@article {pmid40435563,
year = {2025},
author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V},
title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128226},
doi = {10.1016/j.micres.2025.128226},
pmid = {40435563},
issn = {1618-0623},
mesh = {*Gastrointestinal Microbiome/physiology ; *Brassica/metabolism/chemistry ; Fermentation ; Humans ; *Digestion ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Intestine, Large/microbiology/metabolism ; Metabolomics ; Metagenomics ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Polyphenols/metabolism ; Metabolome ; Isothiocyanates/metabolism ; Multiomics ; },
abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.},
}

*Gastrointestinal Microbiome/physiology
*Brassica/metabolism/chemistry
Fermentation
Humans
*Digestion
*Bacteria/classification/metabolism/genetics/isolation & purification
*Intestine, Large/microbiology/metabolism
Metabolomics
Metagenomics
Feces/microbiology
Fatty Acids, Volatile/metabolism
Polyphenols/metabolism
Metabolome
Isothiocyanates/metabolism
Multiomics

@article {pmid40434822,
year = {2025},
author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM},
title = {From air to insight: the evolution of airborne DNA sequencing technologies.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {5},
pages = {},
pmid = {40434822},
issn = {1465-2080},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation & purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.},
}

*High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Sequence Analysis, DNA/methods
*DNA, Environmental/genetics/analysis/isolation & purification
Humans
Environmental Monitoring/methods
Computational Biology/methods
Biodiversity

@article {pmid40433668,
year = {2025},
author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF},
title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1531084},
pmid = {40433668},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Adult ; Biomarkers ; Aged ; },
abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.},
}

Humans
*COVID-19/microbiology/pathology/virology
Cross-Sectional Studies
Disease Susceptibility
*Microbiota
SARS-CoV-2
Female
Male
Severity of Illness Index
Middle Aged
*Respiratory System/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Adult
Biomarkers
Aged

@article {pmid40413859,
year = {2025},
author = {Merchant, M and Mande, SS and Sar, P},
title = {Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions.},
journal = {Chemosphere},
volume = {382},
number = {},
pages = {144429},
doi = {10.1016/j.chemosphere.2025.144429},
pmid = {40413859},
issn = {1879-1298},
mesh = {*Polyethylene/metabolism ; Waste Disposal Facilities ; Biodegradation, Environmental ; Anaerobiosis ; Biotransformation ; Aerobiosis ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; },
abstract = {Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.},
}

*Polyethylene/metabolism
Waste Disposal Facilities
Biodegradation, Environmental
Anaerobiosis
Biotransformation
Aerobiosis
Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
*Microbiota

@article {pmid40393758,
year = {2025},
author = {Jiang, JY and Fan, ZX and Yang, F and Liu, HM and Mao, M and Feng, L and Xiong, F and Li, P},
title = {[Composition of gut microbiota and characteristics of virulence factors genes in overweight or obese children and their relationship with liver metabolic inflammation].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {63},
number = {6},
pages = {642-648},
doi = {10.3760/cma.j.cn112140-20241128-00873},
pmid = {40393758},
issn = {0578-1310},
support = {2023YFS0034//Key R&D Project of Science and Technology Department of Sichuan Province/ ; },
mesh = {Humans ; Male ; Female ; Child ; *Gastrointestinal Microbiome/genetics ; *Virulence Factors/genetics ; Case-Control Studies ; *Pediatric Obesity/microbiology/metabolism ; *Overweight/microbiology/metabolism ; Feces/microbiology ; Inflammation/metabolism ; *Liver/metabolism ; *Obesity/microbiology ; Body Mass Index ; },
abstract = {Objective: To explore the composition of gut microbiome, the characteristics of virulence factor genes and their relationship with liver metabolic inflammation in overweight or obese children. Methods: A case-control design was conducted. From the children who visited the West China Second University Hospital of Sichuan University for medical or physical examinations between August 2021 and April 2022, a total of 23 obese children (obesity group), 8 overweight children (overweight group), and 22 healthy children (control group) were recruited. The body mass index of children was calculated after anthropometric measurements; metabolic inflammation indexes such as the levels of fasting blood glucose and hepatic function and renal function etc. were detected. The composition and abundance of gut microbiota in the feces of the children were detected by metagenomic sequencing technology and the Shannon index and Simpson index were calculated to assess the α diversity of virulence factor genes. The Wilcoxon rank-sum test was used for pairwise comparison between groups. The Spearman's rank correlation test was used for correlation analysis, and the Benjamini-Hochberg method was used to correct the P-value of multiple tests. Results: The obese group included 23 children aged 8.5 (6.3, 11.8) years, of whom 9 (39%) were male. The overweight group consisted of 8 children aged 9.2 (5.5, 12.3) years, of whom 4 were male. The control group comprised 22 children aged 5.3 (5.1, 5.4) years, of whom 10 (45%) were male. The obese group exhibited higher levels of alanine aminotransferase (ALT), gamma-glutamyl transferase (γ-GT), globulin, and uric acid compared to those of the control group (all P<0.05), with ALT also higher than that of the overweight group (P<0.05). The levels of fasting blood glucose, γ-GT, globulin, and uric acid in the overweight group were all higher than those in the control group (all P<0.05). The abundance of Coprococcus A (0.76 (0.00, 3.11) vs. 0.00 (0.00, 0.00), false discovery rate (FDR)<0.05) and Parasutterella (0.89 (0.08, 1.79) vs. 0.00 (0.00, 0.08), FDR<0.05) in the gut of children in the obese group were both higher than those of the control group. The number of virulence factor genes in the obese group was higher than those of the control group (941 (886, 977) vs. 890 (807, 920), P<0.05). The Simpson index and Shannon index of gut microbial virulence factor genes in the obese group were both higher than those of the control group (0.993 (0.992, 0.993) vs. 0.991(0.990, 0.991), (5.50 (5.46, 5.56) vs. 5.37 (5.30, 5.43), both P<0.01). The abundance of gut microbiota virulence factors genes all showed positive correlations with fasting blood glucose, ALT, γ-GT, and uric acid levels in children (all r>0.3, all FDR<0.05). The abundance of 17 gut microbial virulence factor genes were all positively associated with γ-GT levels (all r>0.3, all FDR<0.05). The virulence factor genes (LpxH, LpxB, LpxK) of lipopolysaccharide were all positively correlated with plasma γ-GT and globulin levels (all r>0.3, all FDR<0.05). Conclusions: Overweight or obese children exhibited elevated liver metabolic-inflammatory markers compared to their normal-weight counterparts. Notably, obese children demonstrated gut microbiota dysbiosis accompanied by enrichment of virulence factor genes, which may promote liver metabolic inflammation through pathways such as lipopolysaccharide biosynthesis.},
}

Humans
Male
Female
Child
*Gastrointestinal Microbiome/genetics
*Virulence Factors/genetics
Case-Control Studies
*Pediatric Obesity/microbiology/metabolism
*Overweight/microbiology/metabolism
Feces/microbiology
Inflammation/metabolism
*Liver/metabolism
*Obesity/microbiology
Body Mass Index

@article {pmid40349412,
year = {2025},
author = {Ren, P and You, C and Chen, P and Mei, X and Yang, T and Xu, Y and Wang, X and Shen, Q and Wei, Z},
title = {Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128213},
doi = {10.1016/j.micres.2025.128213},
pmid = {40349412},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Fertilizers/analysis ; Bacteria/classification/genetics/isolation & purification ; China ; Biodiversity ; Lysobacter ; },
abstract = {Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.},
}

*Soil Microbiology
*Soil/chemistry
*Ecosystem
Fertilizers/analysis
Bacteria/classification/genetics/isolation & purification
China
Biodiversity
Lysobacter

@article {pmid40328980,
year = {2025},
author = {Liébana-García, R and López-Almela, I and Olivares, M and Romaní-Pérez, M and Manghi, P and Torres-Mayo, A and Tolosa-Enguís, V and Flor-Duro, A and Bullich-Vilarrubias, C and Rubio, T and Rossini, V and Segata, N and Sanz, Y},
title = {Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.},
journal = {Nature microbiology},
volume = {10},
number = {6},
pages = {1310-1322},
pmid = {40328980},
issn = {2058-5276},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Obesity/immunology/microbiology ; *Immunity, Innate ; Mice ; Humans ; *Metabolic Diseases/immunology/microbiology ; Male ; Macrophages/immunology ; Female ; Mice, Inbred C57BL ; Symbiosis ; Disease Models, Animal ; Metagenome ; },
abstract = {The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Obesity/immunology/microbiology
*Immunity, Innate
Mice
Humans
*Metabolic Diseases/immunology/microbiology
Male
Macrophages/immunology
Female
Mice, Inbred C57BL
Symbiosis
Disease Models, Animal
Metagenome

@article {pmid40246210,
year = {2025},
author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin, and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R},
title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.},
journal = {Biotechnology advances},
volume = {82},
number = {},
pages = {108580},
doi = {10.1016/j.biotechadv.2025.108580},
pmid = {40246210},
issn = {1873-1899},
mesh = {*Symbiosis ; *Soil Microbiology ; *Metagenomics/methods ; Nitrogen/metabolism ; Phosphorus/metabolism ; *Plants/microbiology/metabolism ; Sulfur/metabolism ; *Microbiota ; *Carbon Sequestration ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.},
}

*Symbiosis
*Soil Microbiology
*Metagenomics/methods
Nitrogen/metabolism
Phosphorus/metabolism
*Plants/microbiology/metabolism
Sulfur/metabolism
*Microbiota
*Carbon Sequestration
Soil/chemistry
Carbon/metabolism

@article {pmid40215877,
year = {2025},
author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T},
title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105130},
pmid = {40215877},
issn = {1525-3171},
mesh = {Animals ; *Probiotics/administration & dosage ; *Chickens/physiology/growth & development ; Animal Feed/analysis ; Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; *Lactobacillus plantarum/chemistry ; *Animal Husbandry/methods ; },
abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.},
}

Animals
*Probiotics/administration & dosage
*Chickens/physiology/growth & development
Animal Feed/analysis
Diet/veterinary
*Gastrointestinal Microbiome/drug effects
Animal Nutritional Physiological Phenomena
*Lactobacillus plantarum/chemistry
*Animal Husbandry/methods

@article {pmid40187012,
year = {2025},
author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A},
title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105089},
pmid = {40187012},
issn = {1525-3171},
mesh = {Animals ; Pakistan ; *Chickens/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Feces/microbiology ; Metagenomics ; *Bacteria/isolation & purification/classification/genetics ; *Gastrointestinal Microbiome ; Animal Husbandry ; RNA, Bacterial/analysis ; Farms ; },
abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.},
}

Animals
Pakistan
*Chickens/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Feces/microbiology
Metagenomics
*Bacteria/isolation & purification/classification/genetics
*Gastrointestinal Microbiome
Animal Husbandry
RNA, Bacterial/analysis
Farms

@article {pmid39406574,
year = {2025},
author = {Steinberg, R and Moeller, A and Gisler, A and Mostacci, N and Hilty, M and Usemann, J},
title = {Longitudinal effects of elexacaftor/tezacaftor/ivacaftor on the oropharyngeal metagenome in adolescents with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {24},
number = {3},
pages = {562-570},
doi = {10.1016/j.jcf.2024.10.001},
pmid = {39406574},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology/physiopathology ; Adolescent ; *Aminophenols/therapeutic use/administration & dosage ; Male ; Female ; *Quinolones/therapeutic use/administration & dosage ; Drug Combinations ; *Oropharynx/microbiology ; *Benzodioxoles/therapeutic use/administration & dosage ; *Indoles/therapeutic use/administration & dosage ; Child ; Prospective Studies ; *Metagenome/drug effects ; Longitudinal Studies ; Chloride Channel Agonists/administration & dosage ; Young Adult ; *Pyridines/therapeutic use ; *Pyrrolidines/therapeutic use ; *Pyrazoles/therapeutic use/administration & dosage ; Microbiota/drug effects ; Oxadiazoles/therapeutic use ; },
abstract = {BACKGROUND: Triple modulator therapy elexacaftor/tezacaftor/ivacaftor (ETI) improves lung function and impacts upon the respiratory microbiome in people with Cystic fibrosis (pwCF) with advanced lung disease. However, adolescents with cystic fibrosis (CF) are less colonized with bacterial pathogens than adult pwCF but their microbiota already differs from healthy individuals. The aim of this study was to longitudinally analyze the impact of ETI on the respiratory metagenome in adolescents with predominantly mild CF lung disease.

METHODS: In this prospective observational study, we included pwCF aged 12-20 years with at least one F508del mutation, who collected oropharyngeal swabs before and after initiation of ETI therapy twice per week to biweekly over three months. We performed whole metagenome shotgun sequencing, followed by host DNA filtering and taxonomic profiling. We used linear and additive mixed effects models adjusted for known confounders and corrected for multiple testing to study longitudinal development of the microbiome. We analyzed bacterial diversity, abundance, and strain-level phylogeny.

RESULTS: We analyzed the metagenomic data of 297 swabs of 20 pwCF. Microbiome composition changed after initiation of ETI therapy. We observed a slight diversification of the microbiome over time (Inv Simpson, Coef 0.085, 95 %CI 0.003, 0.17, p = 0.04). Strain-level analysis and clustering showed that strain retention of the most frequent bacterial species is predominant even during ETI therapy.

CONCLUSIONS: During three months of ETI therapy, commensal bacteria increased, which may help to prevent overgrowth of bacterial pathogens.},
}

Humans
*Cystic Fibrosis/drug therapy/microbiology/physiopathology
Adolescent
*Aminophenols/therapeutic use/administration & dosage
Male
Female
*Quinolones/therapeutic use/administration & dosage
Drug Combinations
*Oropharynx/microbiology
*Benzodioxoles/therapeutic use/administration & dosage
*Indoles/therapeutic use/administration & dosage
Child
Prospective Studies
*Metagenome/drug effects
Longitudinal Studies
Chloride Channel Agonists/administration & dosage
Young Adult
*Pyridines/therapeutic use
*Pyrrolidines/therapeutic use
*Pyrazoles/therapeutic use/administration & dosage
Microbiota/drug effects
Oxadiazoles/therapeutic use

@article {pmid40431358,
year = {2025},
author = {Yue, Y and Yang, HJ and Li, C and Ryu, MS and Seo, JW and Jeong, DY and Park, S},
title = {Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.},
journal = {Nutrients},
volume = {17},
number = {10},
pages = {},
pmid = {40431358},
issn = {2072-6643},
support = {2023-3//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats, Sprague-Dawley ; *Soy Foods/microbiology ; Rats ; *Memory/drug effects ; *Neuroinflammatory Diseases ; *Glucose/metabolism ; Scopolamine ; *Fermented Foods ; Water/metabolism ; Neuroprotective Agents/pharmacology ; *Glycine max ; Fermentation ; },
abstract = {Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Male
Rats, Sprague-Dawley
*Soy Foods/microbiology
Rats
*Memory/drug effects
*Neuroinflammatory Diseases
*Glucose/metabolism
Scopolamine
*Fermented Foods
Water/metabolism
Neuroprotective Agents/pharmacology
*Glycine max
Fermentation

@article {pmid40431158,
year = {2025},
author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE},
title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
pmid = {40431158},
issn = {2076-2607},
support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; },
abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.},
}

@article {pmid40431145,
year = {2025},
author = {Jiang, K and Ye, L and Cao, C and Che, G and Wang, Y and Hong, Y},
title = {Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
pmid = {40431145},
issn = {2076-2607},
support = {32360005//National Natural Science Foundation of China/ ; 2022JBQN091//Fundamental Research Funds for the Inner Mongolia Normal University/ ; 2022JBTD010//Fundamental Research Funds for the Inner Mongolia Normal University/ ; },
abstract = {Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.},
}

@article {pmid40431076,
year = {2025},
author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D},
title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {40431076},
issn = {2223-7747},
support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.},
}

@article {pmid40429958,
year = {2025},
author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, Á and Ferrero, MÁ and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N},
title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {10},
pages = {},
pmid = {40429958},
issn = {1422-0067},
mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; },
abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.},
}

Humans
*Celiac Disease/microbiology/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
Biomarkers/metabolism
*Colorectal Neoplasms/microbiology/metabolism
Animals
Metagenomics/methods

@article {pmid40428846,
year = {2025},
author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R},
title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {5},
pages = {},
pmid = {40428846},
issn = {1648-9144},
support = {SRA-882725/CCF/CCF/United States ; },
mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; },
abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.},
}

Humans
Female
*Endometriosis/microbiology/physiopathology
*Feces/microbiology
*Vagina/microbiology
*RNA, Ribosomal, 16S/analysis/genetics
Dysbiosis/microbiology
Adult
Gastrointestinal Microbiome
Metagenomics/methods

@article {pmid40428372,
year = {2025},
author = {Dimitrova, L and Ilieva, Y and Gouliamova, D and Kussovski, V and Hubenov, V and Georgiev, Y and Bratanova, T and Kaleva, M and Zaharieva, MM and Najdenski, H},
title = {Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428372},
issn = {2073-4425},
support = {КP-06-N71/8 from 08.12.2023//National Fund for Scientific Research, Republic of Bulgaria/ ; },
mesh = {*Cellulose/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Microbial Consortia/genetics ; Biodegradation, Environmental ; Bacteria/genetics/isolation & purification/metabolism ; Aerobiosis ; *Bacteria, Anaerobic/genetics/isolation & purification/metabolism ; Methane/metabolism ; Biofuels ; },
abstract = {Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.},
}

*Cellulose/metabolism
*Bioreactors/microbiology
Anaerobiosis
*Microbial Consortia/genetics
Biodegradation, Environmental
Bacteria/genetics/isolation & purification/metabolism
Aerobiosis
*Bacteria, Anaerobic/genetics/isolation & purification/metabolism
Methane/metabolism
Biofuels

@article {pmid40428326,
year = {2025},
author = {Sun, YF and Han, ZX and Yao, XK and Meng, J and Ren, WL and Wang, CK and Yuan, XX and Zeng, YQ and Wang, YF and Sun, ZW and Wang, JW},
title = {Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428326},
issn = {2073-4425},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Physical Conditioning, Animal ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Feces/microbiology
*Physical Conditioning, Animal
*Bacteria/genetics/classification/isolation & purification

@article {pmid40428305,
year = {2025},
author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J},
title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.},
journal = {Genes},
volume = {16},
number = {5},
pages = {},
pmid = {40428305},
issn = {2073-4425},
support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; },
mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.

METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.

RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.

CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.},
}

Animals
*Elephants/microbiology/genetics
*Gastrointestinal Microbiome/genetics
*Diet
China
Metagenomics/methods
Bacteria/genetics/classification

@article {pmid40427823,
year = {2025},
author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG},
title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {5},
pages = {},
pmid = {40427823},
issn = {1660-4601},
support = {PTDC/CTA AMB/29586/2017//Fundação para a Ciência e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; },
mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation & purification/genetics ; },
abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.},
}

*Wastewater/virology
*Computational Biology/methods
*Virome
Portugal
*Metagenomics/methods
*Viruses/classification/isolation & purification/genetics

@article {pmid40427639,
year = {2025},
author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR},
title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).},
journal = {Biomolecules},
volume = {15},
number = {5},
pages = {},
pmid = {40427639},
issn = {2218-273X},
support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; },
mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.},
}

Humans
Child
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Metagenomics/methods
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Metabolomics/methods
Adolescent
*Colitis, Ulcerative/microbiology/genetics/metabolism
*Crohn Disease/microbiology/genetics/metabolism
Biomarkers/metabolism
Transcriptome
Multiomics

@article {pmid40424276,
year = {2025},
author = {Goldman, M and Zhao, C and Pollard, KS},
title = {Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012277},
doi = {10.1371/journal.pcbi.1012277},
pmid = {40424276},
issn = {1553-7358},
mesh = {Humans ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Linear Models ; Metagenome/genetics ; },
abstract = {Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.},
}

Humans
Inflammatory Bowel Diseases/microbiology/genetics
Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics
Computational Biology/methods
Linear Models
Metagenome/genetics

@article {pmid40388589,
year = {2025},
author = {Lei, Z and Wang, H and Zhang, H and Liu, W and He, Z and Wang, Z and Zhang, H and Wang, Y and Tang, Y and Hu, C and Zhao, X},
title = {Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {22},
pages = {13313-13326},
doi = {10.1021/acs.jafc.5c01540},
pmid = {40388589},
issn = {1520-5118},
mesh = {*Selenium/metabolism ; *Solanum lycopersicum/metabolism/microbiology/genetics/growth & development ; Oxidation-Reduction ; Soil Microbiology ; *Methylobacterium/metabolism/genetics/isolation & purification ; *Bacterial Proteins/metabolism/genetics ; Plant Roots/microbiology/metabolism ; Soil/chemistry ; Microbiota ; },
abstract = {Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.},
}

*Selenium/metabolism
*Solanum lycopersicum/metabolism/microbiology/genetics/growth & development
Oxidation-Reduction
Soil Microbiology
*Methylobacterium/metabolism/genetics/isolation & purification
*Bacterial Proteins/metabolism/genetics
Plant Roots/microbiology/metabolism
Soil/chemistry
Microbiota

@article {pmid40306604,
year = {2025},
author = {Lee, SH and Han, C and Shin, C},
title = {IUPHAR review: Microbiota-gut-brain axis and its role in neuropsychiatric disorders.},
journal = {Pharmacological research},
volume = {216},
number = {},
pages = {107749},
doi = {10.1016/j.phrs.2025.107749},
pmid = {40306604},
issn = {1096-1186},
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Brain/metabolism/microbiology ; *Mental Disorders/microbiology/therapy ; *Brain-Gut Axis ; Probiotics/therapeutic use ; Prebiotics ; },
abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.},
}

Humans
*Gastrointestinal Microbiome
Animals
*Brain/metabolism/microbiology
*Mental Disorders/microbiology/therapy
*Brain-Gut Axis
Probiotics/therapeutic use
Prebiotics

@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