to the severity of the disease, whereas Firmicutes were strongly associated with the healthy group of buffaloes. The genus Acinetobacter was most abundant in clinical cases (79%) and least in healthy animals (33%). The present study provides important insights into the microbial population and composition in the milk of mastitis-affected buffaloes. The findings will aid in investigating potential therapeutic ways for reducing antibiotic resistance and treatment costs.},
}

Animals
*Buffaloes/microbiology
*Milk/microbiology
Female
*Microbiota/genetics
*Mastitis/microbiology/veterinary
*Acinetobacter/genetics/isolation & purification/classification
DNA, Bacterial/genetics
Phylogeny
Bacteria/classification/genetics/isolation & purification
Proteobacteria/genetics/isolation & purification/classification
Metagenome

@article {pmid41214576,
year = {2025},
author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W},
title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {460},
pmid = {41214576},
issn = {1471-2377},
support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Levodopa/pharmacokinetics/therapeutic use/blood ; *Parkinson Disease/drug therapy/blood ; Male ; Female ; *Antiparkinson Agents/pharmacokinetics/therapeutic use/blood ; Middle Aged ; *Tyrosine Decarboxylase/genetics/metabolism ; *Gastrointestinal Microbiome/physiology ; Aged ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear. METHODS: The aim of this study was to investigate this relationship in Parkinson’s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography‒tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing. RESULTS: A total of 12 PD patients (age: 58.00 ± 8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0–3.0) and a disease duration of 8.46 ± 4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%±17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics. CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.},
}

Humans
*Levodopa/pharmacokinetics/therapeutic use/blood
*Parkinson Disease/drug therapy/blood
Male
Female
*Antiparkinson Agents/pharmacokinetics/therapeutic use/blood
Middle Aged
*Tyrosine Decarboxylase/genetics/metabolism
*Gastrointestinal Microbiome/physiology
Aged
Feces/microbiology

@article {pmid41266970,
year = {2025},
author = {Jin, L and Xu, Q and Miao, C and Zhan, J and Zhang, Y and Li, M and Cheng, J and Liu, P and Yang, Y and Zhou, H and Hu, Z and Li, F and Wu, C},
title = {Dynamic multi-omics analysis reveals the correlation between aroma compounds and symbiotic microbial community during tobacco leaf aging process.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1745},
pmid = {41266970},
issn = {1471-2229},
support = {110202102033//the Key Grant of China National Tobacco Corporation, China/ ; },
mesh = {Multiomics ; *Plant Leaves/microbiology/physiology/metabolism ; *Nicotiana/microbiology/physiology/metabolism ; *Symbiosis ; *Odorants/analysis ; *Volatile Organic Compounds/metabolism ; Gas Chromatography-Mass Spectrometry ; *Plant Senescence ; Proteomics ; *Microbiota ; },
abstract = {Aging in crops like tea and tobacco involves the production of secondary metabolites, with symbiotic microbes playing a key role. However, their dynamic changes and correlation with metabolites during aging remain poorly understood. This study investigates changes in microbial communities, aroma compounds, and protein expression during tobacco leaf aging using artificial accelerated aging techniques, which combine GC-MS, metagenomics, and metaproteomics methods. We identified 62 aroma compounds with distinct change patterns and observed significant changes in the structure of symbiotic bacteria. Type one, represented by Wolbachia_endosymbiont_of_Diaphorina_citri, increased in abundance from the fourth month, correlating with compounds like 2-Furaldehyde. Type two, represented by Sphingomonas_sp_LK11, showed a bimodal abundance pattern, correlating with compounds like Tabanone. Metaproteomics revealed that protein functions were initially limited to cytoskeleton organization but diversified from the fourth month. Fungi also displayed two distinct clustering patterns, Rhizopus and Mortierella elongata were abundant early on, while Colletotrichum asianum and Trichophyton violaceum appeared later. Rhizopus and other fungi exhibited a significant positive correlation with 24 aroma compounds, including 5-Methylfuran-2(5 H)-one. Linderina pennispora and other fungi showed a significant positive correlation with 28 aroma compounds, including 2-Furaldehyde. The dynamic changes in microbial community structure during aging are closely related to the generation of aroma compounds. Overall, temporal shifts in microbial communities were closely linked to aroma formation. One set of microorganisms, such as Wolbachia_endosymbiont_of_Diaphorina_citri and Linderina pennispora, is positively correlated with 2-Furaldehyde, Isophorone, and 2-Methylbenzofuran. Another set, including Sphingomonas_sp_LK11 and Rhizopus, exhibits a positive correlation with 5-Methylfuran-2(5 H)-one and 1,2-Cyclohexanedione. These findings provide new insights into the biological mechanisms of tobacco leaf aging, and offer new research directions for the development and innovation of future tobacco products.},
}

Multiomics
*Plant Leaves/microbiology/physiology/metabolism
*Nicotiana/microbiology/physiology/metabolism
*Symbiosis
*Odorants/analysis
*Volatile Organic Compounds/metabolism
Gas Chromatography-Mass Spectrometry
*Plant Senescence
Proteomics
*Microbiota

@article {pmid41316248,
year = {2025},
author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N},
title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {6},
pmid = {41316248},
issn = {1479-5876},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/virology/blood ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; Metabolomics ; Case-Control Studies ; },
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent metabolic disorder with complex gut microbiome involvement. While bacterial dysbiosis in NAFLD has been widely studied, the role of the gut virome remains largely unexplored. METHODS: We profiled gut viral communities from 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene repertoires were analyzed. Serum metabolomic data were integrated to assess virus–metabolite interactions, and random forest models were constructed to evaluate the diagnostic potential of viral signatures. RESULTS: Overall viral diversity showed no significant differences between NAFLD and controls, but subtle compositional shifts were detected at the vOTU level, with 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched phages primarily targeted Bacteroides, whereas non-NAFLD-enriched phages were associated with beneficial genera such as Faecalibacterium, Oscillibacter, and Prevotella. Functional annotation revealed a reorganization of viral gene repertoires: genes involved in DNA recombination and horizontal transfer (e.g. int, recD) were depleted, while those related to host interaction and stress response (e.g. xerD, dnaK, hipB) were enriched in NAFLD, indicating enhanced viral persistence and host communication. Serum metabolomic profiling identified 8 differential metabolites, and correlation analysis linked specific vOTUs with altered metabolic pathways. A random forest model based on viral features achieved an AUC of 0.758, outperforming the bacterial model, while integration of viral and bacterial features further improved prediction (AUC = 0.837). CONCLUSION: The gut virome in NAFLD undergoes compositional and functional remodeling characterized by a shift toward host-adaptive, metabolically interactive viral communities. These viral alterations are closely associated with host metabolic changes and demonstrate strong diagnostic potential. Our findings highlight the virome as an overlooked yet critical component of the gut ecosystem in NAFLD pathogenesis and as a promising source of noninvasive biomarkers for disease prediction and monitoring.},
}

Humans
*Non-alcoholic Fatty Liver Disease/virology/blood
*Virome/genetics
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
Metabolomics
Case-Control Studies

@article {pmid41318497,
year = {2025},
author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X},
title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {24},
pmid = {41318497},
issn = {1479-5876},
support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; },
mesh = {*Lupus Erythematosus, Systemic/microbiology ; Humans ; *Mycobiome ; *Microbial Interactions ; *Fungi/genetics ; Bacteria ; *Gastrointestinal Microbiome ; Case-Control Studies ; Feces/microbiology ; },
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a complex autoimmune disorder shaped by host genetics and environmental exposures, including the gut microbiota. While bacterial dysbiosis in SLE is well characterized, the role of the gut mycobiome and its cross-kingdom interactions remains largely unexplored. METHODS: Using fecal metagenomic sequencing from 117 SLE patients and 115 healthy controls (HCs), we established a non-redundant fungal genome catalog and revealed significant alterations in fungal composition, function, and cross-kingdom ecology. RESULTS: Fungal diversity was increased in SLE, with enrichment of potentially pathogenic taxa such as Candida, Malassezia, and Trichophyton, and depletion of commensal genera such as Pichia. Functional analysis showed expanded biosynthetic and redox capacities in SLE-associated fungi, including enrichment of RiPP- and terpene-related biosynthetic gene clusters and oxidative stress–related Pfam domains. Several predicted metabolites—such as kynurenine, phenylacetic acid, secondary bile acids, and acylcarnitines—were linked to immune activation and inflammation, suggesting that fungal metabolism may contribute to immune dysregulation. Network analysis revealed sparser and less centralized fungal–bacterial interactions in SLE, indicating disrupted ecological stability and the emergence of fungal taxa as key structural drivers. Integrating fungal and bacterial profiles markedly improved diagnostic performance (AUC = 0.934), underscoring the complementary predictive value of the gut mycobiome. In contrast, post-treatment samples showed reduced fungal richness but no major compositional shifts. CONCLUSIONS: This study provides a comprehensive, multi-dimensional view of the gut mycobiome in SLE, demonstrating its taxonomic, functional, and ecological remodeling. Our findings highlight the potential contribution of fungal metabolic and redox activities to SLE pathogenesis and support the inclusion of fungi in multi-kingdom microbiome frameworks for disease diagnosis and therapeutic development.},
}

*Lupus Erythematosus, Systemic/microbiology
Humans
*Mycobiome
*Microbial Interactions
*Fungi/genetics
Bacteria
*Gastrointestinal Microbiome
Case-Control Studies
Feces/microbiology

@article {pmid41327018,
year = {2025},
author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D},
title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {28},
pmid = {41327018},
issn = {1471-2229},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; },
mesh = {*Soil Microbiology ; *Curcuma/growth & development ; *Soil/chemistry ; Metagenomics ; Agriculture/methods ; *Microbiota ; Nutrients/analysis ; Bacteria/genetics ; Nitrogen/analysis ; },
abstract = {BACKGROUND: Turmeric (Curcuma longa L.) is a key spice, medicinal and industrially important crop that is increasingly being cultivated under sustainable practices such as natural farming system (NFS). This study compares NFS and conventional/chemical farming system (CFS) in terms of soil physicochemical properties, enzyme activities, microbial diversity, and yield parameters, providing a comprehensive understanding of their ecological and agronomic impacts. RESULTS: Field experiments evaluated nine NFS treatments alongside CFS for high throughput amplicon (16S rRNA and ITS) metagenomics, soil physicochemical properties, enzyme activities, and yield parameters. NFS treatments with ≥ 5 t/ha mulching and 4 t/ha Ghanjeevamrit (i.e. NFS-T6 and NFS-T9) significantly enhanced soil organic carbon (~ 0.25%), nitrogen (~ 239.9 kg/ha), and phosphorus (~ 38.16 kg/ha), alongside elevated enzyme activities like alkaline phosphatase (ALP; ~112.11 µg PNP/g/hr) and protease (PR; ~16.22 µg Tyrosine/g/hr). These treatments also exhibited significantly higher microbial richness and evenness (Shannon index: ~5.09; Simpson index: ~0.981). NFS enriched beneficial bacterial (e.g., Priestia, unclassified Acidobacteria, etc.) and saprophytic fungal genera (e.g., Humicola, Mortierella, etc.), enhancing soil nutrient cycling and soil health. Conversely, CFS enriched chemical-resilient and pathogenic taxa (e.g., Alternaria, Curvularia, etc.). NFS-T5 (40.66 t/ha) and NFS-T9 (40.47 t/ha) yielded over twice the fresh rhizome compared to CFS. NFS treatments recorded higher net returns and Benefit-Cost Ratios (BCRs) of 7.51 to 10.57. Microbial profiling of natural farming (NF) inputs (Beejamrit, Jeevamrit, and Ghanjeevamrit) showed distinct bacterial and fungal communities influencing soil microbiome structure. Co-occurrence network analysis of NF soils revealed that microbial taxa introduced via NF inputs had limited integration into native soil communities, indicating selective incorporation governed by competitive ecological interactions. CONCLUSIONS: Natural farming practices significantly enhanced soil fertility, microbial community structure, enzymatic activity (ALP and PR), and turmeric productivity with superior BCRs. These findings provide scientific evidence supporting natural farming as a viable and sustainable agricultural approach, contributing to improved soil health and crop performance in turmeric cultivation.},
}

*Soil Microbiology
*Curcuma/growth & development
*Soil/chemistry
Metagenomics
Agriculture/methods
*Microbiota
Nutrients/analysis
Bacteria/genetics
Nitrogen/analysis

@article {pmid41350554,
year = {2025},
author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M},
title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {560},
pmid = {41350554},
issn = {2045-2322},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Fragile X Syndrome/microbiology/psychology ; Pilot Projects ; Male ; Child ; Female ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {The gut microbiome (GM) is increasingly recognized as a key modulator of neurodevelopment via the microbiome-gut-brain axis. Fragile X syndrome (FXS), the most common inherited monogenic cause of intellectual disability, shares behavioural and molecular features with other neurodevelopmental disorders (NDDs), yet the role of the GM in FXS remains largely unexplored. In this open-label, single-arm trial, 15 children with genetically confirmed FXS received a daily probiotic formulation containing Lactobacillus casei, Lactobacillus salivarius, and Bifidobacterium breve for 12 weeks. Behavioural analysis and metagenomic sequencing with network and pathway analyses were performed before and after probiotic supplementation. Significant improvements were observed in irritability (-3.9, SD: ± 5.2; p = 0.027), communication (+ 1.7, SD: ± 2.5; p = 0.022), socialization (+ 1.4, SD: ± 2.1; p = 0.033), and adaptive behaviour (+ 1.3, SD: ± 1.4; p = 0.004). While overall microbial diversity remained stable, SparCC network analysis revealed increases in connectivity measures such as edge count and clustering coefficient, indicating denser microbial interactions and greater community coordination after probiotic supplementation. Functional profiling showed trends toward increased microbial activity in fatty acid biosynthesis, NAD salvage, and starch degradation pathways. This pilot study provides initial evidence that probiotics may modulate structural and functional properties of the GM, with potential links to improved behavioural outcomes in children with FXS. Larger, controlled trials are needed to validate the therapeutic potential of GM-targeted interventions in FXS and related NDDs.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Fragile X Syndrome/microbiology/psychology
Pilot Projects
Male
Child
Female
*Gastrointestinal Microbiome/drug effects

@article {pmid41361265,
year = {2025},
author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J},
title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {33},
pmid = {41361265},
issn = {1471-2180},
support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Metagenome ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; Phylogeny ; Genome, Bacterial ; },
abstract = {Antibiotic resistance poses a significant threat to human health, and the human gut microbiota serves as a major reservoir of antibiotic resistance genes (ARGs). In this study, we analyzed 149,515 metagenome-assembled genomes (MAGs) from human gut microbiomes and revealed marked geographic variations in the global distribution of gut-associated ARGs. Asia exhibits the highest diversity of ARGs. At the phylum level, Pseudomonadota was identified as the predominant ARG host among pathogenic bacteria, with its pathogenic strains frequently exhibiting high levels of multidrug resistant strains harboring ≥ 5 ARGs accounting for up to 88.5% and 79.1% in Africa and South America, respectively. Campylobacterota was also recognized as a potential high-risk ARG host phylum. Horizontal gene transfer (HGT) analysis revealed that ARG transmission predominantly occurred within the same phylum, with Bacillota being the most active donor, which was likely influenced by antibiotic selection pressure. Actinomycetota and Bacteroidota were identified as major recipients of interphylum HGT, indicating their greater capacity to acquire exogenous ARGs. Through the integration of deep learning and structural calculation, we also identified a potentially novel class of β-lactam resistance genes. This study provides a comprehensive global landscape of gut-associated resistomes, underscores the critical roles of public health infrastructure, antibiotic misuse, and HGT in shaping antimicrobial resistance (AMR), and offers methodological insights for the discovery of novel ARGs. Our findings highlight urgent challenges and provide a scientific basis for developing global AMR mitigation strategies.},
}

Humans
*Metagenome
*Bacteria/genetics/drug effects/classification/isolation & purification
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
*Genes, Bacterial
Phylogeny
Genome, Bacterial

@article {pmid41382117,
year = {2025},
author = {Wang, Y and Bai, Z and Sun, J and Gong, Q and Miao, W and Niu, Z and Li, X and Xu, J and Lai, Z},
title = {Intestinal congestion-driven gut dysbiosis: a cross-disease hemodynamic mechanism in liver cirrhosis and heart failure.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {79},
pmid = {41382117},
issn = {1479-5876},
support = {SYYYRC-2022006//First Hospital of Shanxi Medical University/ ; 202103021224408//Natural Science Foundation of Shanxi Province/ ; 202203021221248//Natural Science Foundation of Shanxi Province/ ; 202204010931008//Shanxi Provincial Science and Technology Department/ ; YDZJSX2021B012//Shanxi Provincial Science and Technology Department/ ; 82470693//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2023065//Health Commission of Shanxi Province/ ; },
mesh = {Humans ; *Liver Cirrhosis/physiopathology/microbiology/complications ; *Heart Failure/physiopathology/complications/microbiology ; *Dysbiosis/physiopathology/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Intestines/pathology/microbiology/physiopathology ; *Hemodynamics ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; },
abstract = {BACKGROUND: Intestinal congestion is a common pathophysiological feature of both liver cirrhosis and heart failure (HF). This study aimed to investigate whether intestinal congestion induces similar gut microbiota and metabolite alterations under both conditions, and to identify key microbial and metabolic signatures. METHODS: We analyzed 117 cirrhosis patients (uncomplicated cirrhosis, cirrhosis with hepatocellular carcinoma, transjugular intrahepatic portosystemic shunt, and liver transplantation), 75 HF patients, and 31 healthy controls (CG). We performed 16S rRNA sequencing on all samples to assess gut microbial diversity, and subjected six representative samples per group to metagenomic sequencing. We conducted untargeted metabolomics on 30 fecal samples each from the uncomplicated cirrhosis, HF with reduced ejection fraction (HFrEF), and CG groups to profile intestinal metabolites, followed by correlation analyses among representative taxa, clinical characteristics, and key metabolites. RESULTS: Intestinal congestion of different etiologies exhibits similar alterations in the gut microbiota, particularly in patients with uncomplicated cirrhosis and HFrEF. Alterations in Bacteroides were closely associated with the severity of congestion. Veillonella and Lactobacillales were enriched in cirrhotic patients, whereas Coprococcus was uniquely abundant in HFs. Metabolomic analysis revealed significant reductions in tripeptides, anti-inflammatory compounds, and prostaglandin analogs in patients with intestinal congestion. Musacin D and neopterin may serve as potential noninvasive biomarkers for HF and cirrhosis, respectively. CONCLUSION: Intestinal congestion is associated with gut microbiota dysbiosis and metabolic disturbances in cirrhosis and HFs, with specific microbes and metabolites showing potential predictive value for distinguishing underlying diseases.},
}

Humans
*Liver Cirrhosis/physiopathology/microbiology/complications
*Heart Failure/physiopathology/complications/microbiology
*Dysbiosis/physiopathology/microbiology/complications
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Intestines/pathology/microbiology/physiopathology
*Hemodynamics
Feces/microbiology
Metabolomics
Case-Control Studies

@article {pmid41398218,
year = {2025},
author = {Huang, R and Zhang, Y and Arif, M and Song, C and Yang, L},
title = {16S rDNA sequencing of the intestinal metagenome of Wanxi White Goose (Anser cygnoides) with different egg production abilities.},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {12},
pmid = {41398218},
issn = {2730-6844},
support = {202423l10050055//Anhui Province Science and Technology Innovation Project/ ; },
mesh = {Animals ; *Geese/microbiology/genetics/physiology ; *RNA, Ribosomal, 16S/genetics ; *DNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Female ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; *Metagenome ; },
abstract = {OBJECTIVES: The Wanxi White Goose (Anser cygnoides) is a large waterfowl of the Anatidae family and one of the most prominent medium-sized goose breeds in China. This breed has been observed to exhibit several distinctive characteristics, including accelerated early growth, robust stress resistance, substantial egg-laying performance, and elevated down production. The egg-laying performance of Wanxi White Geese is influenced by genetic factors, as well as by environmental and feeding management factors. In this study, the intestinal contents from the high-laying and low-laying Wanxi white geese were collected, and the 16 S amplicon sequencing method was used to evaluate the relationship between the composition of intestinal bacterial communities and their egg-laying ability. DATA DESCRIPTION: The 16 S rDNA sequencing technology was utilized to sequence and identify the microorganisms present in the duodenum, jejunum, ileum, and cecum of Wanxi white geese with varying egg-laying abilities. Four biological replicates were collected from each sample across all sections, resulting in a total of 32 samples for subsequent sequencing studies. All raw DNA sequences were uploaded to the Genome Sequence Archive (GSA) database of the National Genomics Data Center (NGDC), which is under the China National Center for Bioinformation. The accession number assigned to the submission is CRA028174, and the BioProject number is PRJCA043467. The clean read sequencing lengths for most samples ranged from 200 to 450 bp. CLINICAL TRIAL NUMBER: Not applicable.},
}

Animals
*Geese/microbiology/genetics/physiology
*RNA, Ribosomal, 16S/genetics
*DNA, Ribosomal/genetics
Sequence Analysis, DNA
Female
*Gastrointestinal Microbiome
*Intestines/microbiology
*Metagenome

@article {pmid41408163,
year = {2025},
author = {Yang, G and He, W and Ma, B and La, Y and Ma, X and Wu, X and Chu, M and Zhao, M and Liu, X and Zhao, Y and Guo, X and Wang, L and Liang, C},
title = {Effects of dietary supplementation with astragalus polysaccharides on growth performance, serum parameters, and rumen microbial function of yaks.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {64},
pmid = {41408163},
issn = {1471-2180},
support = {CARS-37//Modern Beef Yak Industry Technology System/ ; 25ZYJA008//Central Guidance Funds for Local science and technology Development projects/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/growth & development/blood/microbiology/immunology ; *Polysaccharides/administration & dosage/pharmacology ; *Astragalus Plant/chemistry ; *Dietary Supplements ; Male ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation & purification ; Diet/veterinary ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Astragalus polysaccharide (APS) has become a natural feed additive that has attracted much attention in animal husbandry due to its significant immunomodulatory activity, low toxicity and promotion of animal growth performance. In this study, in order to explore the effects of dietary APS on the growth performance and rumen microorganisms of yaks, 20 male yaks aged 2–3 years were selected and randomly divided into two groups: experimental group (1.0 g/kg APS were added to the diet, AG) and control group (no APS were added to the diet, CG), with 10 yaks in each group. After 60 days of continuous feeding, 5 animals were randomly selected from each group to collect rumen fluid. Comparative analysis of rumen microbial composition, function, and metabolites was conducted using metagenomic and metabolomic approaches. RESULTS: The analysis of yak body weight index showed that the body weight of yak in the AG group was significantly higher than that in the CG group on the 60 th day (P < 0.05). In addition, APS significantly increased the immune indexes of IgA, IgM, IgG, IL-10, IGF1, GH, and NOS in yaks (P < 0.05). Metagenomic analysis showed that the beneficial bacteria (such as Euryarchaeota, Methanobrevibacter and Butyrivibrio) in the rumen of yaks were significantly increased after the addition of astragalus polysaccharides in the experimental group. Differential metabolites were significantly enriched in pathways such as Purine metabolism, Galactose metabolism and Tryptophan metabolism that may have a positive impact on the growth and development of yaks. This may promote the production of immune and growth-related metabolites by regulation, and ultimately enhance the immune function and growth performance of yak. CONCLUSIONS: The results showed that the addition of APS could significantly improve the growth performance and immune function of yak. It can also optimize the rumen microbial community. It shows that polysaccharides such as APS can be used as effective substitutes for antibiotics and other drugs for long-term improvement of yak growth performance and rumen health.},
}

Animals
*Rumen/microbiology
Cattle/growth & development/blood/microbiology/immunology
*Polysaccharides/administration & dosage/pharmacology
*Astragalus Plant/chemistry
*Dietary Supplements
Male
Animal Feed/analysis
Bacteria/classification/genetics/isolation & purification
Diet/veterinary
Metagenomics
Gastrointestinal Microbiome/drug effects

@article {pmid41413769,
year = {2025},
author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F},
title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {70},
pmid = {41413769},
issn = {1471-2180},
support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; },
mesh = {*Feces/microbiology ; Humans ; *Bacteria/genetics/metabolism/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Metagenome ; Butyrates/metabolism ; *Gastrointestinal Microbiome/genetics ; Methylamines/metabolism ; Methane/metabolism ; Phylogeny ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial condition in which the gut microbiome (GM) plays a central role. However, taxonomic associations derived from 16S ribosomal RNA (rRNA) gene studies have yielded inconsistent results, likely due to limited resolution and functional redundancy across taxa. We aimed to identify robust, functionally relevant microbial markers of MASLD using metagenomics and gene-centric profiling. METHODS: We analyzed 554 fecal metagenomes from three independent cohorts. Sequencing reads were quality-controlled and taxonomically profiled with multi-marker gene resolution. We quantified the abundance of over 50 target gene families involved in butyrate, methane, trimethylamine (TMA) and short-chain alcohol (SCAs, i.e., ethanol and propanol) metabolism. Their presence was also determined across complete GM genomes and plasmids. RESULTS: Genes involved in butyrate and methane production tended to show lower abundance in MASLD, particularly in cirrhosis, while TMA- and SCA-producing genes were frequently enriched. These functional shifts were accompanied by the depletion of Agathobacter rectalis. Many of the altered genes were highly accessory and encoded on plasmids, suggesting genome-specific functional divergence driven by horizontal gene transfer. CONCLUSION: MASLD is characterized by a shift toward alcohol- and TMA-producing metabolism, alongside reduced butyrate and methane production -changes driven by accessory and plasmid-borne genes. Gene-centric and mobile genetic element-aware profiling reveals mechanistic microbial contributions to MASLD that remain undetected by taxonomy-based approaches, offering new targets for diagnosis and intervention.},
}

*Feces/microbiology
Humans
*Bacteria/genetics/metabolism/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
*Metagenome
Butyrates/metabolism
*Gastrointestinal Microbiome/genetics
Methylamines/metabolism
Methane/metabolism
Phylogeny

@article {pmid41455901,
year = {2025},
author = {Li, X and Zhao, Y and Wu, K and Li, X and Lv, G and Chen, Y and He, L and Sun, W},
title = {Responses of cotton roots and soil microbiota adaptation to drought hardening.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {184},
pmid = {41455901},
issn = {1471-2229},
support = {2022ZD0115801//National Science and Technology Major Project/ ; },
mesh = {*Gossypium/physiology/microbiology/growth & development ; *Plant Roots/physiology/microbiology ; *Soil Microbiology ; *Droughts ; *Microbiota/physiology ; Drought Resistance ; Adaptation, Physiological ; Rhizosphere ; },
abstract = {BACKGROUND: Global climate change has intensified the frequency and severity of drought events, posing significant threats to agriculture in arid regions. As an important economic crop, cotton is highly vulnerable to drought stress, which adversely affects its growth, yield, and associated soil microbial communities. AIMS: This study aimed to conduct an in-depth investigation the effects of drought hardening on cotton root physiology and rhizosphere microbial dynamics by integrating physiological and metagenomic analyses. By analyzing aboveground responses and yield performance of cotton, this study sought to elucidate the comprehensive impact of drought hardening on cotton growth and yield, with the goal of providing a scientific basis for water-saving irrigation strategies in cotton fields in arid regions. METHODS: The experiment was conducted in 2024 at Huaxing Farm in Changji, Xinjiang, using the Zhongmian 113 variety. The experiment used the field water requirement as the control (CK, including the water for seedling emergence, totaling 4950 m[3]/ha), and set three different drought hardening treatments: mild (D1, with 20% water saving during the seedling stage), moderate (D2, with 30% water saving during the seedling stage), and severe (D3, with 40% water saving during the seedling stage). Compared with the control, the total water savings for the entire growth period of treatments D1, D2, and D3 were 12.5%, 15%, and 17.5%, respectively. RESULTS: Based on the performance of cotton growth, development, and yield, the D1 treatment significantly enhanced the antioxidant capacity of cotton roots and effectively maintained cell membrane integrity. Additionally, the D1 treatment significantly altered the diversity of soil fungi, to some extent, this water management practice optimized the structure of the microbial community, and promoted the formation of the dominant bacterial group, Gemmatimonadales. CONCLUSIONS: The study preliminarily revealed the interaction between Gemmatimonadales and cotton roots during the budding stage. Meanwhile, through a comprehensive analysis of cotton growth characteristics, root physiological and biochemical processes, and yield performance, it was shown that the stress resistance of cotton was enhanced under the D1 treatment. This research provided a scientific basis for water-saving irrigation strategies in cotton fields in arid regions, demonstrating that under the D1 condition, it is possible to enhance the stress resistance of cotton while conserving water.},
}

*Gossypium/physiology/microbiology/growth & development
*Plant Roots/physiology/microbiology
*Soil Microbiology
*Droughts
*Microbiota/physiology
Drought Resistance
Adaptation, Physiological
Rhizosphere

@article {pmid41476181,
year = {2025},
author = {Fedi, S and Ghezzi, D and Firrincieli, A and Lopo, E and Romeo, A and Sauro, F and Cappelletti, M},
title = {Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {126},
pmid = {41476181},
issn = {2045-2322},
mesh = {*Caves/microbiology ; *Bacteria/classification/genetics/metabolism ; Metagenomics ; *Microbiota ; Geologic Sediments/microbiology ; Metagenome ; Phylogeny ; Nitrogen Cycle ; *Ice Cover/microbiology ; Nitrogen/metabolism ; Carbon Cycle ; },
abstract = {Investigating the geomicrobiology of the cryosphere offers insights into past climate dynamics and the potential impacts of ongoing climate change. Here, we present the characterization of the microbial communities inhabiting ice sediments collected at various depths within the Cenote Abyss cave, located in the Italian Alps. First explored in 1994 following the drainage of an overlying lake, this site harbours one of the largest cave glaciers in the Dolomites. Metabarcoding and metagenomic analyses revealed a dominance of cold-adapted bacterial taxa, primarily Actinomycetota, Bacteroidota, and Pseudomonadota, with functional genes linked to distinct steps of the nitrogen cycle varying by cave depth. From the shallowest to the deepest ice cave zones, microbial communities shifted from nitrogen-fixing bacterial genera, including Parafrigobacterium, Polaromonas, and Pedobacter, to a higher prevalence of nitrifying bacteria such as Nitrospira. Functional metagenomic analyses revealed that genes involved in nitrogen and carbon cycling are broadly distributed across the cave depth zones, with the inner samples displaying the highest potential for nitrogen transformations, including complete denitrification pathways. CO2 fixation pathways, including the Calvin–Benson–Bassham and Wood–Ljungdahl cycles, were partially represented and taxonomically diverse across the cave depths. Culturable bacterial strains from all depths demonstrated enzymatic activities relevant to organic matter degradation, while phenotype microarray analysis highlighted the metabolic versatility of the inner microbial community in utilizing organic nitrogen substrates, supporting the higher diversity of the inner cave zone compared to the outer cave zone. These findings underscore the ecological complexity and functional potential of microbial life in subterranean ice, offering insights into biogeochemical processes in cold and nutrient-poor environments with implications for climate change studies.},
}

*Caves/microbiology
*Bacteria/classification/genetics/metabolism
Metagenomics
*Microbiota
Geologic Sediments/microbiology
Metagenome
Phylogeny
Nitrogen Cycle
*Ice Cover/microbiology
Nitrogen/metabolism
Carbon Cycle

@article {pmid41513932,
year = {2026},
author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A},
title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4921},
pmid = {41513932},
issn = {2045-2322},
support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d´Educació, Cultura, Universitats i Ocupació, cofinançat per la Unió Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d´Educació, Cultura, Universitats i Ocupació/ ; },
mesh = {Humans ; *Symbiosis ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; Spain ; *Bacteria/genetics/classification ; Adult ; Child ; Feces/microbiology ; Infant ; Female ; Child, Preschool ; Male ; Phylogeny ; },
abstract = {While a proportion of the microbiota plays a beneficial role, there is no conclusive evidence that the entire microbiome is mutualistic. Here, we have studied the intestinal microbiota of three healthy age groups from the Valencian Region (Spain). We have periodically obtained stool samples to determine the 16S rRNA gene amplicons, metagenomes, and metatranscriptomes, and we have observed that the microbiota’s stability differs with age, being less stable in infants. Regarding analyses of the conserved microbiota across the three age groups throughout the study period, shared genera account for about 60%. In addition, we identified a core of microbial taxa present in all individuals, which could represent mutualistic symbionts. Finally, in a previous study, we detected that tryptophan and indole production by intestinal bacteria decreases substantially with host age. Metagenomics and metatranscriptomics analyses show that tryptophanase mRNA synthesis in the genus Akkermansia is approximately 10 times lower in adults and the elderly than in children, consistent with this enzyme’s low levels or absence in these groups. Consequently, this supports the hypothesis that an uncoupling might occur between some microbiota taxa and the human host at older ages.},
}

Humans
*Symbiosis
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
Metagenome
Metagenomics
Spain
*Bacteria/genetics/classification
Adult
Child
Feces/microbiology
Infant
Female
Child, Preschool
Male
Phylogeny

@article {pmid41591600,
year = {2026},
author = {Bilecen Şen, D and Ertürkmen, P and Alp Baltakesmez, D},
title = {Microbiota and quality profiling of fermented goat meat sausages (sucuk) under nitrite-reduced and mixed-culture strategies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {64},
pmid = {41591600},
issn = {1573-0972},
mesh = {Animals ; Fermentation ; *Meat Products/microbiology/analysis ; Goats ; *Nitrites/metabolism ; *Lactobacillales/isolation & purification/classification/genetics/metabolism ; *Microbiota ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The bioprotective activity of lactic acid bacteria (LAB) to modulate the microbiota and quality of nitrite-reduced fermented goat meat sucuk was investigated. Antagonistic activity of LAB strains against foodborne pathogens was evaluated using agar well diffusion, spot-on lawn, and cross-streak assays. Three LAB isolates affiliated with the genera Weissella, Limosilactobacillus, and Lactiplantibacillus, exhibiting inhibition zones > 18 mm, were selected and applied as a mixed culture (MC; 2:1:1). Sucuk formulations with 150, 75, and 0 ppm sodium nitrite were produced in the presence or absence of a MC and analyzed during fermentation (days 0 and 7) and refrigerated storage (days 7 and 14). Among the treatments, 75 ppm nitrite combined with MC (75-MC) exhibited the highest LAB counts, enhanced acidification (pH 4.7 on fermentation day 7), inhibited pathogens and spoilage microorganisms, and improved moisture and color stability (> 90% of initial L* and a*), with a significant treatment × day interaction (P < 0.05). Metagenomic analysis of the 16 S rRNA (V3–V4) and ITS2 regions revealed a LAB-dominated sucuk microbiota, characterized by Levilactobacillus (69.5%), Lactiplantibacillus (12.1%), Psychrobacter (8.8%), and Lacticaseibacillus (3.0%) among bacteria, and Yarrowia (46%), Kurtzmaniella (11.8%), Geotrichum (6.7%), and Cladosporium (5.5%) among fungi. This microbial composition was associated with enhanced microbial stability and technological quality, while mixed-culture strategies under nitrite-reduced conditions promoted a Lactobacillaceae-enriched microbiota, highlighting their potential role in bioprotection and product quality.},
}

Animals
Fermentation
*Meat Products/microbiology/analysis
Goats
*Nitrites/metabolism
*Lactobacillales/isolation & purification/classification/genetics/metabolism
*Microbiota
Food Microbiology
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
Bacteria/classification/genetics/isolation & purification

@article {pmid41604102,
year = {2026},
author = {Rocha, LBA and Gonçalves, VN and de Oliveira, FS and Corrêa, GR and Senra, EO and Duarte, EB and Lopes, FAC and Silva, MC and Convey, P and Câmara, PEAS and Rosa, LH},
title = {Endolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {46},
pmid = {41604102},
issn = {1678-4405},
mesh = {Metagenomics ; *Fungi/classification/genetics/isolation & purification ; Brazil ; DNA, Fungal/genetics ; *Biodiversity ; *Geologic Sediments/microbiology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We evaluated endolithic fungal diversity associated with rocks sampled at the polyextreme Brazilian São Pedro and São Paulo archipelago using a DNA amplicon metagenomics approach. We detected 808,547 fungal DNA reads grouped into 92 amplicon sequence variants (ASVs). The rocks sampled were geologically characterized as mylonitized peridotites, serpentinized peridotites, and carbonate-matrix sedimentary breccias. Ascomycota was the dominant phylum, followed by Basidiomycota, Mucoromycota, Mortierellomycota and Chytridiomycota. Hortaea werneckii, Cladosporium sp., Simplicillium sp., Blastobotrys serpentis, Penicillium sp., P. simplicissimum, Malassezia restricta, Ascomycota sp., Verrucariaceae sp., and Fungal sp. were the dominant assigned taxa. The endolithic assemblages displayed moderate to low diversity indices. Among the fungal community, only the dominant Fungal sp. occurred in all samples. The data obtained in our environmental DNA (eDNA) amplicon metagenomics approach suggest that the rocks of the isolated equatorial São Pedro and São Paulo archipelago host a complex fungal diversity, including taxa regarded to be cosmopolitan, extremophilic hypersaline and xerophilic, plant pathogens, and human/animal opportunistic pathogens. As eDNA studies do not confirm the presence of viable organisms or propagules, further research using culturing approaches is now required to develop strategies to recover these fungi for physiological, biogeochemical, genetic and potential biotechnological studies.},
}

Metagenomics
*Fungi/classification/genetics/isolation & purification
Brazil
DNA, Fungal/genetics
*Biodiversity
*Geologic Sediments/microbiology
Phylogeny
Sequence Analysis, DNA

@article {pmid42156610,
year = {2026},
author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z},
title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.},
journal = {International journal of clinical oncology},
volume = {31},
number = {7},
pages = {1175-1188},
pmid = {42156610},
issn = {1437-7772},
support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/therapy/pathology ; *Dysbiosis/microbiology/complications ; Disease Progression ; *Gastrointestinal Microbiome/physiology ; Prognosis ; Animals ; },
abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.},
}

Humans
*Stomach Neoplasms/microbiology/therapy/pathology
*Dysbiosis/microbiology/complications
Disease Progression
*Gastrointestinal Microbiome/physiology
Prognosis
Animals

@article {pmid42286668,
year = {2026},
author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA},
title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42286668},
issn = {2049-2618},
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Vitamin B 12/metabolism/biosynthesis ; Cattle ; *Rumen/microbiology ; Microbiota ; Archaea/metabolism/genetics ; Female ; Fermentation ; Dietary Supplements ; Animal Feed/analysis ; Diet/veterinary ; Bacteria/classification/genetics/metabolism ; Rhodophyta ; },
abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.

RESULTS: ASP supplementation reduced CH₄ yield by 54% (g CH₄/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH₄ were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION : ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.},
}

Animals
*Methane/metabolism/biosynthesis
*Vitamin B 12/metabolism/biosynthesis
Cattle
*Rumen/microbiology
Microbiota
Archaea/metabolism/genetics
Female
Fermentation
Dietary Supplements
Animal Feed/analysis
Diet/veterinary
Bacteria/classification/genetics/metabolism
Rhodophyta

@article {pmid42309017,
year = {2026},
author = {Yang, X and Liu, W and Mao, Y and Wang, H},
title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.},
journal = {Ecotoxicology and environmental safety},
volume = {320},
number = {},
pages = {120390},
doi = {10.1016/j.ecoenv.2026.120390},
pmid = {42309017},
issn = {1090-2414},
mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Metabolome/drug effects ; *Plant Roots/drug effects/metabolism/microbiology ; *Soil Pollutants/toxicity ; *Cuminum/drug effects/metabolism/microbiology ; *Lead/toxicity ; Soil Microbiology ; Stress, Physiological ; Soil/chemistry ; },
abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.},
}

*Rhizosphere
*Microbiota/drug effects
*Metabolome/drug effects
*Plant Roots/drug effects/metabolism/microbiology
*Soil Pollutants/toxicity
*Cuminum/drug effects/metabolism/microbiology
*Lead/toxicity
Soil Microbiology
Stress, Physiological
Soil/chemistry

@article {pmid42338489,
year = {2026},
author = {Tang, C and Li, B and Chen, J and Liu, X and She, C},
title = {Causal relationship between gut microbiota and adenomyosis: metagenomics sequencing and Mendelian randomization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1772864},
pmid = {42338489},
issn = {2235-2988},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Adenomyosis/microbiology/etiology ; *Mendelian Randomization Analysis ; *Metagenomics/methods ; Middle Aged ; Adult ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in the pathogenesis of adenomyosis (AM); however, whether this association is causal and through which mechanisms it operates remain largely unknown.

METHODS: To interrogate potential causal relationships, we performed a two-sample Mendelian randomization (MR) analysis leveraging inverse-variance weighting (IVW) as the primary estimator, complemented by MR-Egger, weighted median, and weighted mode approaches, to evaluate the causal effects of gut microbial taxa and microbiota-derived metabolic pathways on AM. We further conducted mediation analyzes to delineate the role of circulating immune-cell phenotypes in this process. In parallel, in an independent clinical cohort, 22 patients with AM and 23 age-matched healthy controls recruited from the health-screening center of our institution were enrolled according to stringent inclusion and exclusion criteria (including antibiotic-use history and long-term local residency) and subjected to shotgun metagenomic sequencing. Significant differences in the types of bacterial communities were observed between the AM group and the control group. Subsequently, the results were cross-compared with those of the MR study using the Linear Discriminant Analysis Effect Size (LEfSe) method, and further verified using the ANCOM-BC method to determine the common microbial characteristics.

RESULTS: MR analysis identified ten microbial taxa and ten metabolic pathways with evidence of potential causal associations with AM. Of these, nine taxa and five pathways were associated with a reduced risk of AM, including Alistipes indistinctus (OR = 0.847, 95% CI = 0.754-0.951, p = 0.005, p~FDR~ > 0.05), Ruminococcus torques (OR = 0.818, 95% CI = 0.712-0.941, p = 0.005, p~FDR~ > 0.05), class Deltaproteobacteria (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), family Desulfovibrionaceae (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), order Desulfovibrionales (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), Parasutterella excrementihominis (OR = 0.875, 95% CI = 0.784-0.977, p = 0.017, p~FDR~ > 0.05), Ruminococcus bromii (OR = 0.836, 95% CI = 0.718-0.972, p = 0.020, p~FDR~ > 0.05), Bacteroides finegoldii (OR = 0.919, 95% CI = 0.855-0.987, p = 0.020, p~FDR~ > 0.05), and the genus Parasutterella (OR = 0.886, 95% CI = 0.797-0.986, p = 0.026, p~FDR~ > 0.05); the five protective pathways comprised dTDP-L-rhamnose biosynthesis (OR = 0.819, 95% CI = 0.674-0.995, p = 0.045, p~FDR~ > 0.05), lactose and galactose degradation (OR = 0.818, 95% CI = 0.689-0.972, p = 0.022, p~FDR~ > 0.05), the reductive TCA cycle (OR = 0.919, 95% CI = 0.851-0.993, p = 0.032, p~FDR~ > 0.05), allantoin degradation to glyoxylate (OR = 0.907, 95% CI = 0.830-0.991, p = 0.030, p~FDR~ > 0.05), and glycolysis I (from glucose-6-phosphate) (OR = 0.850, 95% CI = 0.747-0.967, p = 0.013, p~FDR~ > 0.05).Conversely, one taxon and five pathways were associated with an increased risk of AM: the genus Lactobacillus (OR = 1.083, 95% CI = 1.008-1.164, p = 0.030, p~FDR~ > 0.05), degradation of glucose and glucose-1-phosphate (OR = 1.202, 95% CI = 1.056-1.369, p = 0.005, p~FDR~ > 0.05), peptidoglycan biosynthesis (in Enterococcus faecium) (OR = 1.138, 95% CI = 1.007-1.285, p = 0.039, p~FDR~ > 0.05), pyruvate fermentation to acetone (OR = 1.118, 95% CI = 1.001-1.248, p = 0.048, p~FDR~ > 0.05), glycerol degradation to butanol (OR = 1.118, 95% CI = 1.011-1.237, p = 0.031, p~FDR~ > 0.05), and de novo pyrimidine deoxyribonucleotide biosynthesis (OR = 1.216, 95% CI = 1.063-1.390, p = 0.004, p~FDR~ > 0.05).Mediation analysis revealed that the immune phenotype "CD24 on CD24[+]CD27[+] B cells" mediated the pathway from Ruminococcus bromii to AM, accounting for 32.91% of the total effect (p = 0.020).Shotgun metagenomic profiling of the clinical cohort demonstrated no significant differences in α-diversity or β-diversity between the AM and control groups. At the phylum level, the relative abundance of Desulfobacterota was significantly decreased in the AM group (p< 0.05), and at the genus level, Alistipes was similarly reduced (p< 0.05). LEfSe analysis further indicated enrichment of Escherichia and Clostridium in the AM group, whereas Desulfobacterota and Rikenellaceae were enriched in the Control group. Matching the aforementioned results with the Mendelian randomization (MR) outcomes revealed that Desulfovibrionales and Desulfovibrionaceae constituted the shared microbial taxa. This finding was subsequently re-validated and confirmed using the ANCOM-BC method.

CONCLUSIONS: Integrating genetic causal inference with clinical metagenomic validation, this study provides convergent evidence that specific gut microbial taxa, their associated metabolic pathways, and immune-cell-mediated mechanisms may be causally implicated in the development of AM. These findings offer a framework for future microbiota-targeted preventive and therapeutic strategies against AM.},
}

Humans
Female
*Gastrointestinal Microbiome/genetics
*Adenomyosis/microbiology/etiology
*Mendelian Randomization Analysis
*Metagenomics/methods
Middle Aged
Adult
Bacteria/classification/genetics

@article {pmid42340399,
year = {2026},
author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA},
title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42340399},
issn = {1432-184X},
mesh = {*Groundwater/virology/microbiology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; Metagenomics ; *Virome ; Genome, Viral ; *Bacteria/virology/genetics/classification ; Microbiota ; Phylogeny ; Ecosystem ; },
abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.},
}

*Groundwater/virology/microbiology
*Bacteriophages/genetics/classification/isolation & purification/physiology
Metagenomics
*Virome
Genome, Viral
*Bacteria/virology/genetics/classification
Microbiota
Phylogeny
Ecosystem

@article {pmid42341025,
year = {2026},
author = {Wohl, DL and Belder, PT and Mitchell, BD},
title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350558},
pmid = {42341025},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; },
abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Saliva/microbiology
*Amish
Female
Male
Oral Health
Adult
Middle Aged
Dental Plaque/microbiology
Bacteria/genetics/classification

@article {pmid42342731,
year = {2026},
author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H},
title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42342731},
issn = {2055-5008},
support = {100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 323134//Norges Forskningsråd/ ; 323134//Norges Forskningsråd/ ; },
mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.},
}

*Lignin/metabolism
Metagenomics
Xylans/metabolism
*Carboxylic Acids/metabolism
Anaerobiosis
Fermentation
Ethanol/metabolism
Metabolic Networks and Pathways
*Bacteria/metabolism/classification/genetics
Cellulose/metabolism
Microbial Consortia
Lactic Acid/metabolism
Acetic Acid/metabolism
Carbon Dioxide/metabolism

@article {pmid42343233,
year = {2026},
author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM},
title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690689},
doi = {10.1080/19490976.2026.2690689},
pmid = {42343233},
issn = {1949-0984},
mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration & dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; },
abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.},
}

Humans
*Metabolic Syndrome/metabolism/microbiology/therapy
Female
Middle Aged
*Glucagon-Like Peptide 1/metabolism
Male
*Insulin Resistance
Double-Blind Method
*Probiotics/administration & dosage
*Body Composition
Adult
Akkermansia
*Verrucomicrobia
Gastrointestinal Microbiome
Pasteurization
Prediabetic State/metabolism
Aged

@article {pmid42343765,
year = {2026},
author = {Qiu, X and Lei, Z and Wang, J},
title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {5},
pages = {2103-2113},
doi = {10.13345/j.cjb.250783},
pmid = {42343765},
issn = {1872-2075},
support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; },
mesh = {*Solanum lycopersicum/growth & development/drug effects ; *Plant Roots/growth & development/drug effects ; *Seedlings/growth & development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; },
abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.},
}

*Solanum lycopersicum/growth & development/drug effects
*Plant Roots/growth & development/drug effects
*Seedlings/growth & development/drug effects
*Rhizosphere
*Soil Microbiology
*Graphite/pharmacology
*Microbiota/drug effects
Soil/chemistry
Nitrogen/metabolism

@article {pmid42346116,
year = {2026},
author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M},
title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.},
journal = {Cells},
volume = {15},
number = {12},
pages = {},
pmid = {42346116},
issn = {2073-4409},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.},
}

Humans
Multiomics
*Neurodegenerative Diseases/immunology/metabolism
Animals
*Brain/immunology/metabolism
*Metabolic Diseases/immunology/metabolism
Gastrointestinal Microbiome
Metabolomics

@article {pmid42346775,
year = {2026},
author = {He, Z and Nie, Y and Li, C and Sun, G and Zheng, W and Liu, H and Geng, M and Tian, J and Zhang, Y},
title = {GV-971 Ameliorates Chronic Restraint Stress-Induced Depression-like Phenotypes Accompanied by Reshaping of the Microbiota-Gut-Brain Axis.},
journal = {Marine drugs},
volume = {24},
number = {6},
pages = {},
pmid = {42346775},
issn = {1660-3397},
support = {2024CXPT029, 2025CXPT011//Key R&D Program of Shandong Province, China/ ; ZR2024QH615//Shandong Provincial Natural Science Foundation/ ; SYS202205//Shandong Laboratory Program/ ; },
mesh = {Animals ; *Depression/drug therapy/etiology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Brain-Gut Axis/drug effects ; *Oligosaccharides/pharmacology ; Restraint, Physical ; Disease Models, Animal ; *Antidepressive Agents/pharmacology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; Phenotype ; Hippocampus/drug effects/metabolism ; Intestinal Barrier Function ; },
abstract = {Depression is increasingly linked to microbiota-gut-brain axis dysfunction, yet current monoaminergic antidepressants show limited efficacy. This study investigated the therapeutic potential and underlying mechanisms of GV-971, a marine-derived oligosaccharide, in a chronic restraint stress (CRS) mouse model. We first established that 8 h of daily restraint for 4-8 weeks induces a stable depression-like phenotype characterized by behavioral despair and significant reduction in peripheral monoamine neurotransmitters (5-HT and norepinephrine). GV-971 treatment robustly attenuated CRS-induced depression- and anxiety-like behaviors, restored hippocampal serotonin levels, reduced elevated plasma corticosterone concentrations, and ameliorated CRS-induced adrenal cortical hyperplasia. Mechanistically, GV-971 significantly suppressed neuroinflammation by inhibiting microglial hyperactivation in the prefrontal cortex and hippocampus. Concurrently, it repaired intestinal barrier dysfunction, evidenced by reduced permeability, restored mucosal integrity, and recovered goblet cell numbers. Crucially, integrated shot-gun metagenomics and plasma metabolomics revealed that GV-971 not only reshaped microbial taxonomy but also functionally recalibrated the gut ecosystem. It enriched beneficial taxa (e.g., Bifidobacterium pseudolongum, Bacteroides uniformis) and specific metabolic pathways, leading to increased short-chain fatty acids (valeric and caproic acids) and a significant reduction in plasma levels of tryptophan-kynurenine pathway metabolites, specifically the neurotoxic compounds kynurenine and quinolinic acid. Fecal microbiota transplantation (FMT) from GV-971-treated donors partially recapitulated the antidepressant and gut-protective effects in CRS recipients, confirming a causal role for the remodeled microbiota. Collectively, GV-971 exerts antidepressant effects by coordinately remodeling the gut microbiota, normalizing tryptophan and SCFA metabolism, restoring gut barrier integrity, and dampening central neuroinflammation, supporting its potential as a novel gut-brain axis-targeted therapy for depression.},
}

Animals
*Depression/drug therapy/etiology
*Gastrointestinal Microbiome/drug effects
Male
Mice
*Stress, Psychological/drug therapy
*Brain-Gut Axis/drug effects
*Oligosaccharides/pharmacology
Restraint, Physical
Disease Models, Animal
*Antidepressive Agents/pharmacology
Mice, Inbred C57BL
Brain/drug effects/metabolism
Phenotype
Hippocampus/drug effects/metabolism
Intestinal Barrier Function

@article {pmid42347203,
year = {2026},
author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ},
title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060591},
pmid = {42347203},
issn = {2076-0817},
mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration & dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration & dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration & dosage ; },
abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.},
}

Humans
Child
Pilot Projects
Female
Probiotics/administration & dosage
Male
*Microbiota
*Growth Disorders/microbiology/complications
Mouthwashes/administration & dosage
*Mouth/microbiology
Saliva/microbiology/chemistry
Oral Health
Bacteria/classification/genetics
Oils, Volatile/administration & dosage

@article {pmid42101034,
year = {2026},
author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM},
title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70354},
pmid = {42101034},
issn = {1758-2229},
support = {NA19NOS4190106//Texas General Land Office/ ; },
mesh = {*Estuaries ; *Viruses/classification/genetics/isolation & purification ; Salinity ; *Fresh Water/virology/microbiology ; *Temperature ; Bacteria/genetics/classification ; Microbiota ; Metagenomics ; *Virome ; },
abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.},
}

*Estuaries
*Viruses/classification/genetics/isolation & purification
Salinity
*Fresh Water/virology/microbiology
*Temperature
Bacteria/genetics/classification
Microbiota
Metagenomics
*Virome

@article {pmid42123477,
year = {2026},
author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M},
title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {9},
pages = {},
pmid = {42123477},
issn = {1422-0067},
mesh = {Humans ; *Mineral Waters/therapeutic use ; *Balneology/methods ; Dermatitis, Atopic/therapy ; Psoriasis/therapy ; Animals ; Skin/drug effects ; Skin Microbiome ; *Skin Diseases/therapy ; },
abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.},
}

Humans
*Mineral Waters/therapeutic use
*Balneology/methods
Dermatitis, Atopic/therapy
Psoriasis/therapy
Animals
Skin/drug effects
Skin Microbiome
*Skin Diseases/therapy

@article {pmid42223530,
year = {2026},
author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC},
title = {Predator avoidance promotes interbacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42223530},
issn = {1751-7370},
support = {P20GM103432//Institutional Development Award (IDeA)/ ; R35GM140886/GM/NIGMS NIH HHS/United States ; R01GM149795/GM/NIGMS NIH HHS/United States ; },
mesh = {*Symbiosis ; *Soil Microbiology ; *Myxococcales/physiology/genetics/classification/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; *Microbial Consortia ; Metagenomics ; Escherichia coli/physiology ; Gene Transfer, Horizontal ; Metagenome ; },
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to nonsymbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable interbacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

*Symbiosis
*Soil Microbiology
*Myxococcales/physiology/genetics/classification/isolation & purification
Phylogeny
Sequence Analysis, DNA
*Microbial Consortia
Metagenomics
Escherichia coli/physiology
Gene Transfer, Horizontal
Metagenome

@article {pmid42228562,
year = {2026},
author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N},
title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.},
journal = {Cell reports},
volume = {45},
number = {6},
pages = {117478},
doi = {10.1016/j.celrep.2026.117478},
pmid = {42228562},
issn = {2211-1247},
mesh = {Humans ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Proteolysis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Inflammatory Bowel Diseases/microbiology ; Peptide Hydrolases/metabolism ; Proteomics ; Colitis, Ulcerative/microbiology ; Feces/microbiology ; Pouchitis/microbiology ; },
abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.},
}

Humans
*Anti-Bacterial Agents/adverse effects/pharmacology
*Proteolysis/drug effects
*Gastrointestinal Microbiome/drug effects
*Inflammatory Bowel Diseases/microbiology
Peptide Hydrolases/metabolism
Proteomics
Colitis, Ulcerative/microbiology
Feces/microbiology
Pouchitis/microbiology

@article {pmid42249581,
year = {2026},
author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W},
title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.},
journal = {Microbial biotechnology},
volume = {19},
number = {6},
pages = {e70397},
pmid = {42249581},
issn = {1751-7915},
support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; },
mesh = {*Escherichia coli/genetics ; *Polymorphism, Single Nucleotide ; *Colorectal Neoplasms/microbiology ; Humans ; Genome, Bacterial ; Genetic Markers ; Gastrointestinal Microbiome ; Case-Control Studies ; Chromosome Mapping ; Multilocus Sequence Typing ; },
abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.},
}

*Escherichia coli/genetics
*Polymorphism, Single Nucleotide
*Colorectal Neoplasms/microbiology
Humans
Genome, Bacterial
Genetic Markers
Gastrointestinal Microbiome
Case-Control Studies
Chromosome Mapping
Multilocus Sequence Typing

@article {pmid42290500,
year = {2026},
author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F},
title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.},
journal = {Future microbiology},
volume = {21},
number = {8},
pages = {777-794},
pmid = {42290500},
issn = {1746-0921},
mesh = {*Synbiotics/administration & dosage ; Humans ; *Probiotics/therapeutic use/administration & dosage ; *Liver/metabolism/microbiology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; Animals ; *Liver Diseases/therapy/microbiology ; Proteomics ; Metabolomics ; },
abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.},
}

*Synbiotics/administration & dosage
Humans
*Probiotics/therapeutic use/administration & dosage
*Liver/metabolism/microbiology
Multiomics
*Gastrointestinal Microbiome/physiology
Animals
*Liver Diseases/therapy/microbiology
Proteomics
Metabolomics

@article {pmid42324618,
year = {2026},
author = {Hernandez, JB and Abiodun, M and Hayer, SS and Dickson, T and Ayayee, P and Clayton, JB},
title = {Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2687925},
pmid = {42324618},
issn = {1949-0984},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Metagenome/drug effects ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Callithrix/microbiology ; Metagenomics ; Shotgun Sequencing ; Real-Time Polymerase Chain Reaction ; Genome, Bacterial ; Feces/microbiology ; },
abstract = {Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.},
}

Animals
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Metagenome/drug effects
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Callithrix/microbiology
Metagenomics
Shotgun Sequencing
Real-Time Polymerase Chain Reaction
Genome, Bacterial
Feces/microbiology

@article {pmid42324848,
year = {2026},
author = {Santos-Perdomo, I and Salces-Castellano, A and Moraza, ML and Mateos, E and Muñoz-Barrera, A and González-Montelongo, R and Suárez, D and Vega-Pita, N and Falcón-López, L and Lorenzo-Salazar, JM and Flores, C and Arribas, P and Andújar, C},
title = {Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70166},
pmid = {42324848},
issn = {1755-0998},
support = {CGL2015-74178-JIN//Agencia Estatal de Investigación/ ; PID2021-126883NA-I00//Agencia Estatal de Investigación/ ; PID2022-143291NB-I00//Agencia Estatal de Investigación/ ; RYC2020-029196-I//Agencia Estatal de Investigación/ ; RYC2021-034291-I//Agencia Estatal de Investigación/ ; TESIS2022010039//Agencia Canaria de Investigación, Innovación y Sociedad de la Información/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Spain ; Phylogeography ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; *Metagenomics/methods ; Soil ; },
abstract = {Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Biodiversity
Spain
Phylogeography
High-Throughput Nucleotide Sequencing/methods
Genetic Variation
*Metagenomics/methods
Soil

@article {pmid42330062,
year = {2026},
author = {Mason, CJ and Weaver, M and Kissinger, KR and Johnson, MA and Copeland, DC and Anderson, KE and Geib, SM},
title = {Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: impacts on error rates and sequence distributions.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029526},
doi = {10.1128/msphere.00295-26},
pmid = {42330062},
issn = {2379-5042},
abstract = {The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, errors introduced during library preparation remain a major limitation, particularly during PCR amplification of full-length amplicons, where error accumulation may be elevated due to longer sequence lengths. These challenges are amplified when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated PCR cycle autonormalization for PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional fixed-cycle PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Under the workflow tested here, autonormalized libraries generally retained a high proportion of sequences following denoising and chimera removal, exhibited low residual error rates (<0.005%), and yielded relatively even read distributions across heterogeneous sample inputs. Overamplified reactions (30 cycles) showed elevated residual error rates and greater sequence loss, particularly in samples with higher microbial biodiversity, whereas low-cycle libraries produced more variable read output among specimens. Importantly, the PCR protocol had relatively minor effects on overall community composition compared with specimen type. These results support PCR cycle autonormalization as a useful workflow strategy for heterogeneous full-length 16S library preparation, while also highlighting the importance of library design, pooling strategy, and downstream processing in shaping technical outcomes.IMPORTANCEAmplicon-based sequencing of the 16S rRNA gene is a foundational tool in microbiome research, yet PCR amplification remains a major source of library-preparation error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can underamplify low-biomass samples or overamplify high-titer samples, increasing artifacts and sequence loss during downstream processing. Here, we show that PCR cycle autonormalization can be integrated into a PacBio full-length 16S rRNA workflow and, under the conditions tested, provides low residual error rates and relatively even sample representation across heterogeneous inputs. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale library preparation applications handling diverse specimen types.},
}

@article {pmid42337243,
year = {2026},
author = {Hoskinson, C and Dai, DLY and Petersen, C and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Turvey, SE},
title = {Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42337243},
issn = {2041-1723},
support = {[274CHI] and [EC1-144621]//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; [274CHI] and [EC1-144621]//AllerGen (AllerGen National Center of Excellence)/ ; [274CHI] and [EC1-144621]//Genome Canada (Génome Canada)/ ; },
mesh = {Humans ; *Malassezia/genetics/isolation & purification/physiology ; Infant ; Feces/microbiology ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Mycobiome ; Male ; Female ; Child, Preschool ; *Food Hypersensitivity/microbiology/immunology ; Child ; Metagenome ; Metagenomics ; *Hypersensitivity/microbiology ; },
abstract = {While early-life gut bacterial microbiota maturation has been well studied and linked to childhood disease, the development of the gut mycobiome remains poorly understood. Few studies have defined fungal succession in infancy, and even fewer have integrated fungal and bacterial maturation, allowing interkingdom analysis within the same individuals. In this study, we analyzed a subset of the CHILD Study Cohort (n = 1409 participants) and generated both ITS2 amplicon and shotgun metagenomic sequencing data from infant stool samples (n = 2256 samples). We hypothesized that the infant mycobiome follows predictable developmental trajectories that influence childhood health outcomes. We found that fungi are reliable biomarkers for gut maturation, with the notable emergence of Saccharomyces and Malassezia as some of the strongest indicators across both fungi and bacteria. Fungal composition was strongly associated with infant age (R = 0.79, p < 0.001) and with the later development of both atopic dermatitis (adj. p = 0.029) and food allergy (adj. p = 0.013). Further, differences in fungal development coincided with changes in key gut immune-modulating metabolites such as butyrate and glycerol, indicating the functional importance of infant gut mycobiome maturation in early-life immune development. Together, these results highlight the early life mycobiome as a potential therapeutic target to mitigate allergic disease development.},
}

Humans
*Malassezia/genetics/isolation & purification/physiology
Infant
Feces/microbiology
*Dermatitis, Atopic/microbiology/immunology
*Gastrointestinal Microbiome/genetics
Mycobiome
Male
Female
Child, Preschool
*Food Hypersensitivity/microbiology/immunology
Child
Metagenome
Metagenomics
*Hypersensitivity/microbiology

@article {pmid42338488,
year = {2026},
author = {Chen, B and Chen, J and Feng, Z and Lv, H and Lin, Q and Jiang, G},
title = {Gut microbiota reconstruction after liver transplantation and its association with early postoperative infections in patients with liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1845273},
pmid = {42338488},
issn = {2235-2988},
mesh = {Humans ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Retrospective Studies ; *Postoperative Complications/microbiology ; Dysbiosis/microbiology ; Male ; *Liver Failure/surgery/complications ; Probiotics/administration & dosage/therapeutic use ; Middle Aged ; Metagenomics ; Feces/microbiology ; Adult ; *Bacterial Infections/microbiology/epidemiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Postoperative infection remains a major cause of morbidity after liver transplantation (LT) in patients with liver failure. Increasing evidence suggests that gut microbiota dysbiosis may contribute to infection risk, but its dynamic changes after LT are not fully understood.

METHODS: This retrospective study included 60 patients with liver failure who underwent LT and developed postoperative infection-related risk. Patients were divided into a probiotic group and a non-probiotic group. Fecal samples were collected before transplantation and on postoperative days 7, 14, 21, and 28. Metagenomic sequencing was performed to analyze gut microbial composition, diversity, and antibiotic resistance genes.

RESULTS: The probiotic group showed a significantly lower rate of postoperative bacterial infection, especially intra-abdominal infection. After LT, gut microbiota gradually recovered in both groups, but restoration was faster in the probiotic group. The non-probiotic group showed persistent dysbiosis, characterized by enrichment of opportunistic pathogens such as Enterococcus and Klebsiella, whereas beneficial genera including Bifidobacterium and Lactobacillus were more abundant in the probiotic group. Antibiotic resistance genes were also more enriched in the non-probiotic group.

CONCLUSION: Early postoperative gut microbiota reconstruction is closely associated with infectious complications after LT, and modulation of gut microbiota may help improve postoperative outcomes.},
}

Humans
*Liver Transplantation/adverse effects
Female
*Gastrointestinal Microbiome
Retrospective Studies
*Postoperative Complications/microbiology
Dysbiosis/microbiology
Male
*Liver Failure/surgery/complications
Probiotics/administration & dosage/therapeutic use
Middle Aged
Metagenomics
Feces/microbiology
Adult
*Bacterial Infections/microbiology/epidemiology
Bacteria/classification/genetics/isolation & purification

@article {pmid41201496,
year = {2026},
author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C},
title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.},
journal = {Journal of advanced research},
volume = {85},
number = {},
pages = {137-154},
doi = {10.1016/j.jare.2025.10.048},
pmid = {41201496},
issn = {2090-1224},
mesh = {Animals ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; *Diabetic Retinopathy/drug therapy/metabolism ; Rats ; Proto-Oncogene Proteins c-akt/metabolism ; *Plant Extracts/pharmacology ; *Pomegranate/chemistry ; Vascular Endothelial Growth Factor A/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; *Gastrointestinal Microbiome/drug effects ; Signal Transduction/drug effects ; Male ; Diabetes Mellitus, Experimental/metabolism/complications ; Oxidative Stress/drug effects ; Humans ; Rats, Sprague-Dawley ; Cell Line ; Reactive Oxygen Species/metabolism ; },
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.

OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.

METHODS: PPE was extracted using 50 % ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.

RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1α/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.

CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1α/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.},
}

Animals
Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
*Diabetic Retinopathy/drug therapy/metabolism
Rats
Proto-Oncogene Proteins c-akt/metabolism
*Plant Extracts/pharmacology
*Pomegranate/chemistry
Vascular Endothelial Growth Factor A/metabolism
Phosphatidylinositol 3-Kinases/metabolism
*Gastrointestinal Microbiome/drug effects
Signal Transduction/drug effects
Male
Diabetes Mellitus, Experimental/metabolism/complications
Oxidative Stress/drug effects
Humans
Rats, Sprague-Dawley
Cell Line
Reactive Oxygen Species/metabolism

@article {pmid41861238,
year = {2026},
author = {Loop Yao, M and Dai, Y and Zhang, W},
title = {Natural Products from the Oral Microbiome.},
journal = {Annual review of biochemistry},
volume = {95},
number = {1},
pages = {569-593},
doi = {10.1146/annurev-biochem-051024-050248},
pmid = {41861238},
issn = {1545-4509},
mesh = {Humans ; *Biological Products/metabolism/chemistry ; *Microbiota ; *Mouth/microbiology ; Peptide Synthases/metabolism/genetics ; Polyketide Synthases/metabolism/genetics ; Multigene Family ; *Bacteria/metabolism/genetics ; },
abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.},
}

Humans
*Biological Products/metabolism/chemistry
*Microbiota
*Mouth/microbiology
Peptide Synthases/metabolism/genetics
Polyketide Synthases/metabolism/genetics
Multigene Family
*Bacteria/metabolism/genetics

@article {pmid41966829,
year = {2026},
author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, SÁ and Ferenczi, S and Szőke, Z},
title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104498},
pmid = {41966829},
issn = {2666-1667},
mesh = {Animals ; Glyphosate ; *Mycotoxins/analysis/toxicity ; *Glycine/analogs & derivatives/analysis/blood ; *Deer/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/chemistry/microbiology ; Metagenome/drug effects ; Computational Biology/methods ; Shotgun Sequencing ; Chromatography, Liquid ; },
abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].},
}

Animals
Glyphosate
*Mycotoxins/analysis/toxicity
*Glycine/analogs & derivatives/analysis/blood
*Deer/microbiology
*Gastrointestinal Microbiome/drug effects/genetics
Feces/chemistry/microbiology
Metagenome/drug effects
Computational Biology/methods
Shotgun Sequencing
Chromatography, Liquid

@article {pmid42083059,
year = {2026},
author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B},
title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42083059},
issn = {2049-2618},
support = {284894//Fonds de recherche du Québec/ ; },
mesh = {Humans ; Metagenomics/methods ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/microbiology ; Male ; Female ; *Melanoma/drug therapy/immunology/microbiology ; Feces/microbiology ; Animals ; *Lung Neoplasms/drug therapy/immunology/microbiology ; Colitis/microbiology/chemically induced/immunology ; Middle Aged ; Mice ; Aged ; Bacteria/classification/genetics/isolation & purification ; Ruminococcus/isolation & purification ; Eubacteriales ; },
abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.

RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade ≥ 2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade ≥ 2 irAE had a lower alpha diversity compared to those who did not develop grade ≥ 2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade ≥ 2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin immunofluorescence signal and increased TNF-α and IL-1β expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also maintained after treatment with P. bifermentans < 3 kDa filtered supernatant.

CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.},
}

Humans
Metagenomics/methods
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*Gastrointestinal Microbiome/genetics
*Carcinoma, Non-Small-Cell Lung/drug therapy/immunology/microbiology
Male
Female
*Melanoma/drug therapy/immunology/microbiology
Feces/microbiology
Animals
*Lung Neoplasms/drug therapy/immunology/microbiology
Colitis/microbiology/chemically induced/immunology
Middle Aged
Mice
Aged
Bacteria/classification/genetics/isolation & purification
Ruminococcus/isolation & purification
Eubacteriales

@article {pmid42084683,
year = {2026},
author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M},
title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.},
journal = {Environmental science and pollution research international},
volume = {33},
number = {16},
pages = {7765-7777},
pmid = {42084683},
issn = {1614-7499},
mesh = {*Rivers/microbiology ; India ; Virulence Factors ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Anti-Bacterial Agents ; Water Microbiology ; Bacteria/genetics ; *Microbiota ; Drug Resistance, Bacterial ; },
abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.},
}

*Rivers/microbiology
India
Virulence Factors
*Drug Resistance, Microbial/genetics
Metagenomics
Anti-Bacterial Agents
Water Microbiology
Bacteria/genetics
*Microbiota
Drug Resistance, Bacterial

@article {pmid42014682,
year = {2026},
author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI},
title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42014682},
issn = {2041-1723},
support = {F30 DK142304/DK/NIDDK NIH HHS/United States ; DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Transcriptome ; *Gene Expression Profiling/methods ; Bacteria/genetics/classification ; *Metagenomics/methods ; Germ-Free Life ; },
abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.},
}

Humans
Animals
Mice
Metagenome/genetics
*Microbiota/genetics
*Transcriptome
*Gene Expression Profiling/methods
Bacteria/genetics/classification
*Metagenomics/methods
Germ-Free Life

@article {pmid42014730,
year = {2026},
author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W},
title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42014730},
issn = {2052-4463},
support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; },
mesh = {*Kelp/microbiology ; Aquaculture ; *Microbiota ; *Metagenome ; Phylogeny ; Bacteria/classification/genetics ; Archaea/genetics/classification ; },
abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.},
}

*Kelp/microbiology
Aquaculture
*Microbiota
*Metagenome
Phylogeny
Bacteria/classification/genetics
Archaea/genetics/classification

@article {pmid42034087,
year = {2026},
author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z},
title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.},
journal = {Food chemistry},
volume = {516},
number = {},
pages = {149287},
doi = {10.1016/j.foodchem.2026.149287},
pmid = {42034087},
issn = {1873-7072},
mesh = {*Biogenic Amines/metabolism ; Fermentation ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Sodium Chloride/metabolism/analysis ; *Wine/microbiology/analysis ; Microbiota ; },
abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.},
}

*Biogenic Amines/metabolism
Fermentation
*Bacteria/metabolism/genetics/classification/isolation & purification
*Sodium Chloride/metabolism/analysis
*Wine/microbiology/analysis
Microbiota

@article {pmid42069617,
year = {2026},
author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG},
title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42069617},
issn = {1756-3305},
support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Animals ; *Toxoplasma/isolation & purification/pathogenicity/genetics ; *Arachidonic Acid/metabolism/pharmacology ; *Toxoplasmosis, Animal/parasitology/pathology ; Mice, Inbred C57BL ; Mice ; Gastrointestinal Microbiome ; *Intestines/pathology/parasitology ; Female ; Virulence ; Animals, Wild/parasitology ; },
abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.

METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.

RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.

CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.},
}

Animals
*Toxoplasma/isolation & purification/pathogenicity/genetics
*Arachidonic Acid/metabolism/pharmacology
*Toxoplasmosis, Animal/parasitology/pathology
Mice, Inbred C57BL
Mice
Gastrointestinal Microbiome
*Intestines/pathology/parasitology
Female
Virulence
Animals, Wild/parasitology

@article {pmid42207030,
year = {2026},
author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S},
title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.},
journal = {Food & function},
volume = {17},
number = {12},
pages = {5410-5424},
doi = {10.1039/d6fo01620k},
pmid = {42207030},
issn = {2042-650X},
mesh = {Animals ; Mice ; Liver/metabolism/drug effects ; *Plant Extracts/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Dexamethasone/adverse effects ; *Fatty Liver/chemically induced/drug therapy/metabolism ; *Tea/chemistry ; Mice, Inbred C57BL ; Multiomics ; Camellia sinensis/chemistry ; },
abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.},
}

Animals
Mice
Liver/metabolism/drug effects
*Plant Extracts/pharmacology
Male
*Gastrointestinal Microbiome/drug effects
*Dexamethasone/adverse effects
*Fatty Liver/chemically induced/drug therapy/metabolism
*Tea/chemistry
Mice, Inbred C57BL
Multiomics
Camellia sinensis/chemistry

@article {pmid41566339,
year = {2026},
author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A},
title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {67},
pmid = {41566339},
issn = {2049-2618},
support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Animals ; Swine/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Acinetobacter/isolation & purification/genetics ; Abattoirs ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Food Storage ; Metagenome ; Food Handling ; Food, Processed ; Pseudomonas/isolation & purification/genetics ; Brochothrix/isolation & purification/genetics ; Food Microbiology ; },
abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.},
}

Animals
Swine/microbiology
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification/drug effects
Acinetobacter/isolation & purification/genetics
Abattoirs
*Pork Meat/microbiology
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics
Metagenomics
Food Storage
Metagenome
Food Handling
Food, Processed
Pseudomonas/isolation & purification/genetics
Brochothrix/isolation & purification/genetics
Food Microbiology

@article {pmid41567008,
year = {2026},
author = {Zhao, S and Rogers, MJ and Ding, C and He, J},
title = {Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides.},
journal = {Environmental science & technology},
volume = {60},
number = {4},
pages = {3364-3373},
doi = {10.1021/acs.est.5c14525},
pmid = {41567008},
issn = {1520-5851},
mesh = {*Dehalococcoides/metabolism/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br[-]/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.},
}

*Dehalococcoides/metabolism/genetics
Phylogeny
Biodiversity

@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}

@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}

Humans
*Cognitive Dysfunction/microbiology
*Alzheimer Disease/microbiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
Probiotics/therapeutic use
*Brain

@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {33},
number = {4},
pages = {1447-1458},
pmid = {41569365},
issn = {1614-7499},
mesh = {Portugal ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Soil Pollutants/analysis ; *Microplastics/analysis ; Environmental Monitoring ; *Soil Microbiology ; Bacteria ; Soil/chemistry ; Microbiota ; },
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}

Portugal
*Polycyclic Aromatic Hydrocarbons/analysis
*Soil Pollutants/analysis
*Microplastics/analysis
Environmental Monitoring
*Soil Microbiology
Bacteria
Soil/chemistry
Microbiota

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

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

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

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

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

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

@article {pmid41570486,
year = {2026},
author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K},
title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.},
journal = {Journal of neuroimmunology},
volume = {413},
number = {},
pages = {578870},
doi = {10.1016/j.jneuroim.2026.578870},
pmid = {41570486},
issn = {1872-8421},
mesh = {Humans ; Animals ; *Neuroinflammatory Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology/drug effects ; *Gastrointestinal Microbiome/physiology/drug effects ; *Cognitive Aging/physiology ; *Probiotics/administration & dosage ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; },
abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.},
}

Humans
Animals
*Neuroinflammatory Diseases/metabolism/microbiology
*Brain-Gut Axis/physiology/drug effects
*Gastrointestinal Microbiome/physiology/drug effects
*Cognitive Aging/physiology
*Probiotics/administration & dosage
*Brain/metabolism
*Dysbiosis/metabolism
*Aging

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

*Lakes/microbiology
*Nitrogen Cycle
*Microbiota
Nitrogen
Metagenomics
Metagenome
Proteobacteria
Denitrification
Bacteria

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

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

@article {pmid41572308,
year = {2026},
author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K},
title = {Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {40},
pmid = {41572308},
issn = {1743-422X},
support = {23-75-10125//Russian Science Foundation/ ; },
mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Computational Biology/methods ; Virome ; Genome, Viral ; },
abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.},
}

Humans
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Metagenome
*Gastrointestinal Microbiome
Metagenomics/methods
Computational Biology/methods
Virome
Genome, Viral

@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.},
journal = {Acta neuropsychiatrica},
volume = {38},
number = {},
pages = {e16},
pmid = {41572438},
issn = {1601-5215},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology/genetics ; Metagenomics/methods ; Female ; Dysbiosis/microbiology ; Male ; Adult ; *Cognition/physiology ; Oxidative Stress ; Middle Aged ; },
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune–metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Major Depressive Disorder/microbiology/metabolism/psychology/genetics
Metagenomics/methods
Female
Dysbiosis/microbiology
Male
Adult
*Cognition/physiology
Oxidative Stress
Middle Aged

@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {53},
number = {1},
pages = {34-44},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota/genetics ; *Dysbiosis/microbiology/etiology ; Metagenomics ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; Saliva/microbiology ; *Mouth/microbiology ; Adolescent ; *Dental Debonding ; },
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}

Humans
Longitudinal Studies
*Orthodontic Appliances, Fixed/adverse effects
*Microbiota/genetics
*Dysbiosis/microbiology/etiology
Metagenomics
Female
RNA, Ribosomal, 16S/genetics
Male
Saliva/microbiology
*Mouth/microbiology
Adolescent
*Dental Debonding

@article {pmid41572827,
year = {2025},
author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y},
title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.},
journal = {Immunotherapy},
volume = {17},
number = {17-18},
pages = {1231-1239},
pmid = {41572827},
issn = {1750-7448},
mesh = {Humans ; Multiomics ; *Dysbiosis/metabolism ; *Thrombocytopenia/chemically induced/metabolism ; *Gastrointestinal Microbiome ; *Immune Checkpoint Inhibitors/adverse effects ; Proteomics ; Metabolomics ; Female ; Male ; Middle Aged ; Aged ; *Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.

METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.

RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.

CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.},
}

Humans
Multiomics
*Dysbiosis/metabolism
*Thrombocytopenia/chemically induced/metabolism
*Gastrointestinal Microbiome
*Immune Checkpoint Inhibitors/adverse effects
Proteomics
Metabolomics
Female
Male
Middle Aged
Aged
*Neoplasms/drug therapy

@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {Animals ; Phylogeny ; *Metagenomics ; Tibet ; *Feces/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Cattle/virology ; *Virome/genetics ; Genome, Viral ; *Picornaviridae/genetics/classification/isolation & purification ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}

Animals
Phylogeny
*Metagenomics
Tibet
*Feces/virology
*DNA Viruses/genetics/classification/isolation & purification
Cattle/virology
*Virome/genetics
Genome, Viral
*Picornaviridae/genetics/classification/isolation & purification

@article {pmid41575223,
year = {2026},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41575223},
issn = {1751-7370},
support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; },
mesh = {Humans ; *Plasmids/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Extrachromosomal DNA ; },
abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.},
}

Humans
*Plasmids/genetics
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Metagenome
Extrachromosomal DNA

@article {pmid41576514,
year = {2026},
author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H},
title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106487},
pmid = {41576514},
issn = {1525-3171},
mesh = {Animals ; *Geese/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics ; *Metagenome ; *Animal Husbandry ; Metagenomics ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Farmers ; },
abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.},
}

Animals
*Geese/microbiology
*Gastrointestinal Microbiome
Humans
*Drug Resistance, Microbial/genetics
*Bacteria/drug effects/genetics
*Metagenome
*Animal Husbandry
Metagenomics
Feces/microbiology
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Farmers

@article {pmid41576933,
year = {2026},
author = {Hernandez-Leyva, AJ and Berna, AZ and Bui, MH and Liu, Y and Rosen, AL and Lint, MA and Whiteside, SA and Jaeger, N and McDonough, RT and Joardar, N and Santiago-Borges, J and Tomera, CP and Luo, W and Odom John, AR and Kau, AL},
title = {The gut microbiota shapes the human and murine breath volatilome.},
journal = {Cell metabolism},
volume = {38},
number = {4},
pages = {779-793.e8},
pmid = {41576933},
issn = {1932-7420},
support = {T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 HD109963/HD/NICHD NIH HHS/United States ; R21 AI154370/AI/NIAID NIH HHS/United States ; R33 HD105594/HD/NICHD NIH HHS/United States ; F30 DK127584/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Volatile Organic Compounds/metabolism/analysis ; Breath Tests ; Mice ; *Gastrointestinal Microbiome ; Child ; Female ; Male ; Asthma/microbiology/metabolism ; Gas Chromatography-Mass Spectrometry ; Germ-Free Life ; Child, Preschool ; Mice, Inbred C57BL ; },
abstract = {The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. As a proof of principle, we demonstrated that exhaled breath predicts the abundance of a disease-associated bacterium, Eubacterium siraeum, in children with asthma. Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of non-invasive microbiome diagnostics.},
}

Animals
Humans
*Volatile Organic Compounds/metabolism/analysis
Breath Tests
Mice
*Gastrointestinal Microbiome
Child
Female
Male
Asthma/microbiology/metabolism
Gas Chromatography-Mass Spectrometry
Germ-Free Life
Child, Preschool
Mice, Inbred C57BL

@article {pmid41576939,
year = {2026},
author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H},
title = {Microbiota from young mice restore the function of aged ISCs.},
journal = {Stem cell reports},
volume = {21},
number = {2},
pages = {102788},
pmid = {41576939},
issn = {2213-6711},
support = {R01 DK137771/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Aging ; Mice ; *Intestinal Mucosa/cytology/metabolism/microbiology ; Regeneration ; *Gastrointestinal Microbiome ; *Microbiota ; Basic Helix-Loop-Helix Proteins/metabolism ; Homeostasis ; Akkermansia ; },
abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.},
}

Animals
*Stem Cells/metabolism/cytology
Wnt Signaling Pathway
*Aging
Mice
*Intestinal Mucosa/cytology/metabolism/microbiology
Regeneration
*Gastrointestinal Microbiome
*Microbiota
Basic Helix-Loop-Helix Proteins/metabolism
Homeostasis
Akkermansia

@article {pmid41576942,
year = {2026},
author = {Masi, D and Watanabe, M and Clément, K},
title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.},
journal = {Cell reports. Medicine},
volume = {7},
number = {2},
pages = {102573},
pmid = {41576942},
issn = {2666-3791},
mesh = {*Obesity/microbiology/therapy/metabolism/drug therapy ; Humans ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Multiomics ; *Diet ; },
abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.},
}

*Obesity/microbiology/therapy/metabolism/drug therapy
Humans
Animals
*Gastrointestinal Microbiome/physiology/drug effects
Multiomics
*Diet

@article {pmid41577947,
year = {2026},
author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6583},
pmid = {41577947},
issn = {2045-2322},
support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.},
}

@article {pmid41578124,
year = {2026},
author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M},
title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6070},
pmid = {41578124},
issn = {2045-2322},
support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; },
mesh = {Humans ; *Bacteria/enzymology/genetics ; *Gastrointestinal Microbiome/genetics ; *Neoplasms/microbiology/immunology/therapy ; *Phosphorus-Oxygen Lyases/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; },
abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.},
}

Humans
*Bacteria/enzymology/genetics
*Gastrointestinal Microbiome/genetics
*Neoplasms/microbiology/immunology/therapy
*Phosphorus-Oxygen Lyases/genetics/metabolism
Dinucleoside Phosphates/metabolism

@article {pmid41578762,
year = {2025},
author = {Shen, F and Xu, C and Wang, C},
title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {37},
number = {1},
pages = {62-74},
pmid = {41578762},
issn = {2148-5607},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; Feces/microbiology ; Female ; Male ; *Biomarkers, Tumor/analysis ; *Adenoma/microbiology/diagnosis ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Fusobacterium nucleatum/isolation & purification/genetics ; Aged ; Peptostreptococcus/isolation & purification/genetics ; Disease Progression ; Adult ; Prognosis ; Early Detection of Cancer/methods ; Sensitivity and Specificity ; },
abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.

MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.

RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.

CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression.   Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology
Feces/microbiology
Female
Male
*Biomarkers, Tumor/analysis
*Adenoma/microbiology/diagnosis
Middle Aged
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Fusobacterium nucleatum/isolation & purification/genetics
Aged
Peptostreptococcus/isolation & purification/genetics
Disease Progression
Adult
Prognosis
Early Detection of Cancer/methods
Sensitivity and Specificity

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

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

@article {pmid41581112,
year = {2026},
author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P},
title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {62},
pmid = {41581112},
issn = {1432-8798},
mesh = {*Solanum lycopersicum/virology ; Animals ; *Hemiptera/virology ; Reunion ; Phylogeny ; *Plant Diseases/virology ; Metagenomics ; *Luteoviridae/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; Insect Vectors/virology ; },
abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.},
}

*Solanum lycopersicum/virology
Animals
*Hemiptera/virology
Reunion
Phylogeny
*Plant Diseases/virology
Metagenomics
*Luteoviridae/genetics/classification/isolation & purification
*Virome
Genome, Viral
Insect Vectors/virology

@article {pmid41581442,
year = {2026},
author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W},
title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.},
journal = {Virology},
volume = {617},
number = {},
pages = {110814},
doi = {10.1016/j.virol.2026.110814},
pmid = {41581442},
issn = {1096-0341},
mesh = {Animals ; *Metagenomics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Animals, Wild/virology ; Tibet ; Feces/virology ; *Virome ; RNA, Viral/genetics ; Genetic Variation ; Genome, Viral ; },
abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.},
}

Animals
*Metagenomics
Phylogeny
*RNA Viruses/genetics/classification/isolation & purification
*Animals, Wild/virology
Tibet
Feces/virology
*Virome
RNA, Viral/genetics
Genetic Variation
Genome, Viral

@article {pmid41581489,
year = {2026},
author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J},
title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {147984},
doi = {10.1016/j.foodchem.2026.147984},
pmid = {41581489},
issn = {1873-7072},
mesh = {*Indoles/metabolism ; Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; *Tryptophan/metabolism ; *Ellagic Acid/metabolism/chemistry ; Signal Transduction/drug effects ; Multiomics ; Bacteria/isolation & purification/classification/genetics/metabolism ; Male ; Humans ; Mice ; },
abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.},
}

*Indoles/metabolism
Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
*Tryptophan/metabolism
*Ellagic Acid/metabolism/chemistry
Signal Transduction/drug effects
Multiomics
Bacteria/isolation & purification/classification/genetics/metabolism
Male
Humans
Mice

@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Antimicrobial Peptides/chemistry/pharmacology/economics ; *Biotechnology/economics ; *Aquatic Organisms/chemistry ; Animals ; Humans ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}

*Antimicrobial Peptides/chemistry/pharmacology/economics
*Biotechnology/economics
*Aquatic Organisms/chemistry
Animals
Humans

@article {pmid41582242,
year = {2026},
author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM},
title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5348},
pmid = {41582242},
issn = {2045-2322},
mesh = {*Solanum lycopersicum/virology/genetics/growth & development/microbiology ; *Endophytes/genetics/isolation & purification/classification ; *Begomovirus/pathogenicity ; *Disease Resistance/genetics ; *Plant Diseases/virology/genetics/microbiology ; Genotype ; Bacteria/isolation & purification/classification/genetics ; Fungi/isolation & purification/genetics/classification ; Biodiversity ; },
abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.},
}

*Solanum lycopersicum/virology/genetics/growth & development/microbiology
*Endophytes/genetics/isolation & purification/classification
*Begomovirus/pathogenicity
*Disease Resistance/genetics
*Plant Diseases/virology/genetics/microbiology
Genotype
Bacteria/isolation & purification/classification/genetics
Fungi/isolation & purification/genetics/classification
Biodiversity

@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Blood Pressure ; *Hypertension/microbiology/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; Blood Pressure Monitoring, Ambulatory ; China ; Prospective Studies ; *Metabolome ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}

Humans
*Blood Pressure
*Hypertension/microbiology/blood
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Adult
Blood Pressure Monitoring, Ambulatory
China
Prospective Studies
*Metabolome

@article {pmid41582602,
year = {2026},
author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C},
title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.},
journal = {European journal of haematology},
volume = {116},
number = {5},
pages = {646-662},
pmid = {41582602},
issn = {1600-0609},
support = {//Fundación FERO and the Fundación para la Promoción de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; },
mesh = {Humans ; *Metagenomics/methods ; Shotgun Sequencing ; Female ; Treatment Outcome ; *Microbiota ; *Immunotherapy, Adoptive/adverse effects/methods ; Male ; Middle Aged ; Adult ; *Receptors, Chimeric Antigen/genetics/metabolism ; Aged ; *Lymphoma/therapy/diagnosis/mortality ; Machine Learning ; },
abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis , Bifidobacterium bifidum , and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens , Bifidobacterium bifidum , Bifidobacterium breve , Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.},
}

Humans
*Metagenomics/methods
Shotgun Sequencing
Female
Treatment Outcome
*Microbiota
*Immunotherapy, Adoptive/adverse effects/methods
Male
Middle Aged
Adult
*Receptors, Chimeric Antigen/genetics/metabolism
Aged
*Lymphoma/therapy/diagnosis/mortality
Machine Learning

@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Aged ; Female ; Male ; *Soybean Proteins/administration & dosage/pharmacology ; *Sarcopenia/diet therapy ; *Muscle, Skeletal/physiology ; Aged, 80 and over ; Fatty Acids, Volatile ; Feces/microbiology ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Aged
Female
Male
*Soybean Proteins/administration & dosage/pharmacology
*Sarcopenia/diet therapy
*Muscle, Skeletal/physiology
Aged, 80 and over
Fatty Acids, Volatile
Feces/microbiology

@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics ; Female ; Cross-Sectional Studies ; Retrospective Studies ; *Microbiota ; Male ; *Inflammation/microbiology ; *Abscess/microbiology ; Severity of Illness Index ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Aged ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}

Humans
*Metagenomics
Female
Cross-Sectional Studies
Retrospective Studies
*Microbiota
Male
*Inflammation/microbiology
*Abscess/microbiology
Severity of Illness Index
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Aged

@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}