@article {pmid40426500,
year = {2025},
author = {Tóth, AG and Tóth, DL and Remport, L and Tóth, I and Németh, T and Dubecz, A and Patai, ÁV and Wagenhoffer, Z and Makrai, L and Solymosi, N},
title = {A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
pmid = {40426500},
issn = {2079-6382},
support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020/ ; 2024-2.1.2-EKÖP-2024-00018//Ministry of Culture and Innovation of Hungary/ ; },
abstract = {Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.},
}

@article {pmid40392941,
year = {2025},
author = {Feng, C and Liang, Z and Liao, X and Lin, K and Zhai, Y and Liu, G and Malpei, F and Hu, A},
title = {Microbial Dynamics on Different Microplastics in Coastal Urban Aquatic Ecosystems: The Critical Roles of Extracellular Polymeric Substances.},
journal = {Environmental science & technology},
volume = {59},
number = {21},
pages = {10554-10566},
doi = {10.1021/acs.est.5c03796},
pmid = {40392941},
issn = {1520-5851},
mesh = {*Microplastics ; Ecosystem ; Extracellular Polymeric Substance Matrix ; Bacteria ; Water Pollutants, Chemical ; Microbiota ; },
abstract = {Microplastics (MPs) serve as carriers for microbial community colonization, forming unique ecosystems known as plastispheres in urban aquatic ecosystems. However, interactions among microbes, extracellular polymeric substances (EPS), and MPs remain poorly understood. This study investigates microbial consortia and their EPS secretion behaviors across various plastispheres at two representative coastal urban water sites. Permutational multivariate analysis of variance revealed that MP type significantly influenced microbial community structures in reservoir environments (R[2] = 0.60, p < 0.001), highlighting the pronounced impact of MP types in high-quality urban waters. Specific microbial phyla and genera were identified as key contributors to EPS compositional variations across different plastispheres. Hierarchical partitioning results identified Acidobacteria, Nitrospirae, and Planctomycetes as influential phyla positively affecting EPS composition. Spearman correlation analysis pinpointed Robiginitialea (positive correlation) and Fimbriiglobus (negative correlation) as critical genera influencing EPS dynamics. Moreover, EPS-related gene abundance corresponded closely with observed EPS compositional differences. Dominant genes associated with protein biosynthesis included xapD in reservoirs and glnA in bays, while glmS and eno were predominant for polysaccharide biosynthesis in bays. This research advances our understanding of microbial-EPS-MP interactions in urban water systems, offering critical insights into ecological remediation and risk assessment of MP pollution.},
}

*Microplastics
Ecosystem
Extracellular Polymeric Substance Matrix
Bacteria
Water Pollutants, Chemical
Microbiota

@article {pmid40237492,
year = {2025},
author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L},
title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.},
journal = {Microbiology spectrum},
volume = {13},
number = {6},
pages = {e0298424},
doi = {10.1128/spectrum.02984-24},
pmid = {40237492},
issn = {2165-0497},
mesh = {*Candida albicans/growth & development/drug effects/metabolism ; Female ; Humans ; *Vagina/microbiology ; *Lactobacillus/metabolism/genetics/classification ; Candidiasis, Vulvovaginal/microbiology ; Microbiota ; Antibiosis ; Adult ; Microbial Interactions ; Metagenomics ; },
abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.},
}

*Candida albicans/growth & development/drug effects/metabolism
Female
Humans
*Vagina/microbiology
*Lactobacillus/metabolism/genetics/classification
Candidiasis, Vulvovaginal/microbiology
Microbiota
Antibiosis
Adult
Microbial Interactions
Metagenomics

@article {pmid40426336,
year = {2025},
author = {Wang, Y and Zhou, K and Zhang, Y and Li, C and Zhang, Y and Ren, X and Mi, C and Ma, L and Duan, Y and Liu, M and Ping, G and Tian, X and Song, Z},
title = {The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.},
journal = {Helicobacter},
volume = {30},
number = {3},
pages = {e70047},
doi = {10.1111/hel.70047},
pmid = {40426336},
issn = {1523-5378},
support = {82170562//National Natural Science Foundation of China/ ; 7232199//Beijing Natural Science Foundation/ ; BYSYZD2023008//Key Clinical Projects of Peking University Third Hospital/ ; },
mesh = {Humans ; *Feces/microbiology ; Cross-Sectional Studies ; *Helicobacter Infections/microbiology ; Male ; Middle Aged ; Female ; *Gastric Juice/microbiology ; Adult ; *Helicobacter pylori/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification ; Aged ; *Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Metagenomics ; },
abstract = {BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.

METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).

RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.

CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.},
}

Humans
*Feces/microbiology
Cross-Sectional Studies
*Helicobacter Infections/microbiology
Male
Middle Aged
Female
*Gastric Juice/microbiology
Adult
*Helicobacter pylori/physiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Bacteria/classification/genetics/isolation & purification
Aged
*Gastrointestinal Tract/microbiology
Dysbiosis/microbiology
Metagenomics

@article {pmid40424445,
year = {2025},
author = {Li, W and Cai, J and Chen, G and Liu, Y and Wu, X and Bai, Y and Wu, Y and Wang, T},
title = {Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324786},
pmid = {40424445},
issn = {1932-6203},
mesh = {*Soil Microbiology ; China ; Soil/chemistry ; *Microbiota ; Forests ; Ecosystem ; *Environmental Restoration and Remediation ; },
abstract = {Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.},
}

*Soil Microbiology
China
Soil/chemistry
*Microbiota
Forests
Ecosystem
*Environmental Restoration and Remediation

@article {pmid40423870,
year = {2025},
author = {Zhang, M and Zhang, H and Hong, A and Huang, J and Yang, L and Long, Y and Yu, Z},
title = {Dynamic changes of dental plaque and saliva microbiota in OSCC progression.},
journal = {Clinical oral investigations},
volume = {29},
number = {6},
pages = {314},
pmid = {40423870},
issn = {1436-3771},
support = {32170071//This work was funded by the National Natural Science Foundation of China/ ; 82273466//This work was funded by the National Natural Science Foundation of China/ ; 2023ZJ1120//Hunan Provincial Science and Technology Department/ ; 2024JJ2039//Natural Science Foundation of Hunan Province/ ; 2024JJ8117//Natural Science Foundation of Hunan Province/ ; },
mesh = {Humans ; *Saliva/microbiology ; Disease Progression ; *Dental Plaque/microbiology ; *Mouth Neoplasms/microbiology/pathology ; *Carcinoma, Squamous Cell/microbiology/pathology ; Female ; *Microbiota ; Male ; Middle Aged ; Neoplasm Staging ; Metagenomics ; },
abstract = {OBJECTIVES: To elucidate the changes in microbial composition and genomics in saliva and dental plaque during the progression of Oral Squamous Cell Carcinoma (OSCC), and to identify virulence factors and pathways associated with tumor differentiation in OSCC patients.

MATERIALS AND METHODS: Using metagenomic sequencing, 64 saliva and dental plaque samples from OSCC patients at different stages of differentiation were examined.

RESULTS: The results showed notable differences in the microbial composition and genomic profiles across ecological regions and differentiation degrees. Notably, the relative abundance of specific microbes, such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Haemophilus parainfluenzae, increased in poorly differentiated OSCC. Microbial alpha diversity in dental plaque and saliva correlates with tumor T staging. Dental plaque microbiota shows higher specialization, especially in poorly differentiated tumors. Both microbiota types become more stable with advanced T staging. Genomic analysis reveals increased virulence factors in poorly differentiated stages.Subsequently, functional pathway analysis and tracing of pathogens reveal specific microbial mechanisms in oral cancer pathogenesis. Certain oral pathogens may promote tumorigenesis by secreting factors like GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GspG (a gingipain precursor), and AllS (a lysine-specific gingipain precursor).

CONCLUSIONS: OSCC progression is associated with altered microbial composition, diversity, and genomic profiles in saliva and dental plaque. Poorly differentiated stages show higher abundance of pathogens and virulence factors, implicating them in tumorigenesis.

CLINICAL RELEVANCE: Understanding the microbial and genomic changes in saliva and dental plaque during OSCC progression could aid in developing new diagnostic biomarkers and targeted therapies, potentially enhancing early detection, treatment efficacy, and patient prognosis. Maintaining oral microbiota homeostasis may also help prevent oral cancer.},
}

Humans
*Saliva/microbiology
Disease Progression
*Dental Plaque/microbiology
*Mouth Neoplasms/microbiology/pathology
*Carcinoma, Squamous Cell/microbiology/pathology
Female
*Microbiota
Male
Middle Aged
Neoplasm Staging
Metagenomics

@article {pmid40372916,
year = {2025},
author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV},
title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115684},
doi = {10.1016/j.celrep.2025.115684},
pmid = {40372916},
issn = {2211-1247},
mesh = {Animals ; *Gastrointestinal Microbiome ; *DNA Methylation ; *Dendritic Cells/metabolism/immunology ; *Asthma/microbiology/immunology/genetics/pathology ; Mice ; Female ; Mice, Inbred C57BL ; *Bacteria ; Epigenesis, Genetic ; *Particulate Matter ; },
abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.},
}

Animals
*Gastrointestinal Microbiome
*DNA Methylation
*Dendritic Cells/metabolism/immunology
*Asthma/microbiology/immunology/genetics/pathology
Mice
Female
Mice, Inbred C57BL
*Bacteria
Epigenesis, Genetic
*Particulate Matter

@article {pmid40260991,
year = {2025},
author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F},
title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.},
journal = {Molecular nutrition & food research},
volume = {69},
number = {11},
pages = {e70046},
doi = {10.1002/mnfr.70046},
pmid = {40260991},
issn = {1613-4133},
support = {//Instituto de Salud Carlos III/ ; //Centro de investigación Biomédica en Red/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Acute Coronary Syndrome/microbiology/diet therapy/metabolism ; Male ; Female ; Middle Aged ; Dysbiosis/microbiology/diet therapy ; *Diet ; Aged ; Feces/microbiology ; Inflammation ; Case-Control Studies ; },
abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Acute Coronary Syndrome/microbiology/diet therapy/metabolism
Male
Female
Middle Aged
Dysbiosis/microbiology/diet therapy
*Diet
Aged
Feces/microbiology
Inflammation
Case-Control Studies

@article {pmid40420833,
year = {2025},
author = {Clasen, F and Yildirim, S and Arıkan, M and Garcia-Guevara, F and Hanoğlu, L and Yılmaz, NH and Şen, A and Celik, HK and Neslihan, AA and Demir, TK and Temel, Z and Mardinoglu, A and Moyes, DL and Uhlen, M and Shoaie, S},
title = {Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2506843},
pmid = {40420833},
issn = {1949-0984},
mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; *Brain/physiopathology/microbiology ; Male ; Female ; Aged ; *Bacteria/genetics/classification/pathogenicity/isolation & purification ; Metagenomics ; Virulence ; Virulence Factors/genetics/metabolism ; Saliva/microbiology/chemistry ; Middle Aged ; },
abstract = {The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.},
}

Humans
*Parkinson Disease/microbiology/physiopathology
*Cognitive Dysfunction/microbiology/physiopathology
*Gastrointestinal Microbiome
*Mouth/microbiology
*Brain/physiopathology/microbiology
Male
Female
Aged
*Bacteria/genetics/classification/pathogenicity/isolation & purification
Metagenomics
Virulence
Virulence Factors/genetics/metabolism
Saliva/microbiology/chemistry
Middle Aged

@article {pmid40419960,
year = {2025},
author = {Shen, Q and Fan, X and Sun, Y and Gao, H and Su, X},
title = {TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {136},
pmid = {40419960},
issn = {1471-2105},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Algorithms ; Machine Learning ; Humans ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S-based approach often lead to profiling discrepancies, particularly at the species level, compromising the accuracy and reliability of findings.

RESULTS: To address this issue, we present TaxaCal (Taxonomic Calibrator), a machine learning algorithm designed to calibrate species-level taxonomy profiles in 16S amplicon data using a two-tier correction strategy. Validation on in-house produced and public datasets shows that TaxaCal effectively reduces biases in amplicon sequencing, mitigating discrepancies between microbial profiles derived from 16S and WGS. Moreover, TaxaCal enables seamless cross-platform comparisons between these two sequencing approaches, significantly improving disease detection in 16S-based microbiome data.

CONCLUSIONS: Therefore, TaxaCal offers a cost-effective solution for generating high-resolution microbiome species profiles that closely align with WGS results, enhancing the utility of 16S-based profiling in microbiome research. As microbiome-based diagnostics continue to evolve, TaxaCal has the potential to be a crucial tool in advancing the utility of 16S sequencing in clinical and research settings.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Metagenomics/methods
Algorithms
Machine Learning
Humans
*Bacteria/genetics/classification
Sequence Analysis, DNA/methods

@article {pmid40419790,
year = {2025},
author = {Wang, D and Duan, Y and He, L and Jiang, J and Xian, J and Yuan, K and Zhang, R and Zhang, H and Wang, J and Li, N and Huang, M and Hu, C and Lu, S and Luo, Z and Deng, T and Zhang, Z and Chen, B and Li, W},
title = {Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {804},
pmid = {40419790},
issn = {2399-3642},
support = {82102301//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/mortality ; Male ; Female ; Metagenomics/methods ; Middle Aged ; Severity of Illness Index ; *SARS-CoV-2/genetics ; *Microbiota ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Sputum/microbiology ; Adult ; Transcriptome ; *Respiratory System/microbiology ; },
abstract = {The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.},
}

Humans
*COVID-19/microbiology/virology/mortality
Male
Female
Metagenomics/methods
Middle Aged
Severity of Illness Index
*SARS-CoV-2/genetics
*Microbiota
Aged
Bronchoalveolar Lavage Fluid/microbiology
Sputum/microbiology
Adult
Transcriptome
*Respiratory System/microbiology

@article {pmid40373900,
year = {2025},
author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F},
title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {313},
number = {},
pages = {144153},
doi = {10.1016/j.ijbiomac.2025.144153},
pmid = {40373900},
issn = {1879-0003},
mesh = {*Polysaccharide-Lyases/chemistry/metabolism/genetics ; Humans ; *Gastrointestinal Microbiome ; Hyaluronic Acid/metabolism ; Substrate Specificity ; Enzyme Stability ; Hydrogen-Ion Concentration ; Temperature ; Amino Acid Sequence ; },
abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.},
}

*Polysaccharide-Lyases/chemistry/metabolism/genetics
Humans
*Gastrointestinal Microbiome
Hyaluronic Acid/metabolism
Substrate Specificity
Enzyme Stability
Hydrogen-Ion Concentration
Temperature
Amino Acid Sequence

@article {pmid40367885,
year = {2025},
author = {Mo, S and Wu, X and Kashif, M and Zeng, S and Sang, Y and Meng, C and He, S and Jiang, C},
title = {Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118128},
doi = {10.1016/j.marpolbul.2025.118128},
pmid = {40367885},
issn = {1879-3363},
mesh = {*Wetlands ; *Carbon Cycle ; *Sulfates/metabolism ; *Introduced Species ; *Poaceae/physiology ; Geologic Sediments/microbiology ; Ecosystem ; *Rhizophoraceae ; },
abstract = {Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.},
}

*Wetlands
*Carbon Cycle
*Sulfates/metabolism
*Introduced Species
*Poaceae/physiology
Geologic Sediments/microbiology
Ecosystem
*Rhizophoraceae

@article {pmid40344797,
year = {2025},
author = {Chen, Y and Liu, Q and Xu, XW},
title = {Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118121},
doi = {10.1016/j.marpolbul.2025.118121},
pmid = {40344797},
issn = {1879-3363},
mesh = {*Estuaries ; Rivers/microbiology ; China ; *Nitrogen Cycle ; *Microbiota ; Nitrogen ; Seawater/microbiology ; Spatio-Temporal Analysis ; Bacteria/metabolism ; Environmental Monitoring ; Salinity ; Denitrification ; },
abstract = {Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.},
}

*Estuaries
Rivers/microbiology
China
*Nitrogen Cycle
*Microbiota
Nitrogen
Seawater/microbiology
Spatio-Temporal Analysis
Bacteria/metabolism
Environmental Monitoring
Salinity
Denitrification

@article {pmid40315739,
year = {2025},
author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X},
title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.},
journal = {Journal of reproductive immunology},
volume = {169},
number = {},
pages = {104535},
doi = {10.1016/j.jri.2025.104535},
pmid = {40315739},
issn = {1872-7603},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Young Adult ; *Bacteria/genetics ; },
abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.

METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.

CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.},
}

Humans
Female
Pregnancy
*Placenta/microbiology
*Gastrointestinal Microbiome
*Mouth/microbiology
Adult
RNA, Ribosomal, 16S/genetics
*Microbiota
Young Adult
*Bacteria/genetics

@article {pmid40419614,
year = {2025},
author = {Lu, W and Hua, J and Zhang, M and Yan, L and Zhao, H and Lv, X},
title = {Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18398},
pmid = {40419614},
issn = {2045-2322},
support = {[2021]1146//Joint Research on Improved Beef Cattle Breeds in Anhui Province/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Buffaloes/microbiology ; Female ; Male ; *Metagenomics/methods ; *Metagenome ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Phylogeny ; *Microbiota ; },
abstract = {In this study, the composition of the rumen microbiota and its functional characteristics were investigated using a metagenomic approach in Dongliu buffalo. This study compared the rumen microbial communities of six female and four male Dongliu buffaloes of similar age, weight and lifestyle. Taxonomic analysis identified 964 genera across 52 phyla, dominated by Bacteroidota (47.54%) and Bacillota (28.20%). While alpha and beta diversity showed no sex differences (PERMANOVA P = 0.82), males exhibited higher Fibrobacter at the genus level (P = 0.02). Functional profiling revealed 429 KEGG pathways, with carbohydrate metabolism (11.17%) and amino acid metabolism (9.74%) as dominant processes. Males showed enrichment in cellulose-degrading enzymes (EC2.4.1.20, EC1.2.1.90, EC2.7.1.58) and CAZymes (GH94, GT35), while females had higher Bacteroides abundance (P = 0.01) and CAZymes like CBM47. Core cellulolytic genera (Prevotella, Ruminococcus) demonstrated male-biased GH/CBM activity, linked to enhanced fiber degradation. COG annotation highlighted carbohydrate metabolism as central, with sex-specific functional partitioning in replication (female-enriched) and secondary metabolism (male-enriched). Network analysis revealed Prevotella's dominance in CAZymeme contributions and functional specialization in lignocellulose degradation pathways, suggesting sex-driven microbial adaptation to dietary fiber utilization.},
}

Animals
*Rumen/microbiology
*Buffaloes/microbiology
Female
Male
*Metagenomics/methods
*Metagenome
*Gastrointestinal Microbiome
*Bacteria/genetics/classification
Phylogeny
*Microbiota

@article {pmid40415955,
year = {2025},
author = {Guo, Y and Lin, L and Zhang, M and Yu, Y and Wang, Y and Cao, J and Li, Y and Sun, X and Guan, M and Wen, S and Wang, X and Fang, Z and Duan, W and Duan, J and Huang, T and Xia, W and Guo, S and Wei, F and Zheng, D and Huang, X},
title = {Salivary mycobiome alterations in HIV-infected MSM: dominance of Pseudogymnoascus and functional shifts across disease stages.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1564891},
pmid = {40415955},
issn = {2235-2988},
mesh = {Humans ; Male ; *Saliva/microbiology ; Cross-Sectional Studies ; *HIV Infections/microbiology/complications ; *Mycobiome ; Adult ; *Homosexuality, Male ; Middle Aged ; CD4 Lymphocyte Count ; *Fungi/classification/genetics/isolation & purification ; Disease Progression ; Metagenomics ; },
abstract = {BACKGROUND: Oral health is increasingly recognized as a crucial determinant of overall health in people living with HIV/AIDS (PLWHA). Specifically, the oral mycobiome may play a pivotal role in HIV-associated oral complications. However, the fungal species involved and their potential as biomarkers for HIV-related oral conditions remain poorly understood. This study investigates salivary fungal profiles in PLWHA who have sex with men (MSM), focusing on diversity, functional shifts, and correlations with disease progression.

METHODS: A cross-sectional study included 25 MSM participants divided into five groups: HIV-negative controls (n = 5) and four HIV-positive groups stratified by CD4 count: Stage 0 (HIV RNA-positive/antibody-negative; n = 5), Stage 1 (CD4 ≥500 cells/μL; n = 5), Stage 2 (CD4 200-499 cells/μL; n = 5), and Stage 3 (CD4 <200 cells/μL or opportunistic infections; n = 5). Saliva samples were collected and analyzed using metagenomic sequencing (Illumina NovaSeq platform). Bioinformatic analyses included genome assembly (MEGAHIT), gene clustering (CD-HIT), gene abundance calculation (SOAPaligner), species annotation (BLASTP), and KEGG pathway annotation (KOBAS 2.0). Statistical analyses (Kruskal-Wallis tests, Spearman's correlation) assessed associations between fungal profiles, CD4 count, and viral loads.

RESULTS: A total of 51 fungal genera were identified, with Pseudogymnoascus being the most abundant. Functional analysis revealed 113 shared KEGG pathways, of which 69 were unique to Stage 3, primarily related to metabolic and disease-related processes. Notably, Auricularia exhibited a positive correlation with CD4 count (P ≤ 0.01), while Mucor showed a negative correlation (P = 0.0299).

CONCLUSIONS: Salivary mycobiome composition and function shift significantly across HIV stages, reflecting immune decline. Pseudogymnoascus dominance challenges conventional views of oral fungal ecology in immunocompromised hosts. These findings highlight the mycobiome's diagnostic potential for monitoring HIV-related oral health. Longitudinal studies are needed to validate clinical relevance.},
}

Humans
Male
*Saliva/microbiology
Cross-Sectional Studies
*HIV Infections/microbiology/complications
*Mycobiome
Adult
*Homosexuality, Male
Middle Aged
CD4 Lymphocyte Count
*Fungi/classification/genetics/isolation & purification
Disease Progression
Metagenomics

@article {pmid40414991,
year = {2025},
author = {Rashid, MH and Pascottini, OB and Xie, L and Niazi, M and Lietaer, L and Comlekcioglu, U and Opsomer, G},
title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18274},
pmid = {40414991},
issn = {2045-2322},
support = {2(3)/HRD/OSS-III/2022/HEC/83//Higher Education Commission, Pakistan/ ; KP 2020; FFB200048//Ghent University, Belgium/ ; BOF17/DOC/269//Ghent University, Belgium/ ; 12Y5220N//University of Antwerp, Belgium/ ; CSC; 202206300032//China Scholarship Council/ ; },
mesh = {Animals ; Cattle ; Female ; *Endometritis/microbiology/veterinary ; *Cattle Diseases/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Postpartum Period ; *Uterus/microbiology ; Bacteria/genetics/classification/isolation & purification ; *Microbial Interactions ; Metagenome ; },
abstract = {Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.},
}

Animals
Cattle
Female
*Endometritis/microbiology/veterinary
*Cattle Diseases/microbiology
*Microbiota/genetics
Metagenomics/methods
Postpartum Period
*Uterus/microbiology
Bacteria/genetics/classification/isolation & purification
*Microbial Interactions
Metagenome

@article {pmid40414843,
year = {2025},
author = {Thompson, TP and Rice, CJ and Athanasakis, E and Mawhinney, J and Gilmore, BF and Fitzgerald, P and Skvortsov, T and Kelly, SA},
title = {The effect of sample type and location on industrial workplace sink and hand dryer microbiomes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {325},
pmid = {40414843},
issn = {1471-2180},
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Humans ; Workplace ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Hand Disinfection ; Hand/microbiology ; Metagenomics ; },
abstract = {One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.},
}

*Microbiota/genetics
*Bacteria/genetics/classification/drug effects/isolation & purification
Humans
Workplace
Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Hand Disinfection
Hand/microbiology
Metagenomics

@article {pmid40413728,
year = {2025},
author = {Kousgaard, SJ and Dall, SM and Albertsen, M and Nielsen, HL and Thorlacius-Ussing, O},
title = {Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2510464},
pmid = {40413728},
issn = {1949-0984},
mesh = {Humans ; *Pouchitis/therapy/microbiology ; *Fecal Microbiota Transplantation/adverse effects/methods ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Quality of Life ; Chronic Disease/therapy ; Gastrointestinal Microbiome ; Proof of Concept Study ; Treatment Outcome ; Tissue Donors ; Denmark ; },
abstract = {Chronic pouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) with limited treatment options. In this case series, we aimed to investigate clinical and microbiome changes, as well as adverse events, associated with using fecal microbiota transplantation (FMT) from a donor with a normal functioning IPAA to induce remission in patients with chronic pouchitis. Methods The study was a case-series including a 4-week intervention period and 12-month follow-up. Patients with chronic pouchitis who met the inclusion criteria were recruited from the Department of Gastrointestinal Surgery at Aalborg University Hospital, Denmark. Participants received FMT derived from a donor with a normal functioning IPAA. Treatment was administered by enema daily for two weeks, then every other day for two more weeks. Disease severity and quality of life (QoL) were accessed at baseline and 30-day follow-up. Clinical remission was defined as Pouchitis Disease Activity Index (PDAI) <7. Fecal samples from participants, healthy donors, and the IPAA donor were analyzed using shotgun metagenomic sequencing. Results Three patients with chronic pouchitis were included and completed the treatment protocol and follow-up visits. At the 30-day follow-up, all participants achieved clinical remission with reduced endoscopic inflammation. The median total PDAI score decreased from 8 (range 10-8) at baseline to 6 (range 6-5) at 30 days. Two participants reported improved QoL, while one reported no change. Few mild, self-limited adverse events were reported by all participants during treatment, with no serious events. Principal component analysis of fecal samples distinguished two clusters: healthy donors and the IPAA donor, with participant samples forming a separate cluster Conclusion We observed that all participants achieved clinical remission with reduced endoscopic inflammation following a 4-week FMT intervention. Adverse events were mild and self-limited. Metagenomic analysis revealed distinct microbiome clusters between IPAA donor and recipients, both of which differed from those of healthy donors.},
}

Humans
*Pouchitis/therapy/microbiology
*Fecal Microbiota Transplantation/adverse effects/methods
Male
Female
Adult
Middle Aged
Feces/microbiology
Quality of Life
Chronic Disease/therapy
Gastrointestinal Microbiome
Proof of Concept Study
Treatment Outcome
Tissue Donors
Denmark

@article {pmid40228693,
year = {2025},
author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY},
title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.},
journal = {Environmental research},
volume = {277},
number = {},
pages = {121559},
doi = {10.1016/j.envres.2025.121559},
pmid = {40228693},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology/chemistry ; Aquaculture ; *Carbon/metabolism ; *Kelp ; Microbiota ; *Carbon Cycle ; },
abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.},
}

*Geologic Sediments/microbiology/chemistry
Aquaculture
*Carbon/metabolism
*Kelp
Microbiota
*Carbon Cycle

@article {pmid40222470,
year = {2025},
author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z},
title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.},
journal = {Environmental research},
volume = {277},
number = {},
pages = {121602},
doi = {10.1016/j.envres.2025.121602},
pmid = {40222470},
issn = {1096-0953},
mesh = {*Ammonia/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; Oxidation-Reduction ; Metagenome ; Microbiota ; },
abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2 %) was higher than ammonia-oxidizing bacteria (AOB, 12.0 %), but lower than ammonia-oxidizing archaea (AOA, 64.8 %). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.},
}

*Ammonia/metabolism
*Geologic Sediments/microbiology
*Wetlands
Archaea/metabolism/genetics
*Bacteria/metabolism/genetics
Oxidation-Reduction
Metagenome
Microbiota

@article {pmid40203979,
year = {2025},
author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M},
title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.},
journal = {Environmental research},
volume = {277},
number = {},
pages = {121563},
doi = {10.1016/j.envres.2025.121563},
pmid = {40203979},
issn = {1096-0953},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; *Plankton/metabolism ; *Bacteria/metabolism/genetics ; RNA, Ribosomal, 16S ; Microbiota ; Seawater/microbiology ; },
abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Water Pollutants, Chemical/metabolism
Biodegradation, Environmental
*Plankton/metabolism
*Bacteria/metabolism/genetics
RNA, Ribosomal, 16S
Microbiota
Seawater/microbiology

@article {pmid40413726,
year = {2025},
author = {Zhang, DY and Li, D and Chen, SJ and Zhang, LJ and Zhu, XL and Chen, FD and Chen, C and Wang, Q and Du, Y and Xiong, JX and Huang, SM and Zhang, XD and Lv, YT and Zeng, F and Chen, RX and Huang, X and Mao, F and Zhou, S and Yao, Q and Huang, Y and Chen, R and Mo, Y and Xie, Y and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Bai, FH},
title = {Bacteroides uniformis-generated hexadecanedioic acid ameliorates metabolic-associated fatty liver disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508433},
pmid = {40413726},
issn = {1949-0984},
mesh = {Humans ; Gastrointestinal Microbiome ; Animals ; *Bacteroides/metabolism/genetics ; Mice ; Male ; Female ; Middle Aged ; Feces/microbiology ; Liver/metabolism ; *Fatty Liver/microbiology/metabolism ; Fecal Microbiota Transplantation ; Prospective Studies ; Adult ; Metabolomics ; Mice, Inbred C57BL ; },
abstract = {Gut microbiota exerts a pivotal influence on the development of Metabolic Associated Fatty Liver Disease (MAFLD), although the specific contributions of individual bacterial strains and their metabolites remain poorly defined. We conducted stool shotgun metagenomic sequencing and plasma untargeted metabolomics in a large prospective cohort comprising 120 MAFLD patients and 120 matched healthy controls. The mechanisms and microbial-derived metabolites involved in MAFLD were further investigated through multi-omics analyses in vitro and in vivo. Distinct differences were identified in both the microbial community structure and metabolomic profiles between MAFLD patients and healthy controls. Bacteroides uniformis (B. uniformis) was the most significantly depleted species in MAFLD and negatively correlated with hepatic steatosis and BMI. MAFLD was characterized by marked disruptions in fatty acid and amino acid metabolism. Combined analysis of metabolomic and metagenomic data achieved high diagnostic accuracy for MAFLD and hepatic steatosis severity (AUC = 0.93). Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B. uniformis administration alleviate disease progression by inhibiting intestinal fat absorption, FFA from eWAT influx into liver via the gut-liver axis, and IRE1α-XBP1s-mediated flipogenesis and ferroptosis, as confirmed by hepatic transcriptomic and proteomic analyses. Hexadecanedioic acid (HDA), potentially identified as a key metabolite produced by B. uniformis, ameliorated MAFLD symptoms. Mechanistically, B. uniformis-derived HDA also inhibited fat absorption and transported, and entered the liver via the portal vein to suppress IRE1α-XBP1s-mediated flipogenesis and ferroptosis. B. uniformis and its potential putative metabolite HDA may contribute to MAFLD progression modulation, through regulation of the IRE1α-XBP1s axis. This study provides new insights into the gut-liver axis in MAFLD and offers promising therapeutic targets based on specific microbes and their metabolites.},
}

Humans
Gastrointestinal Microbiome
Animals
*Bacteroides/metabolism/genetics
Mice
Male
Female
Middle Aged
Feces/microbiology
Liver/metabolism
*Fatty Liver/microbiology/metabolism
Fecal Microbiota Transplantation
Prospective Studies
Adult
Metabolomics
Mice, Inbred C57BL

@article {pmid40413611,
year = {2025},
author = {Ju, J and He, J and Ye, B and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Liu, L and Li, Y and Xia, M and Liu, Y},
title = {Microbial metabolism mediates the deteriorative effects of sedentary behaviour on insulin resistance.},
journal = {Clinical and translational medicine},
volume = {15},
number = {5},
pages = {e70348},
pmid = {40413611},
issn = {2001-1326},
support = {2023YFC3606300//National Key Research and Development Program of China/ ; 82330105//Key Project of National Natural Science Foundation of China/ ; Overseas//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; },
mesh = {*Insulin Resistance/physiology ; Humans ; *Sedentary Behavior ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; },
abstract = {BACKGROUND: Prolonged sedentary time is a strong risk factor for insulin resistance. Recent evidence indicates that gut microbiota may influence the regulation of insulin sensitivity and demonstrates a distinct profile between sedentary and physically active individuals. However, whether and how microbial metabolism mediates the progression of insulin resistance induced by prolonged sedentary time remains unclear.

METHODS: 560 male participants without hypoglycaemic therapy were included, and insulin resistance was evaluated using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). The gut microbiota was identified through metagenomics, host genetic data were obtained using a genotyping array, and plasma metabolites were quantified by liquid chromatography mass spectrometry.

RESULTS: A panel of 15 sedentary-related species and 38 sedentary-associated metabolic capacities accounted for 31.68% and 21.48% of the sedentary time-related variation in HOMA-IR, respectively. Specifically, decreased Roseburia sp. CAG:471, Intestinibacter bartlettii, and Firmicutes bacterium CAG:83, but increased Bacteroides xylanisolvens related to longer sedentary time, were causally linked to the development of insulin resistance. Furthermore, integrative analysis with metabolomics identified reduced L-citrulline and L-serine, resulting from a suppression of arginine biosynthesis as key microbial effectors linking longer sedentary time to enhanced insulin resistance.

CONCLUSIONS: In summary, our findings provide insights into the mediating role of gut microbiota on the progression of insulin resistance induced by excessive sedentary time, and highlight the possibility of counteracting the detrimental effect of prolonged sedentary time on insulin resistance by microbiota-modifying interventions.

KEY POINTS: Prolonged sedentary time leads to a depletion of Roseburia sp. CAG:471 and Firmicutes bacterium CAG:83, and suppresses arginine biosynthesis. Decreased L-citrulline and L-serine function as key microbial effectors mediating the adverse effect of sedentary time on insulin sensitivity. Targeting gut microbiota holds promise to combat insulin resistance induced by excessive sedentary time.},
}

*Insulin Resistance/physiology
Humans
*Sedentary Behavior
Male
*Gastrointestinal Microbiome/physiology
Adult

@article {pmid40413198,
year = {2025},
author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL},
title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {858},
pmid = {40413198},
issn = {2052-4463},
support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; },
abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.},
}

*Soil Microbiology
*Groundwater
Agriculture
*Metagenome
Microbiota
Bacteria/genetics/classification
Metagenomics
California
Archaea/genetics
Soil

@article {pmid40412963,
year = {2025},
author = {Wang, C and Tian, Z and Luan, X and Zhang, H and Zhang, Y and Yang, M},
title = {Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure.},
journal = {Journal of environmental sciences (China)},
volume = {156},
number = {},
pages = {647-659},
doi = {10.1016/j.jes.2024.10.008},
pmid = {40412963},
issn = {1001-0742},
mesh = {*Biofilms/drug effects ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.},
}

*Biofilms/drug effects
Plasmids/genetics
*Anti-Bacterial Agents/pharmacology
Bacteriophages/genetics
*Drug Resistance, Microbial/genetics
*Microbiota/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics

@article {pmid40280386,
year = {2025},
author = {An, X and Zhao, R and Wang, L and Xiao, X and Xu, Z and Zhang, S and Xie, D and Xiao, Y and Zhang, Q},
title = {Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.},
journal = {Environmental research},
volume = {278},
number = {},
pages = {121688},
doi = {10.1016/j.envres.2025.121688},
pmid = {40280386},
issn = {1096-0953},
mesh = {*Thiocyanates/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Networks and Pathways ; *Water Pollutants, Chemical/metabolism ; *Bacteria/metabolism ; Thiobacillus/metabolism/genetics ; },
abstract = {Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.},
}

*Thiocyanates/metabolism
Biodegradation, Environmental
*Microbial Consortia
Metabolic Networks and Pathways
*Water Pollutants, Chemical/metabolism
*Bacteria/metabolism
Thiobacillus/metabolism/genetics

@article {pmid40254251,
year = {2025},
author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS},
title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.},
journal = {Journal of invertebrate pathology},
volume = {211},
number = {},
pages = {108341},
doi = {10.1016/j.jip.2025.108341},
pmid = {40254251},
issn = {1096-0805},
mesh = {Animals ; Bees/virology/parasitology ; *Varroidae/virology ; *Virome ; Metagenomics ; Taiwan ; *RNA Viruses/isolation & purification/genetics ; *Insect Viruses/genetics/isolation & purification ; },
abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by an ecto-parasite that has spread worldwide, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.},
}

Animals
Bees/virology/parasitology
*Varroidae/virology
*Virome
Metagenomics
Taiwan
*RNA Viruses/isolation & purification/genetics
*Insect Viruses/genetics/isolation & purification

@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
mesh = {Humans ; *Metabolic Syndrome/microbiology ; Brazil/epidemiology ; Male ; Female ; *Saliva/microbiology ; Middle Aged ; Adult ; *Microbiota ; Body Mass Index ; Waist Circumference ; Triglycerides/blood ; Obesity ; },
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}

Humans
*Metabolic Syndrome/microbiology
Brazil/epidemiology
Male
Female
*Saliva/microbiology
Middle Aged
Adult
*Microbiota
Body Mass Index
Waist Circumference
Triglycerides/blood
Obesity

@article {pmid40410832,
year = {2025},
author = {Chu, B and Ge, S and He, W and Sun, X and Ma, J and Yang, X and Lv, C and Xu, P and Zhao, X and Wu, K},
title = {Gut symbiotic bacteria enhance reproduction in Spodoptera frugiperda (J.E. Smith) by regulating juvenile hormone III and 20-hydroxyecdysone pathways.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {132},
pmid = {40410832},
issn = {2049-2618},
support = {2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &Technology Fundamental Resources Investigation Program/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; },
mesh = {Animals ; *Spodoptera/microbiology/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Ecdysterone/metabolism ; *Symbiosis ; Female ; Reproduction ; Enterobacter/isolation & purification/physiology ; Larva/microbiology ; Enterococcus/isolation & purification/physiology/genetics ; Klebsiella/isolation & purification/genetics/physiology ; Bacteria/classification/genetics ; *Juvenile Hormones/metabolism ; },
abstract = {BACKGROUND: The insect gut microbiota forms a complex, multifunctional system that significantly affects phenotypic traits linked to environmental adaptation. Strong reproductive potential underpins the migratory success, population growth and destructive impact of the fall armyworm, Spodoptera frugiperda (J.E. Smith). However, the precise role of gut bacteria in S. frugiperda reproductive processes, distribution and transmission dynamics remains unclear.

RESULTS: We examined the gut microbiota of S. frugiperda a major invasive agricultural pest, identifying Enterococcus, Enterobacter, and Klebsiella as core microorganisms present throughout its life cycle. These microbes showed heightened activity during the egg stage, early larval stages and pre-oviposition period in females. Using an axenic insect re-infection system, Enterococcus quebecensis FAW181, Klebsiella michiganensis FAW071 and Enterobacter hormaechei FAW049 were found to significantly enhance host fecundity, increasing egg production by 62.73%, 59.95%, and 56.71%, respectively. Metagenomic and haemolymph metabolomic analyses revealed a positive correlation between gut symbiotic bacteria and hormone metabolism in female S. frugiperda. Further analysis of metabolites in the insect hormone biosynthesis pathway, along with exogenous injection of juvenile hormone III and 20-hydroxyecdysone, revealed that gut microbes regulate these hormones, maintaining levels equivalent to those in control insects. This regulation supports improved fecundity in S. frugiperda, aiding rapid colonization and population expansion.

CONCLUSIONS: These findings emphasize the pivotal role of gut bacteria E. quebecensis FAW181, E. hormaechei FAW049, and K. michiganensis FAW071 in enhancing S. frugiperda reproduction by modulating JH III levels through JHAMT regulation and concurrently modulating the levels of 20E and its precursors via PHM. Our results provide novel insights into microbe-host symbiosis and pest management strategies for alien invasive species. Video Abstract.},
}

Animals
*Spodoptera/microbiology/physiology/metabolism
*Gastrointestinal Microbiome/physiology
*Ecdysterone/metabolism
*Symbiosis
Female
Reproduction
Enterobacter/isolation & purification/physiology
Larva/microbiology
Enterococcus/isolation & purification/physiology/genetics
Klebsiella/isolation & purification/genetics/physiology
Bacteria/classification/genetics
*Juvenile Hormones/metabolism

@article {pmid40410138,
year = {2025},
author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Yarze, JC and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Association of distinct microbial and metabolic signatures with microscopic colitis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4644},
pmid = {40410138},
issn = {2041-1723},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; P30DK043351//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01AG068390//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Metabolome ; Feces/microbiology ; *Colitis, Microscopic/microbiology/metabolism ; Aged ; Adult ; Case-Control Studies ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diarrhea/microbiology/metabolism ; Metabolomics ; Metagenomics ; Biomarkers/metabolism ; },
abstract = {Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.},
}

Humans
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Metabolome
Feces/microbiology
*Colitis, Microscopic/microbiology/metabolism
Aged
Adult
Case-Control Studies
Bacteria/classification/genetics/isolation & purification/metabolism
Diarrhea/microbiology/metabolism
Metabolomics
Metagenomics
Biomarkers/metabolism

@article {pmid40410126,
year = {2025},
author = {Su, C and Zhou, H and Wang, Y and Duan, X and Jiang, T and Zhang, C and Gao, H and Kong, L and Wang, M and Guo, C},
title = {Contrasting Effects of Atmospheric Particulate Matter Deposition on Free-Living and Particle-Associated Bacteria in the South China Sea.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12533},
pmid = {40410126},
issn = {1520-5851},
abstract = {Atmospheric particulate matter (PM) deposition has become an important nutrient source in marine ecosystems, increasing particulate organic carbon and resource heterogeneity. However, their effects on marine bacterial communities remain unclear. In this study, by conducting on-board microcosm experiments with anthropogenic East Asian PM in the oligotrophic South China Sea, the response of particle-associated (PA) bacteria was investigated and compared with its free-living (FL) counterparts. Results showed that PM input increased nutrient heterogeneity, shifting bacterial community composition and lifestyle. Copiotrophic PA bacteria became more abundant and contributed a disproportionately higher percentage to total bacterial production despite a decline in total bacterial abundance. FL bacteria showed increased diversity, shifting from oligotrophs to copiotrophs, while PA bacteria displayed reduced diversity and nondirectional compositional changes, suggesting their distinct assembly mechanisms in response to external nutrient inputs. Metagenomic analysis further revealed that PM drives a shift toward a copiotrophic, particle-attached lifestyle with upregulated pathways for chemotaxis, motility, and biofilm formation. Notably, PM addition also increased the relative abundance of oil-degrading taxa. These findings reveal the complexity of microbial responses to environmental perturbations and underscore the need to consider unique ecological niches and bacterial lifestyles.},
}

@article {pmid40409349,
year = {2025},
author = {Zhou, S and Wang, K and Huang, J and Xu, Z and Yuan, Q and Liu, L and Wang, Z and Miao, J and Wang, H and Wang, T and Guan, W and Ding, C},
title = {Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508949},
doi = {10.1080/19490976.2025.2508949},
pmid = {40409349},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/metabolism/drug therapy/pathology/microbiology ; Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Indoles/metabolism/pharmacology/administration & dosage ; STAT3 Transcription Factor/metabolism ; Cell Proliferation/drug effects ; Tryptophan/metabolism ; Cell Line, Tumor ; Male ; Female ; Receptors, Aryl Hydrocarbon/metabolism ; Cell Movement/drug effects ; Apoptosis/drug effects ; Metabolic Reprogramming ; },
abstract = {Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.},
}

*Colorectal Neoplasms/metabolism/drug therapy/pathology/microbiology
Humans
Animals
Gastrointestinal Microbiome/drug effects
Mice
*Indoles/metabolism/pharmacology/administration & dosage
STAT3 Transcription Factor/metabolism
Cell Proliferation/drug effects
Tryptophan/metabolism
Cell Line, Tumor
Male
Female
Receptors, Aryl Hydrocarbon/metabolism
Cell Movement/drug effects
Apoptosis/drug effects
Metabolic Reprogramming

@article {pmid40407096,
year = {2025},
author = {Creskey, M and Silva Angulo, F and Wu, Q and Tamming, L and Fekete, EEF and Cheng, K and Ning, Z and Wang, A and Brito Rodrigues, P and de Rezende Rodovalho, V and Ramirez Vinolo, MA and Figeys, D and Li, X and Trottein, F and Zhang, X},
title = {Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505117},
doi = {10.1080/19490976.2025.2505117},
pmid = {40407096},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology ; Cricetinae ; *Proteomics/methods ; SARS-CoV-2 ; Feces/microbiology ; Age Factors ; Metagenomics ; Disease Models, Animal ; Mesocricetus ; Male ; },
abstract = {The gut microbiome's pivotal role in health and disease is well established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32,419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the interactions between the microbiome and host in SARS-CoV-2 infection. Altogether, this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.},
}

Animals
*Gastrointestinal Microbiome
*COVID-19/microbiology/virology
Cricetinae
*Proteomics/methods
SARS-CoV-2
Feces/microbiology
Age Factors
Metagenomics
Disease Models, Animal
Mesocricetus
Male

@article {pmid40406519,
year = {2025},
author = {Song, T and Yin, L and Zhou, X and Tao, X and Tie, D and Zhang, J and Jiang, L},
title = {Microbiota profiling from biopsied tissues in complex infections: a diagnostic and prognostic analysis through metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1567981},
pmid = {40406519},
issn = {2235-2988},
mesh = {Humans ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Prognosis ; *High-Throughput Nucleotide Sequencing/methods ; Biopsy ; Adult ; Aged ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Coinfection/microbiology/diagnosis ; Fungi/isolation & purification/genetics/classification ; Viruses/isolation & purification/genetics/classification ; Aged, 80 and over ; Sensitivity and Specificity ; *Communicable Diseases/diagnosis/microbiology ; },
abstract = {BACKGROUND: Infectious diseases that require tissue biopsy are usually more difficult to diagnose through conventional microbiological tests (CMT), and knowledge of the infection microbiota pattern from biopsied tissues remains incomplete. Our study aimed to investigate the diagnostic and prognostic value of metagenomic next-generation sequencing (mNGS), characterize the microbiota profile from biopsied tissues, and examine its relationship with clinical outcomes.

METHODS: This retrospective cohort study included 110 patients who underwent tissue biopsy and sent both mNGS and CMT due to suspected complex infection. Microbiota patterns were illustrated via unsupervised hierarchical clustering analysis. Multivariate regression analysis was used to investigate the effect measures.

RESULTS: The sensitivity of mNGS was significantly higher than that of CMT regarding bacteria (87.23% vs 40.43%, P=0.01), viruses (100% vs 5.56%, P<0.001), and fungi (87.5% vs 28.6%, P=0.04). Polymicrobial infection accounted for 45.2% (33/73) of the infection samples. In skeletal articular biopsied tissues, Staphylococcus presented the highest mean abundance among different species of bacteria (21.2% of all bacterial reads, standard deviation (SD) 38.9). Anaerobic bacteria (24.0%, SD 25.9) represented the most common bacteria in biopsied tissue from the lung or mediastinum. The presence of gram-negative bacteria (adjusted OR 5.21, 95% CI 1.39-19.43, P=0.01), Enterobacteriaceae (adjusted OR 5.71, 95% CI 1.17-28.03, P=0.03) and Staphylococcus (adjusted OR 8.64, 95% CI 1.95-38.34, P=0.005) was associated with an increased risk of treatment failure. Early mNGS sampling within 7 days after admission was associated with a significantly decreased risk of all-cause mortality (HR 0.18, 95% CI 0.04-0.94; P=0.04), treatment failure (OR 0.17, 95% CI 0.05-0.66; P=0.01), and increased probability of clinical resolution (OR 3.03, 95% CI 1.24-7.40; P=0.01).

CONCLUSION: mNGS demonstrates significant diagnostic and prognostic efficacy in patients undergoing tissue biopsy for suspected complex infections. The presence of Gram-negative bacteria, Enterobacteriaceae, and Staphylococcus is associated with a higher probability of treatment failure, which underscores the advantage of using mNGS to guide more aggressive antibiotic strategies.},
}

Humans
Male
Retrospective Studies
Female
Middle Aged
*Metagenomics/methods
Prognosis
*High-Throughput Nucleotide Sequencing/methods
Biopsy
Adult
Aged
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Coinfection/microbiology/diagnosis
Fungi/isolation & purification/genetics/classification
Viruses/isolation & purification/genetics/classification
Aged, 80 and over
Sensitivity and Specificity
*Communicable Diseases/diagnosis/microbiology

@article {pmid40405096,
year = {2025},
author = {Yasmin, A and Rahman, MS and Kador, SM and Ahmed, MM and Moon, MEK and Akhter, H and Sultana, M and Begum, A},
title = {Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {318},
pmid = {40405096},
issn = {1471-2180},
mesh = {Bangladesh ; Animals ; *Bacteria/genetics/classification/isolation & purification/drug effects/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Farms ; *Poultry/microbiology ; *Microbiota/genetics ; *Metagenomics ; *Poultry Diseases/transmission/microbiology ; Biodiversity ; Soil Microbiology ; DNA, Bacterial/genetics ; },
abstract = {The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems-cloacal swabs, droppings, feed, hand swabs, soil, and water-in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (p < 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as Enterobacter (26.62% in hand swabs), Acinetobacter (30.87% in cloacal swabs), and Shigella (22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like Lactobacillus (36.89% in feed) and Enterococcus (10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (Enterobacter, Acinetobacter, Shigella, Pseudomonas) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.},
}

Bangladesh
Animals
*Bacteria/genetics/classification/isolation & purification/drug effects/pathogenicity
RNA, Ribosomal, 16S/genetics
Farms
*Poultry/microbiology
*Microbiota/genetics
*Metagenomics
*Poultry Diseases/transmission/microbiology
Biodiversity
Soil Microbiology
DNA, Bacterial/genetics

@article {pmid40405076,
year = {2025},
author = {Li, J and Chen, Z and Yan, X and Chen, Q and Chen, C and Liu, H and Shen, J},
title = {Effects of USP25 knockout on the gut microbial diversity and composition in mice.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {315},
pmid = {40405076},
issn = {1471-2180},
support = {2022J011443//Natural Science Foundation of Fujian Province/ ; 2024J011450//Natural Science Foundation of Fujian Province/ ; 2024112//Medical Research Foundation of Putian University/ ; 2024104//Medical Research Foundation of Putian University/ ; 82301785//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Mice, Inbred C57BL ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Ubiquitin Thiolesterase/genetics/deficiency ; Biodiversity ; Male ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in host health. Recent study revealed that ubiquitin-specific protease 25 (USP25) deficiency affected colonic immune responses and resistance to certain bacterial infection. This study aimed to investigate the impact of USP25 gene deletion on the gut microbiota of mice, utilizing 16 S rRNA amplicon sequencing and metagenomic sequencing to provide a comprehensive analysis of microbial diversity, composition and functional characteristics.

METHODS: We collected fecal samples from 10 wild type (WT) C57BL/6J mice and 10 USP25[-/-] mice (C57BL/6J-Usp25[em1]cyagen) for 16 S rRNA amplicon sequencing. Subsequently, the 6 of the 20 samples underwent further analysis using metagenomic sequencing.

RESULTS: Our results revealed significant differences in the gut microbiota between USP25 knockout (KO) mice and wild-type (WT) controls, with KO mice exhibiting 1,858 unique amplicon sequence variants (ASVs) compared to 1,723 in WT mice. Notably, the KO group displayed a higher tendency for biofilm formation and a greater proportion of gram-negative bacteria, while the WT group demonstrated enhanced stress tolerance and a higher presence of gram-positive bacteria. Functional prediction analyses indicated an increase in antibiotic resistance genes in the KO mice, particularly for tetracycline, cephalosporin, and sulfonamides, suggesting a potential risk for clinical antibiotic treatment efficacy. Moreover, KEGG pathway enrichment analysis revealed significant enrichment for fructose and mannose metabolism, streptomycin biosynthesis in the KO group. Furthermore, an increase in protective microbes alongside a decrease in potential pathogens in the KO microbiota hinted at altered immune responses due to USP25 deletion.

CONCLUSION: Our findings elucidate the essential role of USP25 in modulating gut microbiota composition and function, providing insights for future therapeutic strategies targeting gut microbiota in disease contexts.

CLINICAL TRAIL NUMBER: Not applicable.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice, Knockout
Mice
Mice, Inbred C57BL
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
*Ubiquitin Thiolesterase/genetics/deficiency
Biodiversity
Male

@article {pmid40404683,
year = {2025},
author = {Terbtothakun, P and Visedthorn, S and Klomkliew, P and Chanchaem, P and Sawaswong, V and Sivapornnukul, P and Sunantawanit, S and Khamwut, A and Rotcheewaphan, S and Kaewsapsak, P and Payungporn, S},
title = {Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17772},
pmid = {40404683},
issn = {2045-2322},
support = {HEA_FF_68_100_3000_016//Thailand Science research and Innovation Fund, Chulalongkorn University/ ; B05-F640122//The National Science, Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources and Institutional Development, Research and Innovation/ ; GA68/047//The Ratchadapisek Sompotch Fund, Faculty of Medicine, Chulalongkorn University/ ; },
mesh = {Humans ; *Sputum/microbiology ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis/microbiology/diagnosis ; *Fungi/genetics/isolation & purification/classification ; *Bacteria/genetics/classification/isolation & purification ; Male ; Female ; Mycobacterium tuberculosis/genetics/isolation & purification ; Middle Aged ; Adult ; },
abstract = {Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes.},
}

Humans
*Sputum/microbiology
*Metagenomics/methods
*Nanopore Sequencing/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Tuberculosis/microbiology/diagnosis
*Fungi/genetics/isolation & purification/classification
*Bacteria/genetics/classification/isolation & purification
Male
Female
Mycobacterium tuberculosis/genetics/isolation & purification
Middle Aged
Adult

@article {pmid40404632,
year = {2025},
author = {Dillard, LR and Glass, EM and Kolling, GL and Thomas-White, K and Wever, F and Markowitz, R and Lyttle, D and Papin, JA},
title = {Genome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4768},
pmid = {40404632},
issn = {2041-1723},
support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; NRT-ROL 2021791//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 5T32GM136615-03//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1842490//National Science Foundation (NSF)/ ; },
mesh = {*Vaginosis, Bacterial/microbiology/metabolism ; Humans ; Female ; *Metabolic Networks and Pathways/genetics ; Vagina/microbiology ; Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metabolomics ; Metagenomics ; Genome, Bacterial ; Computer Simulation ; },
abstract = {Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women's health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, and Aerrococcus christenssii) on the spent media of Gardnerella species and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships.},
}

*Vaginosis, Bacterial/microbiology/metabolism
Humans
Female
*Metabolic Networks and Pathways/genetics
Vagina/microbiology
Microbiota/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Metabolomics
Metagenomics
Genome, Bacterial
Computer Simulation

@article {pmid40401771,
year = {2025},
author = {Callens, M and Le Berre, G and Van den Bulcke, L and Lolivier, M and Derycke, S},
title = {An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14126},
doi = {10.1111/1755-0998.14126},
pmid = {40401771},
issn = {1755-0998},
support = {RT/24/DNASense_ILVO//Belgian Federal Science Policy Office/ ; //Biodiversa+/ ; //Belgian Federal Public Service Economy/ ; BAR0159//Directorate-General for Regional Policy of the European Union/ ; },
abstract = {DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.},
}

@article {pmid40399402,
year = {2025},
author = {Jarmukhanov, Z and Vinogradova, E and Mukhanbetzhanov, N and Kozhakhmetov, S and Khassenbekova, D and Kushugulova, A},
title = {Parity influences postpartum adaptations in the maternal gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17636},
pmid = {40399402},
issn = {2045-2322},
support = {AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Female ; Humans ; *Gastrointestinal Microbiome ; *Postpartum Period/physiology ; Pregnancy ; Adult ; *Parity ; *Adaptation, Physiological ; Bacteria/genetics/classification ; Milk, Human ; },
abstract = {The gut microbiome undergoes substantial modifications during pregnancy, yet its postpartum adaptations remain poorly understood, particularly with respect to the influence of parity. Here, we investigated the impact of childbirth history on maternal gut microbiome composition and function one month postpartum. By conducting metagenomic sequencing analysis on 60 participants (34 postpartum mothers and 26 controls), we demonstrated significant differences in microbial diversity and community structure between postpartum mothers and control, as well as subtle differences between first-time mothers and multiple-birth mothers. We identified parity-specific signatures, with first-time mothers showing enrichment in Dysosmobacter welbionis, Candidatus Saccharibacteria, and Anaerotruncus species. Functional analysis revealed distinct metabolic reprogramming patterns, including increased amino acid biosynthesis and modified fermentation pathways supporting postpartum recovery. We observed significant correlations between specific bacterial taxa and metabolic pathways, particularly in energy metabolism and immune modulation. Notably, the enhanced capacity for short-chain fatty acid production in primiparous mothers, mediated by Anaerotruncus and Dysosmobacter welbionis, suggests a potential role in shaping breast milk composition, which may influence neonatal development. These findings establish the concept of parity-dependent microbiome programming and provide insights into the biological mechanisms underlying maternal adaptation to pregnancy and childbirth.},
}

Female
Humans
*Gastrointestinal Microbiome
*Postpartum Period/physiology
Pregnancy
Adult
*Parity
*Adaptation, Physiological
Bacteria/genetics/classification
Milk, Human

@article {pmid40397921,
year = {2025},
author = {Abdillah, A and Ravaux, I and Mokhtari, S and Ranque, S},
title = {Do Malassezia yeasts colonize the guts of people living with HIV?.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322982},
pmid = {40397921},
issn = {1932-6203},
mesh = {Humans ; *Malassezia/isolation & purification/genetics ; *HIV Infections/microbiology/complications/immunology ; Female ; Male ; Adult ; Feces/microbiology ; Middle Aged ; Immunocompromised Host ; Metagenomics ; *Gastrointestinal Microbiome ; Prospective Studies ; },
abstract = {Malassezia yeasts are commensals of human skin. In contrast to culture-based studies, metagenomic studies have detected abundant Malassezia reads in the gut, especially in patients living with HIV. Whether Malassezia colonizes and persists in the gut remains an open question. This study aimed to describe the influence of HIV-associated immunodeficiency on gut colonization by Malassezia and to assess whether Malassezia are alive. Stool samples were prospectively collected over one-five visits from ten controls and 23 patients living with HIV (10 had CD4 < 200/mm3 and 13 had CD4 > 500/mm3). Each sample was cultured and subjected to Malassezia viability PCR and both fungal and bacterial metabarcoding. Abundant M. furfur colonies were cultured from an HIV-immunocompromised patient. M. furfur and M. globosa were isolated in very low quantities from healthy volunteers. Viability Malassezia-specific qPCR was positive in three HIV-immunocompromised patients. Metagenomic analyses showed that Malassezia reads were significantly more abundant in immunocompromised patients living with HIV and erratic over time in all participants. Our findings emphasise that Malassezia are rarely cultured from human stool samples, despite the use of specific culture media. Although HIV-related immunosuppression appears to be associated with the presence of Malassezia, these yeasts do not persist and colonise the gut, even in immunocompromised patients.},
}

Humans
*Malassezia/isolation & purification/genetics
*HIV Infections/microbiology/complications/immunology
Female
Male
Adult
Feces/microbiology
Middle Aged
Immunocompromised Host
Metagenomics
*Gastrointestinal Microbiome
Prospective Studies

@article {pmid40396743,
year = {2025},
author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X},
title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0157124},
doi = {10.1128/msystems.01571-24},
pmid = {40396743},
issn = {2379-5077},
abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.

IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.},
}

@article {pmid40396732,
year = {2025},
author = {Xin, T and Ye, Q and Hu, D},
title = {A relationship between body size and the gut microbiome suggests a conservation strategy.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0029425},
doi = {10.1128/spectrum.00294-25},
pmid = {40396732},
issn = {2165-0497},
abstract = {A key goal of conservation is to protect the biodiversity of wild species to support their continued evolution and survival. Conservation practice has long been guided by genetic, ecological, and demographic indicators of risk. Cope's rule suggests that species tend to evolve larger body sizes over time. Here, we provide strong evidence to support the inclusion of body size when formulating wildlife conservation strategies. The gut microbiome can mirror the physiological and environmental adaptation status of the host. This study established a connection between body size and the gut microbiome in the Felidae family using 70 fecal samples collected from 18 individuals through metagenomic data analysis and mining metagenome-assembled genomes (MAGs). Two enterotypes were identified in the Felidae gut: Bacteroides and Clostridium. Medium-sized felids predominantly harbored Clostridium, associated with pathogenicity, whereas large and small felids harbored both beneficial Bacteroides and pathogenic Clostridium. Species that evolved larger body sizes over time exhibited distinct changes in gut microbial communities, such as enhanced nutrient extraction and metabolic capabilities. Larger felids exhibited a more diverse, stable gut microbiome engaged in metabolic processes and extensive host interactions, indicating an evolved functional role in various biological processes. Conversely, that of smaller felids is less diverse, with more viruses and pathogenic elements primarily involved in chemical synthesis. These findings provide essential insights for developing conservation strategies that consider the nutritional needs of different-sized feline species, control the transmission of pathogens, and allocate resources based on their unique gut microbiome characteristics.IMPORTANCEBody size is a fundamental trait that varies greatly among taxa and has important implications for life history and ecology. Cope's rule suggests that species tend to evolve larger body sizes over time. However, its correlation to body size evolution remains unclear. This study aimed to establish a connection between body size and the gut microbiome in the Felidae family through metagenomic data analysis. Our results support Cope's rule, illustrating that increased body size correlates with shifts in the gut microbiome, enhancing survival and adaptability.},
}

@article {pmid40396204,
year = {2025},
author = {Zöggeler, T and Kavallar, AM and Pollio, AR and Aldrian, D and Decristoforo, C and Scholl-Bürgi, S and Müller, T and Vogel, GF},
title = {Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508951},
pmid = {40396204},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; *Fatty Liver/microbiology ; Male ; Metagenomics ; Female ; *Obesity/microbiology ; Adolescent ; Shotgun Sequencing ; },
abstract = {Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.},
}

Humans
*Gastrointestinal Microbiome/genetics
Child
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
*Pediatric Obesity/microbiology/complications
*Fatty Liver/microbiology
Male
Metagenomics
Female
*Obesity/microbiology
Adolescent
Shotgun Sequencing

@article {pmid40392071,
year = {2025},
author = {You, Q and Wang, K and Zhao, Z and Zhou, H and Lan, Z and Liang, H and Deng, R and Li, W and Shen, S and Wang, R and Zhang, K and Zheng, D and Sun, J},
title = {Reduction of Bacteroides fragilis in Gut Microbiome of Chronic Hepatitis B Patients Promotes Liver Injury.},
journal = {Journal of medical virology},
volume = {97},
number = {5},
pages = {e70395},
doi = {10.1002/jmv.70395},
pmid = {40392071},
issn = {1096-9071},
support = {//This study was supported by the Guangzhou Science and Technology Plan Project (Grant 2024B03J0326), the Guangdong Basic and Applied Basic Research Foundation of Guangzhou Joint Fund (Grant 2022B1515120039), the National Natural Science Foundation of China (Grant U22A20274), and the Guangdong Basic and Applied Basic Research Foundation (Grant 2023A1515010437)./ ; },
mesh = {Humans ; *Bacteroides fragilis/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/microbiology/complications/pathology ; Male ; Female ; Adult ; Case-Control Studies ; Animals ; Middle Aged ; Mice ; Liver/pathology ; Alanine Transaminase/blood ; Metagenomics ; Disease Models, Animal ; },
abstract = {In chronic hepatitis B (CHB) patients under antiviral treatment, liver injury, as evidenced by elevated alanine transaminase (ALT), is associated with unfavorable outcomes and needs effective treatment. The interaction between gut microbiota and liver injury in CHB patients remains unclear. Using a case-control design, 28 cases with elevated ALT and 28 matched controls with normal ALT were randomly selected from CHB patients with viral control. Clinical characteristics were comparable between groups. Metagenomic sequencing revealed that Bacteroides fragilis was decreased in cases and exhibited the greatest disparity between cases and controls. Mice colonized by gut microbiota from cases exhibited more severe liver damage in both LPS-induced and MCD diet-induced liver injury models, and had a lower abundance of B. fragilis compared to mice colonized by gut microbiota from controls. Oral gavage of B. fragilis improved both LPS-induced and MCD diet-induced liver injury. Metabolomics analysis revealed that the levels of 7-Ketolithocholic acid (7-Keto-LCA) were positively correlated with B. fragilis and significantly increased in the cultural supernatant of B. fragilis. Consistently, 7-Keto-LCA exerted protective effects against both LPS-induced and MCD diet-induced liver damage. Targeting gut microbiota might be a promising therapeutic treatment for alleviation residual liver inflammation in CHB patients with viral control.},
}

Humans
*Bacteroides fragilis/isolation & purification/genetics
*Gastrointestinal Microbiome
*Hepatitis B, Chronic/microbiology/complications/pathology
Male
Female
Adult
Case-Control Studies
Animals
Middle Aged
Mice
Liver/pathology
Alanine Transaminase/blood
Metagenomics
Disease Models, Animal

@article {pmid40391128,
year = {2025},
author = {Yatera, K and Wang, Z and Shibata, Y and Ishikawa, N and Homma, T and Fukushima, K and Hataji, O and Inoue, Y and Kawabata, H and Miki, K and Sato, K and Tobino, K and Yoshida, M and Ishii, T and Ito, R and Kobayashi, T and Kawamatsu, S and Compton, CH and Jones, PW},
title = {Sputum Microbiome, Potentially Pathogenic Organisms, and Clinical Outcomes in Japanese Patients with COPD and Moderate Airflow Limitation: The Prospective AERIS-J Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {20},
number = {},
pages = {1477-1492},
pmid = {40391128},
issn = {1178-2005},
mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/pathogenicity/genetics/isolation & purification ; Disease Progression ; Forced Expiratory Volume ; Japan/epidemiology ; *Lung/microbiology/physiopathology ; *Microbiota ; Prospective Studies ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Severity of Illness Index ; *Sputum/microbiology ; East Asian People ; },
abstract = {BACKGROUND: In Western studies, lung microbiome changes are reported in patients with chronic obstructive pulmonary disease (COPD) and are associated with poorer outcomes, but similar studies in Asian patients or those with less severe COPD are limited.

METHODS: The Acute Exacerbation and Respiratory InfectionS in COPD Japan (AERIS-J; jRCT1080224632/NCT03957577) was a prospective, non-interventional study to evaluate sputum microbiome diversity at baseline and after 12 months (V2; exploratory analysis), in patients aged 40-80 years with stable COPD (June 2019-June 2022). Baseline sputum potentially pathogenic organisms (PPOs) were identified. Blood cell counts and COPD Assessment Test (CAT) scores were collected at baseline and COPD symptoms measured over 12 months using the Evaluating Respiratory Symptoms in COPD and EXAcerbations of Chronic pulmonary disease Tool, collected by eDiary.

RESULTS: Patients (N=63) had a mean age of 72.8 years, and percent predicted post-bronchodilator forced expiratory volume in 1 second was 58.3%; 92% were male. Across 62 baseline sputum samples, microbiome composition was similar between 16S rRNA/metagenomic datasets. Patients graded Global Initiative for Chronic Obstructive Lung Disease (GOLD) III versus GOLD I/II had minimal differences in their microbial taxonomic profile and no differences in microbial diversity (Wilcoxon P=0.71). Alpha diversity (Shannon index) positively correlated with blood basophils (rho=0.41; P=0.0019) and negatively correlated with CAT score (rho=0.36; P=0.0069). Alpha diversity and sputum (rho: -0.0637; P=0.7836) or blood (rho: 0.1739; P=0.2043) eosinophils were not correlated. No difference in alpha (P=0.5) or beta (P=0.3) diversity or Operational Taxonomic Unit (Anosim R=-0.024; P=0.892) was observed between PPO-positive or -negative sputum.

CONCLUSION: A less diverse microbiome correlated with poorer health status and lower blood basophils in patients with COPD and moderate airflow limitation. There was no relationship between PPO presence and microbiome diversity.},
}

Adult
Aged
Aged, 80 and over
Female
Humans
Male
Middle Aged
*Bacteria/pathogenicity/genetics/isolation & purification
Disease Progression
Forced Expiratory Volume
Japan/epidemiology
*Lung/microbiology/physiopathology
*Microbiota
Prospective Studies
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis
Severity of Illness Index
*Sputum/microbiology
East Asian People

@article {pmid40350102,
year = {2025},
author = {El-Son, MAM and Elbahnaswy, S and Khormi, MA and Aborasain, AM and Abdelhaffez, HH and Zahran, E},
title = {Harnessing the fish gut microbiome and immune system to enhance disease resistance in aquaculture.},
journal = {Fish & shellfish immunology},
volume = {163},
number = {},
pages = {110394},
doi = {10.1016/j.fsi.2025.110394},
pmid = {40350102},
issn = {1095-9947},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Aquaculture/methods ; *Fishes/immunology/microbiology ; *Disease Resistance/immunology ; Probiotics/administration & dosage ; *Fish Diseases/immunology/prevention & control/microbiology ; Prebiotics/administration & dosage ; Diet/veterinary ; },
abstract = {The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Aquaculture/methods
*Fishes/immunology/microbiology
*Disease Resistance/immunology
Probiotics/administration & dosage
*Fish Diseases/immunology/prevention & control/microbiology
Prebiotics/administration & dosage
Diet/veterinary

@article {pmid40338094,
year = {2025},
author = {Tanaka, M and Toyonaga, T and Nakagawa, F and Iwamoto, T and Hasegawa, Y and Komatsu, A and Sumiyoshi, N and Shibuya, N and Minemura, A and Ariyoshi, T and Matsumoto, A and Oka, K and Shimoda, M and Saruta, M},
title = {Dietary 3-aminobenzoic acid enhances intestinal barrier integrity and attenuates experimental colitis.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {328},
number = {6},
pages = {G801-G810},
doi = {10.1152/ajpgi.00406.2024},
pmid = {40338094},
issn = {1522-1547},
support = {21K15985//Kaken Pharmaceutical (Kaken)/ ; },
mesh = {Humans ; Animals ; Caco-2 Cells ; *Intestinal Mucosa/metabolism/drug effects ; Mice ; Gastrointestinal Microbiome/drug effects ; Permeability/drug effects ; Male ; *Colitis, Ulcerative/metabolism/drug therapy ; Mice, Inbred C57BL ; Female ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism/drug effects/pathology ; },
abstract = {Disruption of intestinal epithelial integrity and increased permeability is central to the pathogenesis of ulcerative colitis (UC). In this study, we identified 3-aminobenzoic acid (3-ABA), a dietary component abundant in azuki beans, soybeans, and chickpeas as a regulator of epithelial permeability and inflammation in the colon. Screening 119 gut microbial metabolites revealed the ability of 4-ABA, a structural isomer of 3-ABA, to enhance barrier function in Caco2 cells. Further analysis of structural isomers identified 3-ABA as the most effective, significantly increasing transepithelial electrical resistance and reducing epithelial permeability. Using liquid chromatography-mass spectrometry, 3-ABA was detected in dietary beans and human fecal samples. Fecal 3-ABA levels were significantly lower in patients with UC compared with healthy individuals. Metagenomic and functional prediction analyses revealed dysbiosis in patients with UC, characterized by an enrichment of bacterial genes involved in ABA degradation. Gene expression analysis of 3-ABA-stimulated Caco2 cells demonstrated upregulation of tight junction molecules, such as CLDN1 and TJP1, enhancing epithelial barrier integrity. In a dextran sodium sulfate-induced colitis mouse model, rectal 3-ABA administration ameliorated colitis by enhancing epithelial barrier function and reducing inflammation. These findings highlight 3-ABA's potential as a dietary therapeutic agent for UC, offering a novel strategy to enhance intestinal integrity and mitigate inflammation.NEW & NOTEWORTHY Increased intestinal epithelial permeability is central to the pathogenesis of ulcerative colitis (UC). 3-Aminobenzoic acid (3-ABA), a dietary component abundant in beans, decreased epithelial permeability and attenuated colonic inflammation in a mouse experimental colitis model. Reduced fecal 3-ABA levels in patients with UC were associated with dysbiosis-driven accelerated degradation. These findings highlight the therapeutic potential of 3-ABA in UC by targeting colonic epithelium.},
}

Humans
Animals
Caco-2 Cells
*Intestinal Mucosa/metabolism/drug effects
Mice
Gastrointestinal Microbiome/drug effects
Permeability/drug effects
Male
*Colitis, Ulcerative/metabolism/drug therapy
Mice, Inbred C57BL
Female
*Colitis/metabolism
Disease Models, Animal
Colon/metabolism/drug effects/pathology

@article {pmid40390177,
year = {2025},
author = {Ren, Z and Wang, M and Yu, J and Zhang, L and Lin, Z and Li, X and Zhang, Y},
title = {Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70110},
doi = {10.1111/1462-2920.70110},
pmid = {40390177},
issn = {1462-2920},
support = {42301132//National Natural Science Foundation of China/ ; NKL2023-QN02//Key Laboratory of Lake and Watershed Science for Water Security/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation & purification ; *Lakes/microbiology ; Phylogeny ; Biodiversity ; Tibet ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Archaea/metabolism/classification/genetics/isolation & purification
*Lakes/microbiology
Phylogeny
Biodiversity
Tibet
RNA, Ribosomal, 16S/genetics

@article {pmid40390128,
year = {2025},
author = {Liao, H and Wen, C and Huang, D and Liu, C and Gao, T and Du, Q and Yang, QE and Jin, L and Ju, F and Yuan, MM and Tang, X and Yu, P and Zhou, S and Alvarez, PJ and Friman, VP},
title = {Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {127},
pmid = {40390128},
issn = {2049-2618},
support = {42277357//National Natural Science Foundation of China/ ; },
mesh = {*Streptomyces/virology/genetics/drug effects ; *Soil Microbiology ; *Bacteriophages/physiology/genetics ; Metagenomics/methods ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; China ; *Drug Resistance, Bacterial/genetics ; Sewage/virology ; },
abstract = {BACKGROUND: Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.

RESULTS: Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.

CONCLUSION: Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.},
}

*Streptomyces/virology/genetics/drug effects
*Soil Microbiology
*Bacteriophages/physiology/genetics
Metagenomics/methods
Microbiota/genetics
Anti-Bacterial Agents/pharmacology
Soil/chemistry
China
*Drug Resistance, Bacterial/genetics
Sewage/virology

@article {pmid40390033,
year = {2025},
author = {Teng, T and Huang, F and Xu, M and Li, X and Zhang, L and Yin, B and Cai, Y and Chen, F and Zhang, L and Zhang, J and Geng, A and Chen, C and Yu, X and Sui, J and Zhu, ZJ and Guo, K and Zhang, C and Zhou, X},
title = {Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {128},
pmid = {40390033},
issn = {2049-2618},
support = {82301714//the National Natural Science Foundation of China/ ; 22425404//the National Natural Science Foundation of China/ ; 82271565//the National Natural Science Foundation of China/ ; 2023TQ0398//the China Postdoctoral Science Foundation/ ; CSTB2023NSCQ-BHX0106//Natural Science Foundation of Chongqing, China/ ; 2208013341918508//Postdoctoral Innovation Talents Support Program of Chongqing, China/ ; 2022YFC3400702//National Key R&D Program of China/ ; 2024YFC2707800//National Key R&D Program of China/ ; 2022ZD0212900//STI2030-Major Projects/ ; },
mesh = {Humans ; Adolescent ; Child ; *Gastrointestinal Microbiome/physiology ; Male ; *Depressive Disorder, Major/microbiology/metabolism ; Female ; *Amino Acids/deficiency/blood/metabolism ; Magnetic Resonance Imaging ; Animals ; Rats ; Brain/diagnostic imaging/metabolism ; Feces/microbiology ; Metagenomics/methods ; Metabolomics/methods ; *Depression/microbiology ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.

RESULTS: We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value < 0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value = 0.001, M[2] = 0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.

CONCLUSIONS: Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.},
}

Humans
Adolescent
Child
*Gastrointestinal Microbiome/physiology
Male
*Depressive Disorder, Major/microbiology/metabolism
Female
*Amino Acids/deficiency/blood/metabolism
Magnetic Resonance Imaging
Animals
Rats
Brain/diagnostic imaging/metabolism
Feces/microbiology
Metagenomics/methods
Metabolomics/methods
*Depression/microbiology

@article {pmid40389724,
year = {2025},
author = {Yang, M and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Yu, L},
title = {Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {766},
pmid = {40389724},
issn = {2399-3642},
support = {202449CE340009, 202201AU070043, 202101BA070001-174//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 202501AU070008//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 2025J0753//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; 2023J0827//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; },
mesh = {*Endophytes/physiology ; *Plant Diseases/microbiology ; *Amorphophallus/microbiology ; *Microbiota ; *Disease Resistance ; *Adaptation, Physiological ; Stress, Physiological ; *Bacteria ; },
abstract = {Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.},
}

*Endophytes/physiology
*Plant Diseases/microbiology
*Amorphophallus/microbiology
*Microbiota
*Disease Resistance
*Adaptation, Physiological
Stress, Physiological
*Bacteria

@article {pmid40298412,
year = {2025},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {mSphere},
volume = {10},
number = {5},
pages = {e0085724},
doi = {10.1128/msphere.00857-24},
pmid = {40298412},
issn = {2379-5042},
support = {R35GM151155/NH/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Case-Control Studies ; Liver Cirrhosis/microbiology ; Genome, Bacterial ; },
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.},
}

*Metagenomics/methods
Humans
*Gastrointestinal Microbiome/genetics
*Metagenome
Case-Control Studies
Liver Cirrhosis/microbiology
Genome, Bacterial

@article {pmid40261045,
year = {2025},
author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD},
title = {TEAL-Seq: targeted expression analysis sequencing.},
journal = {mSphere},
volume = {10},
number = {5},
pages = {e0098424},
doi = {10.1128/msphere.00984-24},
pmid = {40261045},
issn = {2379-5042},
mesh = {Humans ; *Staphylococcus aureus/genetics ; *Microbiota/genetics ; *Staphylococcus epidermidis/genetics ; *Gene Expression Profiling/methods ; Metagenome ; Skin/microbiology ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; },
abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.},
}

Humans
*Staphylococcus aureus/genetics
*Microbiota/genetics
*Staphylococcus epidermidis/genetics
*Gene Expression Profiling/methods
Metagenome
Skin/microbiology
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods

@article {pmid40178790,
year = {2025},
author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W},
title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).},
journal = {Science China. Life sciences},
volume = {68},
number = {6},
pages = {1541-1554},
pmid = {40178790},
issn = {1869-1889},
mesh = {China ; *Spacecraft ; *Microbiota/genetics ; Humans ; *Space Flight ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Astronauts ; },
abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.},
}

China
*Spacecraft
*Microbiota/genetics
Humans
*Space Flight
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
Astronauts

@article {pmid40389466,
year = {2025},
author = {Salehi, M and Laitinen, V and Bhanushali, S and Bengtsson-Palme, J and Collignon, P and Beggs, JJ and Pärnänen, K and Lahti, L},
title = {Gender differences in global antimicrobial resistance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {79},
pmid = {40389466},
issn = {2055-5008},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 330887//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 348439//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 20220114//Alhopuro Foundation/ ; 20220114//Alhopuro Foundation/ ; 2019-00299//Swedish Research Council/ ; FFL21-0174//Swedish Foundation for Strategic Research/ ; KAW 2020.0239//Data-Driven Life Science/ ; },
mesh = {Humans ; Female ; Male ; Sex Factors ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Adult ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Global Health ; Middle Aged ; },
abstract = {Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.},
}

Humans
Female
Male
Sex Factors
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/genetics
Adult
*Drug Resistance, Bacterial/genetics
Metagenome
Global Health
Middle Aged

@article {pmid40388544,
year = {2025},
author = {Kohnert, E and Kreutz, C},
title = {Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321452},
pmid = {40388544},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Benchmarking ; Computer Simulation ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; },
abstract = {Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Benchmarking
Computer Simulation
Humans
*Metagenomics/methods
Computational Biology/methods

@article {pmid40388308,
year = {2025},
author = {Wang, S and Kong, F and Dai, D and Li, C and Hao, Y and Wang, E and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40388308},
issn = {2047-217X},
support = {2022YFD1301400//National Key Research and Development Program/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Female ; *Peripartum Period/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Pregnancy ; },
abstract = {BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Feces/microbiology
*Gastrointestinal Microbiome
Female
*Peripartum Period/metabolism
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Pregnancy

@article {pmid40131463,
year = {2025},
author = {Liu, H and Gan, Y and He, B and Liu, H and Zhuo, H and Tang, J and Xie, B and Shen, G and Ren, H and Jiang, X},
title = {mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {34},
number = {5},
pages = {1709-1721},
pmid = {40131463},
issn = {1432-0932},
mesh = {Humans ; *Intervertebral Disc Degeneration/microbiology ; Male ; Female ; Middle Aged ; *Intervertebral Disc/microbiology ; *Microbiota ; Adult ; *Lumbar Vertebrae/microbiology ; Aged ; },
abstract = {OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.

METHODS: A total of 104 patients with lumbar disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including α diversity analysis, β diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.

RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann ≤ 4) and young patients (age < 45 years) had more abundant microbial communities in disc tissue (P < 0.05). Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P < 0.01). There was a negative correlation between pseudomonas thermotolerans and modified Pfirrmann classification (P < 0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P < 0.05). Staphylococcus arlettae was negatively correlated with age (P < 0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P < 0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P < 0.05), and Pseudomonas had a significant negative correlation with age (P < 0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.

CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.},
}

Humans
*Intervertebral Disc Degeneration/microbiology
Male
Female
Middle Aged
*Intervertebral Disc/microbiology
*Microbiota
Adult
*Lumbar Vertebrae/microbiology
Aged

@article {pmid40045177,
year = {2025},
author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S},
title = {Gut microbiome in colorectal cancer: metagenomics from bench to bedside.},
journal = {JNCI cancer spectrum},
volume = {9},
number = {3},
pages = {},
doi = {10.1093/jncics/pkaf026},
pmid = {40045177},
issn = {2515-5091},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Precision Medicine ; Prognosis ; },
abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approach.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/diagnosis
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Precision Medicine
Prognosis

@article {pmid39470619,
year = {2025},
author = {Liu, X and Luo, Y and Chen, X and Wu, M and Xu, X and Tian, J and Gao, Y and Zhu, J and Wang, Z and Zhou, Y and Zhang, Y and Wang, X and Li, W and Lu, Q and Yao, X},
title = {Fecal microbiota transplantation against moderate-to-severe atopic dermatitis: A randomized, double-blind controlled explorer trial.},
journal = {Allergy},
volume = {80},
number = {5},
pages = {1377-1388},
doi = {10.1111/all.16372},
pmid = {39470619},
issn = {1398-9995},
support = {//Nanjing Incubation Program for National Clinical Research Center/ ; //National Key Research and Development Program of China/ ; //CAMS Innovation Fund for Medical Sciences/ ; //Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; //National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Dermatitis, Atopic/therapy/diagnosis/immunology ; *Fecal Microbiota Transplantation/methods/adverse effects ; Male ; Adult ; Female ; Double-Blind Method ; Severity of Illness Index ; Treatment Outcome ; Middle Aged ; Gastrointestinal Microbiome ; Young Adult ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a novel treatment for inflammatory diseases. Herein, we assess its safety, efficacy, and immunological impact in patients with moderate-to-severe atopic dermatitis (AD).

METHODS: In this randomized, double-blind, placebo-controlled clinical trial, we performed the efficacy and safety assessment of FMT for moderate-to-severe adult patients with AD. All patients received FMT or placebo once a week for 3 weeks, in addition to their standard background treatments. Patients underwent disease severity assessments at weeks 0, 1, 2, 4, 8, 12, and 16, and blood and fecal samples were collected for immunologic analysis and metagenomic shotgun sequencing, respectively. Safety was monitored throughout the trial.

RESULTS: Improvements in eczema area and severity index (EASI) scores and percentage of patients achieving EASI 50 (50% reduction in EASI score) were greater in patients treated with FMT than in placebo-treated patients. No serious adverse reactions occurred during the trial. FMT treatment decreased the Th2 and Th17 cell proportions among the peripheral blood mononuclear cells, and the levels of TNF-α, and total IgE in serum. By contrast, the expression levels of IL-12p70 and perforin on NK cells were increased. Moreover, FMT altered the abundance of species and functional pathways of the gut microbiota in the patients, especially the abundance of Megamonas funiformis and the pathway for 1,4-dihydroxy-6-naphthoate biosynthesis II.

CONCLUSION: FMT was a safe and effective therapy in moderate-to-severe adult patients with AD; the treatment changed the gut microbiota compositions and functions.},
}

Humans
*Dermatitis, Atopic/therapy/diagnosis/immunology
*Fecal Microbiota Transplantation/methods/adverse effects
Male
Adult
Female
Double-Blind Method
Severity of Illness Index
Treatment Outcome
Middle Aged
Gastrointestinal Microbiome
Young Adult

@article {pmid40387602,
year = {2025},
author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J},
title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e70013},
pmid = {40387602},
issn = {1550-7408},
support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovación y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation & purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; },
abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.},
}

Animals
Phylogeny
*Sea Cucumbers/parasitology
*Apicomplexa/genetics/classification/isolation & purification
Host Specificity
Female
Host-Parasite Interactions
Genome, Mitochondrial

@article {pmid40382475,
year = {2025},
author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG},
title = {The Microbial Ecology of Antarctic Sponges.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {44},
pmid = {40382475},
issn = {1432-184X},
mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.},
}

*Porifera/microbiology
Animals
Antarctic Regions
*Microbiota
Symbiosis
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Ecosystem
Fungi/classification/genetics/isolation & purification

@article {pmid40382365,
year = {2025},
author = {Schilling, M and Jagdev, M and Thomas, H and Johnson, N},
title = {Metagenomic analysis of mosquitoes from Kangerlussuaq, Greenland reveals a unique virome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17141},
pmid = {40382365},
issn = {2045-2322},
mesh = {Animals ; Greenland ; *Virome/genetics ; *Metagenomics/methods ; *Aedes/virology/genetics ; *Mosquito Vectors/virology ; Metagenome ; Phylogeny ; *Culicidae/virology ; Climate Change ; },
abstract = {Climate change is dramatically affecting vector ecology in extreme environments such as the Arctic. However, little is known about the current status of viruses of arthropod vectors located in such northerly locations. As part of a field survey on the role of wildlife in international movement of zoonotic pathogens, we sampled mammalophilic mosquitoes near the settlement of Kangerlussuaq, Greenland in July 2022 and July 2023 to investigate their virome. The majority of mosquitoes were identified as either Aedes impiger or Aedes nigripes. Metagenomic analysis of RNA extracted from species pools detected a number of novel RNA viruses belonging to a range of different virus families, including Flaviviridae, Orthomyxoviridae, Bunyavirales, Totiviridae and Rhabdoviridae. However, the sequence identities when compared to previously published, were as low as 34% at the amino acid level. Furthermore, a comparison of virome diversity between Aedes species emphasises the uniqueness of both Aedes impiger and Aedes nigripes from this secluded ecosystem. It also highlights the need to better understand the viromes of potential pathogen vectors as the impacts of climate change are experienced in such northerly ecosystems.},
}

Animals
Greenland
*Virome/genetics
*Metagenomics/methods
*Aedes/virology/genetics
*Mosquito Vectors/virology
Metagenome
Phylogeny
*Culicidae/virology
Climate Change

@article {pmid40382068,
year = {2025},
author = {Zhang, Z and Ran, X and Guo, Z and Hou, Q and Qu, D and Wang, C and Xu, Y and Wang, Y},
title = {Microbial diversity, functional properties, and flavor characteristics of high-temperature Daqu with different colors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {212},
number = {},
pages = {116406},
doi = {10.1016/j.foodres.2025.116406},
pmid = {40382068},
issn = {1873-7145},
mesh = {Color ; *Taste ; *Food Microbiology ; *Hot Temperature ; Odorants/analysis ; Humans ; *Bacteria/classification/genetics ; *Microbiota ; China ; },
abstract = {High-temperature Daqu (HTD) plays a crucial role in the quality of sauce-flavor baijiu. Daqu of different colors serves distinct functions in the baijiu brewing process. However, indicators for distinguishing among different-colored Daqu remain insufficient. This study investigated the microbial community structures, physicochemical properties, and E-sensory characteristics of different-colored HTD from Shandong Province. The results revealed significant differences in microbial communities among the three HTD types (P < 0.05). Kroppenstedtia eburnea, three Bacillus species, and Weizmannia coagulans were significantly enriched in white Daqu; an unclassified Staphylococcus species dominated in black Daqu; and Aspergillus oryzae, Aspergillus fumigatus, and Proteus mirabilis were highly abundant in yellow Daqu. Compared to HTD from Guizhou and Hubei, Shandong HTD was characterized by microbial species such as Proteus mirabilis and Bacillus velezensis. Using metagenomic analysis, we, for the first time, identified Thermomyces lanuginosus, Lentibacillus daqui, and an unclassified Thermoascus species as potential major contributors to pyrazine synthesis in HTD. The primary differences among the three colored Shandong Daqu types lay in their aroma profiles rather than taste. Electronic nose and electronic tongue analyses demonstrated that the W6S and W3S sensors effectively distinguished black and white Daqu, respectively, marking a novel application of these technologies in Daqu analysis. Acidity was identified as a key factor influencing microbial community structure, flavor characteristics, and enzyme activities, with a nonlinear relationship observed between acidity and enzyme activities. This study highlights the microbial and sensory distinctions among different-colored HTD and provides effective indicators for distinguishing these three types of Daqu.},
}

Color
*Taste
*Food Microbiology
*Hot Temperature
Odorants/analysis
Humans
*Bacteria/classification/genetics
*Microbiota
China

@article {pmid40380272,
year = {2025},
author = {Zhang, S and Zheng, N and Zhao, S and Wang, J},
title = {Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {124},
pmid = {40380272},
issn = {2049-2618},
support = {2023M743835//Project Funded by China Postdoctoral Science Foundation/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 2022YFD1301000//National Key Research and Development Program of China/ ; 2004DA125184G2406//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/chemistry ; *Urease/antagonists & inhibitors/metabolism/chemistry ; *Rumen/microbiology ; *Urea/metabolism ; Disulfides/pharmacology ; *Nitrogen/metabolism ; Cattle ; Molecular Docking Simulation ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/drug effects/classification/genetics ; Enzyme Inhibitors/pharmacology ; },
abstract = {BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.

RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77 ± 1.21 μM. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.

CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.},
}

Animals
*Sulfinic Acids/pharmacology/chemistry
*Urease/antagonists & inhibitors/metabolism/chemistry
*Rumen/microbiology
*Urea/metabolism
Disulfides/pharmacology
*Nitrogen/metabolism
Cattle
Molecular Docking Simulation
*Gastrointestinal Microbiome/drug effects
*Bacteria/metabolism/drug effects/classification/genetics
Enzyme Inhibitors/pharmacology

@article {pmid40378832,
year = {2025},
author = {Sarhan, MS and Antonello, G and Weissensteiner, H and Mengoni, C and Mascalzoni, D and Waldron, L and Segata, N and Fuchsberger, C},
title = {Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?.},
journal = {Cell},
volume = {188},
number = {10},
pages = {2561-2566},
doi = {10.1016/j.cell.2025.03.023},
pmid = {40378832},
issn = {1097-4172},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Metagenome ; *Metagenomics/ethics ; Privacy ; Microbiota ; *Genetic Privacy/ethics ; },
abstract = {Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.},
}

Humans
*DNA, Mitochondrial/genetics
*Metagenome
*Metagenomics/ethics
Privacy
Microbiota
*Genetic Privacy/ethics

@article {pmid40377187,
year = {2025},
author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM},
title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {40377187},
issn = {2050-084X},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; 1746045//National Science Foundation Graduate Research Fellowship Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; },
abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Stress, Physiological
Metagenome
*Bacteria/metabolism/genetics/classification

@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
mesh = {*Glycine max/microbiology/physiology/growth & development ; *Rhizosphere ; *Floods ; *Microbiota ; Plant Roots/microbiology ; Seeds ; *Soil Microbiology ; },
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}

*Glycine max/microbiology/physiology/growth & development
*Rhizosphere
*Floods
*Microbiota
Plant Roots/microbiology
Seeds
*Soil Microbiology

@article {pmid40354675,
year = {2025},
author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S},
title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156653},
doi = {10.1016/j.phymed.2025.156653},
pmid = {40354675},
issn = {1618-095X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; *Obesity/drug therapy/metabolism ; *Platycodon/chemistry ; Diet, High-Fat/adverse effects ; Mice ; Fatty Acids, Volatile/metabolism ; *Anti-Obesity Agents/pharmacology ; Drugs, Chinese Herbal ; },
abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.

PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.

STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.

RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.

CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Male
Mice, Inbred C57BL
*Polysaccharides/pharmacology
*Obesity/drug therapy/metabolism
*Platycodon/chemistry
Diet, High-Fat/adverse effects
Mice
Fatty Acids, Volatile/metabolism
*Anti-Obesity Agents/pharmacology
Drugs, Chinese Herbal

@article {pmid40311598,
year = {2025},
author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G},
title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156656},
doi = {10.1016/j.phymed.2025.156656},
pmid = {40311598},
issn = {1618-095X},
mesh = {Animals ; *Asthma/drug therapy/microbiology ; *T-Lymphocytes, Regulatory/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; Mice, Inbred C57BL ; *Interleukin-17/metabolism/genetics ; Mice ; Histones/metabolism ; Cell Differentiation/drug effects ; Male ; Acetylation ; Disease Models, Animal ; Histone Deacetylases/metabolism ; Lung/drug effects/pathology ; },
abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.

PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.

METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.

RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.

CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.},
}

Animals
*Asthma/drug therapy/microbiology
*T-Lymphocytes, Regulatory/drug effects
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology
Mice, Inbred C57BL
*Interleukin-17/metabolism/genetics
Mice
Histones/metabolism
Cell Differentiation/drug effects
Male
Acetylation
Disease Models, Animal
Histone Deacetylases/metabolism
Lung/drug effects/pathology

@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
mesh = {*Meat Products/microbiology/analysis ; *Food Microbiology ; *Sodium Chloride/analysis ; *Food Handling/methods ; Animals ; Metagenomics ; Microbiota ; Bacteria ; Food Preservation/methods ; },
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}

*Meat Products/microbiology/analysis
*Food Microbiology
*Sodium Chloride/analysis
*Food Handling/methods
Animals
Metagenomics
Microbiota
Bacteria
Food Preservation/methods

@article {pmid40372371,
year = {2025},
author = {Li, X and He, N and Wang, H and Wu, Z and Wang, M and Liang, H and Xiao, L and Yang, Z and Li, C and Xu, P and Dai, T and Li, S and Zou, Y},
title = {Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.},
journal = {Journal of applied microbiology},
volume = {136},
number = {5},
pages = {},
doi = {10.1093/jambio/lxaf119},
pmid = {40372371},
issn = {1365-2672},
support = {XMHT20220104017//Shenzhen Municipal Government of China/ ; },
mesh = {Animals ; *Colitis, Ulcerative/therapy/chemically induced/microbiology ; Mice ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Cytokines/metabolism/blood ; Dextran Sulfate/adverse effects ; *Faecalibacterium/physiology/genetics ; Humans ; Disease Models, Animal ; Colon/microbiology ; Male ; Female ; Mice, Inbred C57BL ; },
abstract = {AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.

METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1β, IL-6, and TNF-α, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.

CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.},
}

Animals
*Colitis, Ulcerative/therapy/chemically induced/microbiology
Mice
*Gastrointestinal Microbiome
Feces/microbiology
*Probiotics/administration & dosage/therapeutic use
Cytokines/metabolism/blood
Dextran Sulfate/adverse effects
*Faecalibacterium/physiology/genetics
Humans
Disease Models, Animal
Colon/microbiology
Male
Female
Mice, Inbred C57BL

@article {pmid40371968,
year = {2025},
author = {Jansen, D and Deleu, S and Caenepeel, C and Marcelis, T and Simsek, C and Falony, G and Machiels, K and Sabino, J and Raes, J and Vermeire, S and Matthijnssens, J},
title = {Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499575},
pmid = {40371968},
issn = {1949-0984},
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/virology/microbiology ; *Virome ; Male ; Female ; Feces/virology ; Adult ; Gastrointestinal Microbiome ; Middle Aged ; *Bacteriophages/genetics/isolation & purification/classification ; Young Adult ; },
abstract = {Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.},
}

Humans
*Fecal Microbiota Transplantation
*Colitis, Ulcerative/therapy/virology/microbiology
*Virome
Male
Female
Feces/virology
Adult
Gastrointestinal Microbiome
Middle Aged
*Bacteriophages/genetics/isolation & purification/classification
Young Adult

@article {pmid40369676,
year = {2025},
author = {Zhang, Y and Liu, H and Jing, H},
title = {Community differences and potential function along the particle size spectrum of microbes in the twilight zone.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {121},
pmid = {40369676},
issn = {2049-2618},
support = {424QN341//the Hainan Provincial Natural Science Foundation of China/ ; JRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; 2023YFC2812804//the National Key R&D Program of China/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; },
mesh = {Particle Size ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seawater/microbiology/chemistry ; *Microbiota/genetics ; Metagenomics/methods ; Carbon/metabolism ; Metagenome ; },
abstract = {BACKGROUND: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

RESULTS: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

CONCLUSION: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.},
}

Particle Size
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seawater/microbiology/chemistry
*Microbiota/genetics
Metagenomics/methods
Carbon/metabolism
Metagenome

@article {pmid40368959,
year = {2025},
author = {Song, XL and Wang, ZJ and Yin, XW and Sun, YL and Jang, DJ and Hong, SK},
title = {The impact of nitrogen deposition on nitrogen metabolism in ryegrass lawn with different soil nutrient levels.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16755},
pmid = {40368959},
issn = {2045-2322},
mesh = {*Nitrogen/metabolism ; *Lolium/metabolism ; *Soil/chemistry ; Soil Microbiology ; Nitrogen Fixation ; Nitrification ; *Nutrients/metabolism ; Denitrification ; Nitrogen Cycle ; Microbiota ; Nitrates/metabolism ; },
abstract = {Nitrogen deposition is a crucial factor in global change, which is widespread across various regions globally. It has drawn extensive attention due to its direct modification of soil nitrogen retention and nitrogen species distribution, thereby influencing nitrogen metabolism across entire ecosystems. Previous studies on its influence on nitrogen metabolism have not reached a consensus. In an urban ryegrass lawn mesocosm experiment, we set two levels of nitrogen deposition and soil nutrients respectively, aiming to study the impacts of these factors on the N-cycling process through metagenomic analysis. The results demonstrated nitrogen deposition increased nitrification, nitrogen fixation, denitrification, and dissimilatory nitrate reduction, but decreased assimilatory nitrate reduction in the nitrogen metabolism process by changing soil nitrogen availability and the abundance of N-cycling functional genes in the soil microbial community. The soil nutrient levels exhibited effects opposite to those of nitrogen deposition, negatively impacting nitrification, denitrification, and nitrogen fixation in the nitrogen metabolism process. This work further elucidates the impacts of nitrogen deposition on the ecological functions of the ryegrass lawn with different soil nutrient levels, and predicts the potential impacts of intensified nitrogen deposition on these ecological functions. It provides valuable theoretical support for understanding and evaluating complex ecological interactions.},
}

*Nitrogen/metabolism
*Lolium/metabolism
*Soil/chemistry
Soil Microbiology
Nitrogen Fixation
Nitrification
*Nutrients/metabolism
Denitrification
Nitrogen Cycle
Microbiota
Nitrates/metabolism

@article {pmid40368948,
year = {2025},
author = {Serivichyaswat, PT and Scholte, T and Wilms, T and Stranddorf, L and van der Valk, T},
title = {Metagenomic biodiversity assessment within an offshore wind farm.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16786},
pmid = {40368948},
issn = {2045-2322},
mesh = {*Biodiversity ; *Metagenomics/methods ; North Sea ; Animals ; *Wind ; Seawater ; *DNA, Environmental/genetics/analysis ; Ecosystem ; *Metagenome ; Denmark ; },
abstract = {Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.},
}

*Biodiversity
*Metagenomics/methods
North Sea
Animals
*Wind
Seawater
*DNA, Environmental/genetics/analysis
Ecosystem
*Metagenome
Denmark

@article {pmid40367945,
year = {2025},
author = {Antonaru, LA and Rad-Menéndez, C and Mbedi, S and Sparmann, S and Pope, M and Oliver, T and Wu, S and Green, DH and Gugger, M and Nürnberg, DJ},
title = {Evolution of far-red light photoacclimation in cyanobacteria.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.04.038},
pmid = {40367945},
issn = {1879-0445},
abstract = {Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.},
}

@article {pmid40339893,
year = {2025},
author = {Zhang, L and Wang, S and Jia, Y and Liu, Z and Yao, J and Chen, Y},
title = {Alterations in microbial communities and antibiotic resistance genes pre- and post-sludge bulking in a wastewater treatment plant.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {376},
number = {},
pages = {126391},
doi = {10.1016/j.envpol.2025.126391},
pmid = {40339893},
issn = {1873-6424},
mesh = {*Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; *Sewage/microbiology ; RNA, Ribosomal, 16S ; *Microbiota ; Bacteria/genetics ; Genes, Bacterial ; },
abstract = {Sludge bulking is a common issue in wastewater treatment plants (WWTPs) that can disrupt microbial communities and potentially impact the abundance and spread of antibiotic resistance genes (ARGs) within treatment systems. This study employed high-throughput 16S rRNA gene sequencing and metagenomic sequencing to examine the changes in microbial communities and ARGs in a WWTP during non-bulking and bulking periods. The results indicated that bacterial diversity decreased in bulking sludge while maintaining a high removal efficiency of conventional pollutants. Significant differences were detected at the bacterial genus level between non-bulking and bulking sludge (p < 0.05). The proliferation of Candidatus_Microthrix contributed to sludge bulking, while Micropruina improved sludge settleability. When treating wastewater with the same water quality and quantity, anaerobic/anoxic/oxic (A[2]/O) exhibited the highest resistance to sludge bulking, followed by Bardenpho and the Carrousel oxidation ditch. The abundance of ARGs in bulking sludge (28.15-43.63 ppm) was lower than that in non-bulking sludge (51.72-59.01 ppm). The ARGs removal efficiency reached 96.24 % and 94.34 % during bulking and non-bulking periods, respectively. Network analysis revealed that Candidatus_Microthrix was positively correlated with aadS and tetX, and norank_f_Saprospiraceae exhibited positive correlations with vanRO and ANT(3″)-Iia. These findings provide valuable insights into the impacts of sludge bulking on WWTP performance and ARGs dynamics, informing evidence-based policies for sustainable wastewater treatment.},
}

*Waste Disposal, Fluid/methods
*Wastewater/microbiology
*Drug Resistance, Microbial/genetics
*Sewage/microbiology
RNA, Ribosomal, 16S
*Microbiota
Bacteria/genetics
Genes, Bacterial

@article {pmid40222673,
year = {2025},
author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL},
title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.},
journal = {Journal of dairy science},
volume = {108},
number = {6},
pages = {5705-5718},
doi = {10.3168/jds.2025-26395},
pmid = {40222673},
issn = {1525-3198},
mesh = {Animals ; *Milk/microbiology ; *Bacteriocins/pharmacology ; Pasteurization ; *Microbiota/drug effects ; Food Preservation/methods ; },
abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2× MIC (low concentration), and treatment group with the addition of 4× MIC RSQ01 (high concentration). Integrated 16S ribosomal DNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, whereas probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and AA) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.},
}

Animals
*Milk/microbiology
*Bacteriocins/pharmacology
Pasteurization
*Microbiota/drug effects
Food Preservation/methods

@article {pmid40185271,
year = {2025},
author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A},
title = {From sewage to genomes: Expanding our understanding of the urban and semi-urban wastewater RNA virome.},
journal = {Environmental research},
volume = {276},
number = {},
pages = {121509},
doi = {10.1016/j.envres.2025.121509},
pmid = {40185271},
issn = {1096-0953},
mesh = {*Wastewater/virology ; *Virome ; *Sewage/virology ; *RNA Viruses/genetics ; Chile ; *Genome, Viral ; Phylogeny ; Environmental Monitoring ; RNA, Viral ; Metagenomics ; },
abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90 % of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54 % of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.},
}

*Wastewater/virology
*Virome
*Sewage/virology
*RNA Viruses/genetics
Chile
*Genome, Viral
Phylogeny
Environmental Monitoring
RNA, Viral
Metagenomics

@article {pmid40174744,
year = {2025},
author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W},
title = {Thermal environment driving specific microbial species to form the visible biofilms on the UNESCO World Heritage Dazu Rock Carvings.},
journal = {Environmental research},
volume = {276},
number = {},
pages = {121510},
doi = {10.1016/j.envres.2025.121510},
pmid = {40174744},
issn = {1096-0953},
mesh = {*Biofilms/growth & development ; Bacteria/classification ; Fungi ; *Microbiota ; Temperature ; },
abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4 °C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.},
}

*Biofilms/growth & development
Bacteria/classification
Fungi
*Microbiota
Temperature

@article {pmid40366862,
year = {2025},
author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y},
title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505269},
pmid = {40366862},
issn = {1949-0984},
support = {R01 AI116596/AI/NIAID NIH HHS/United States ; T32 DK007760/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology ; *Clostridium Infections/microbiology ; Feces/microbiology ; Female ; Male ; *Clostridioides difficile/genetics/physiology ; Metagenomics ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Carrier State/microbiology ; Aged, 80 and over ; },
abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Diarrhea/microbiology
*Clostridium Infections/microbiology
Feces/microbiology
Female
Male
*Clostridioides difficile/genetics/physiology
Metagenomics
Middle Aged
Aged
*Bacteria/classification/genetics/isolation & purification
Adult
*Carrier State/microbiology
Aged, 80 and over

@article {pmid40366141,
year = {2025},
author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M},
title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0034225},
doi = {10.1128/msystems.00342-25},
pmid = {40366141},
issn = {2379-5077},
abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.

IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.},
}

@article {pmid40365061,
year = {2025},
author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L},
title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1571684},
pmid = {40365061},
issn = {1664-302X},
abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.},
}

@article {pmid40363788,
year = {2025},
author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z},
title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
pmid = {40363788},
issn = {1420-3049},
support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; },
abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Polysaccharides/pharmacology/chemistry/therapeutic use
Animals
*Hypoglycemic Agents/pharmacology/chemistry/therapeutic use
Signal Transduction/drug effects
Insulin Resistance
Glucose/metabolism

@article {pmid40362493,
year = {2025},
author = {Žukienė, G and Narutytė, R and Rudaitis, V},
title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
pmid = {40362493},
issn = {1422-0067},
mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.},
}

Humans
Female
*Papillomavirus Infections/complications/microbiology/virology
*Vagina/microbiology/virology
*Microbiota/genetics
Metagenomics/methods
*Uterine Cervical Dysplasia/microbiology/virology/etiology
Papillomaviridae
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40362462,
year = {2025},
author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R},
title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
pmid = {40362462},
issn = {1422-0067},
support = {xxxxx//AFRRI/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; },
abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.},
}

Animals
Male
Female
Mice
*Metabolomics/methods
*Metagenomics/methods
*Radiation, Ionizing
*Colon/radiation effects/metabolism/microbiology
*Gastrointestinal Microbiome/radiation effects
Sex Factors
Whole-Body Irradiation/adverse effects
Mice, Inbred C57BL

@article {pmid40334798,
year = {2025},
author = {Zhu, X and Chen, L and Yang, P and Luo, S and Teng, M and Zhu, W and Li, Y and Zhao, D and Wang, N and Chen, X and Cheng, M and Tu, H and Huang, W and Yang, F and Wang, L and Liu, X and Ning, K},
title = {Microbiome catalog and dynamics of the Chinese liquor fermentation process.},
journal = {Bioresource technology},
volume = {431},
number = {},
pages = {132620},
doi = {10.1016/j.biortech.2025.132620},
pmid = {40334798},
issn = {1873-2976},
mesh = {*Fermentation ; *Microbiota/genetics ; *Alcoholic Beverages/microbiology ; Multigene Family ; China ; Bacillus licheniformis/genetics/metabolism ; },
abstract = {Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems.},
}

*Fermentation
*Microbiota/genetics
*Alcoholic Beverages/microbiology
Multigene Family
China
Bacillus licheniformis/genetics/metabolism

@article {pmid40361215,
year = {2025},
author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q},
title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {537},
pmid = {40361215},
issn = {1479-5876},
support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.

METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.

RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.

CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.},
}

Humans
*Gastritis, Atrophic/microbiology/metabolism
Chronic Disease
Middle Aged
Female
Male
RNA, Ribosomal, 16S/genetics
Metabolome
*Stomach/microbiology
Metabolomics
*Microbiota
Bacteria/genetics/metabolism
Adult
Aged
*Gastrointestinal Microbiome

@article {pmid40360994,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {475},
pmid = {40360994},
issn = {1471-2164},
support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; },
mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; },
abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.},
}

Animals
*Liver/metabolism
*Gastrointestinal Microbiome
*Caudata/physiology/genetics/microbiology
Heat-Shock Response
Transcriptome
Gene Expression Profiling
Energy Metabolism
Larva

@article {pmid40360555,
year = {2025},
author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S},
title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {78},
pmid = {40360555},
issn = {2055-5008},
support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; },
abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Bacterial
Metagenome
*Microbiota/drug effects
Microbial Sensitivity Tests
Metagenomics

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods