@article {pmid40953029,
year = {2025},
author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB},
title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330251},
pmid = {40953029},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Male ; Female ; Aged ; *Hydrocephalus, Normal Pressure/microbiology ; Alzheimer Disease/microbiology ; Aged, 80 and over ; Dysbiosis/microbiology ; Case-Control Studies ; Middle Aged ; },
abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Male
Female
Aged
*Hydrocephalus, Normal Pressure/microbiology
Alzheimer Disease/microbiology
Aged, 80 and over
Dysbiosis/microbiology
Case-Control Studies
Middle Aged

@article {pmid40948444,
year = {2025},
author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A},
title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559019},
doi = {10.1080/19490976.2025.2559019},
pmid = {40948444},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation & purification/classification ; *Plasmids/genetics ; Feces/microbiology/virology ; *Clostridium Infections/therapy/microbiology ; *Bacteria/genetics/classification/virology/isolation & purification ; Clostridioides difficile/genetics ; Male ; Female ; Middle Aged ; },
abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.},
}

*Fecal Microbiota Transplantation
Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteriophages/genetics/isolation & purification/classification
*Plasmids/genetics
Feces/microbiology/virology
*Clostridium Infections/therapy/microbiology
*Bacteria/genetics/classification/virology/isolation & purification
Clostridioides difficile/genetics
Male
Female
Middle Aged

@article {pmid40946204,
year = {2025},
author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF},
title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {5},
pages = {e70277},
pmid = {40946204},
issn = {1541-4337},
support = {//Diversey/ ; },
mesh = {*Listeria monocytogenes/growth & development/physiology/isolation & purification ; *Food Microbiology ; *Food Handling ; Microbiota ; Biofilms ; },
abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.},
}

*Listeria monocytogenes/growth & development/physiology/isolation & purification
*Food Microbiology
*Food Handling
Microbiota
Biofilms

@article {pmid40944761,
year = {2025},
author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U},
title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.},
journal = {Neurosurgical review},
volume = {48},
number = {1},
pages = {641},
pmid = {40944761},
issn = {1437-2320},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Adult ; *Brain Neoplasms/microbiology/metabolism ; Cross-Sectional Studies ; *Pituitary Neoplasms/microbiology/metabolism ; Aged ; },
abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Male
Middle Aged
Adult
*Brain Neoplasms/microbiology/metabolism
Cross-Sectional Studies
*Pituitary Neoplasms/microbiology/metabolism
Aged

@article {pmid40943581,
year = {2025},
author = {Gałęcki, R and Nowak, A and Szulc, J},
title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943581},
issn = {1422-0067},
support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; },
mesh = {Animals ; *Tenebrio/chemistry ; *Gastrointestinal Microbiome/genetics ; Rats ; Rats, Wistar ; *Metagenomics/methods ; *Animal Feed ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Male ; Feces/microbiology ; },
abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.},
}

Animals
*Tenebrio/chemistry
*Gastrointestinal Microbiome/genetics
Rats
Rats, Wistar
*Metagenomics/methods
*Animal Feed
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Male
Feces/microbiology

@article {pmid40943165,
year = {2025},
author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J},
title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943165},
issn = {1422-0067},
support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; },
mesh = {Animals ; Horses ; *Gastrointestinal Microbiome/drug effects/genetics ; *Milk/metabolism ; *Metagenomics/methods ; Mice ; *Anti-Inflammatory Agents/pharmacology ; Female ; Cytokines/metabolism ; },
abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.},
}

Animals
Horses
*Gastrointestinal Microbiome/drug effects/genetics
*Milk/metabolism
*Metagenomics/methods
Mice
*Anti-Inflammatory Agents/pharmacology
Female
Cytokines/metabolism

@article {pmid40897066,
year = {2025},
author = {Slobodkina, GB and Merkel, AY and Kondrasheva, KV and Stroeva, AR and Bonch-Osmolovskaya, EA and Davranov, KD and Slobodkin, AI},
title = {Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {5},
pages = {126650},
doi = {10.1016/j.syapm.2025.126650},
pmid = {40897066},
issn = {1618-0984},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Uzbekistan ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenomics ; Metagenome ; *Rivers/microbiology ; *Bacteria/classification/genetics/metabolism ; Groundwater/microbiology ; *Microbiota ; Geologic Sediments/microbiology ; Hot Springs/microbiology ; },
abstract = {Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum[Ts] gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus[Ts] gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.},
}

RNA, Ribosomal, 16S/genetics
Phylogeny
Uzbekistan
DNA, Bacterial/genetics
Sequence Analysis, DNA
Metagenomics
Metagenome
*Rivers/microbiology
*Bacteria/classification/genetics/metabolism
Groundwater/microbiology
*Microbiota
Geologic Sediments/microbiology
Hot Springs/microbiology

@article {pmid40882554,
year = {2025},
author = {Balamurugan, J and Jagadeesan, H and Vijayakumar, M},
title = {A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.},
journal = {Journal of contaminant hydrology},
volume = {275},
number = {},
pages = {104703},
doi = {10.1016/j.jconhyd.2025.104703},
pmid = {40882554},
issn = {1873-6009},
mesh = {*Azo Compounds/metabolism ; Biodegradation, Environmental ; *Microbiota ; Metagenomics ; *Plants/microbiology/metabolism ; *Coloring Agents/metabolism ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; },
abstract = {Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.},
}

*Azo Compounds/metabolism
Biodegradation, Environmental
*Microbiota
Metagenomics
*Plants/microbiology/metabolism
*Coloring Agents/metabolism
*Water Pollutants, Chemical/metabolism
Bacteria/metabolism/genetics

@article {pmid40880079,
year = {2025},
author = {Tang, Y and Oliver, A and Alkan, Z and Korf, I and Huang, L and Kable, ME and Lemay, DG},
title = {Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.},
journal = {Food & function},
volume = {16},
number = {18},
pages = {7393-7407},
doi = {10.1039/d5fo01640a},
pmid = {40880079},
issn = {2042-650X},
mesh = {Humans ; *Lactose/metabolism ; *Lactase/genetics/metabolism ; Male ; Female ; Adult ; Genotype ; Middle Aged ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; United States ; Polymorphism, Single Nucleotide ; Yogurt ; Diet ; Lactose Intolerance/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Lactase persistence is a genetically inherited trait that enables continued lactose digestion into adulthood. Lactase non-persistence (LNP) individuals often experience incomplete lactose digestion, allowing undigested lactose to reach the colon, where it may shape microbial composition and function. We investigated the relationship between the lactase persistence (LP) genotype, lactose consumption, and the taxonomic and functional profiles of the fecal microbiome. Participants from the USDA Nutritional Phenotyping Study, a cross-sectional observational study designed to assess how dietary factors impact human health, whose fecal microbiome profile was measured using shotgun metagenomic sequencing (n = 330) were included in this analysis. Fecal SCFA levels were measured using GC-MS. Fecal microbiome taxonomy and gene abundance were quantified using shotgun metagenomic sequencing. Lactose consumption and yogurt intake were estimated based on Automated Self-Administered 24h Dietary Assessment Tool (ASA24®) dietary recalls or Food Frequency Questionnaire. The LP/LNP genotype was determined by a single nucleotide polymorphism (SNP ID: rs4988235). Several genera of lactic acid bacteria (Veillonella, Lactobacillus, Lacticaseibacillus, and Lactococcus) were differentially abundant between recent high-lactose consuming (>10.0 g lactose per day) and low-lactose consuming (<3.3 g lactose per day) individuals. Among the LNP participants who self-identified as Caucasian or Hispanic, high-lactose consumers (>10.0 g per day via 24-h recall) had significantly higher relative abundances of lactic acid bacteria and lactate-utilizing bacteria (Lacticaseibacillus, Lactobacillus, Megamonas, and Veillonella) than low-lactose consumers (<3.3 g per day). Independent of lactose intake, LNP participants had a higher abundance of fecal microbial β-galactosidase genes than LP participants. Among the LNP participants, those with high recent lactose consumption also showed a significant shift towards more fecal propionate. The abundance of the yogurt-associated microbe, Streptococcus thermophilus, was positively associated with yogurt intake independent of the genotype. Alternative milk consumption was significantly negatively associated with fecal SCFAs both in the full cohort and the Caucasian/Hispanic subset, regardless of the genotype. Our results suggest that functional and persistent host lactase enzymes may work to competitively exclude lactic acid bacteria, contributing to a smaller realized niche for lactic acid bacteria in LP individuals compared to LNP individuals. However, regardless of the host genotype, consumption of alternative milk may be associated with reduced production of health-promoting intestinal metabolites, such as SCFAs.},
}

Humans
*Lactose/metabolism
*Lactase/genetics/metabolism
Male
Female
Adult
Genotype
Middle Aged
Feces/microbiology
Cross-Sectional Studies
*Gastrointestinal Microbiome
United States
Polymorphism, Single Nucleotide
Yogurt
Diet
Lactose Intolerance/genetics
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40855911,
year = {2025},
author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y},
title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.},
journal = {Food & function},
volume = {16},
number = {18},
pages = {7266-7282},
doi = {10.1039/d5fo01536g},
pmid = {40855911},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Oryza/chemistry ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Male ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; *Peptides/pharmacology ; *Hyperlipidemias/metabolism/drug therapy ; *Plant Proteins/pharmacology/chemistry ; },
abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Oryza/chemistry
*Lipid Metabolism/drug effects
*Liver/metabolism/drug effects
Male
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
*Peptides/pharmacology
*Hyperlipidemias/metabolism/drug therapy
*Plant Proteins/pharmacology/chemistry

@article {pmid40816065,
year = {2025},
author = {Kim, E and Song, TC and Yang, SM and Kim, J and Kim, HY},
title = {Comparative analysis of microbial diversity and fatty acids in raw milk from different production systems.},
journal = {Food chemistry},
volume = {493},
number = {Pt 3},
pages = {145899},
doi = {10.1016/j.foodchem.2025.145899},
pmid = {40816065},
issn = {1873-7072},
mesh = {*Milk/microbiology/chemistry ; Animals ; *Fatty Acids/analysis/metabolism/chemistry ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Cattle ; Microbiota ; },
abstract = {This study investigated how differences in raw milk obtained from different milk production practices, such as conventional, antibiotic-free, and organic, influence microbial community structure and fatty acid profiles, potentially affecting milk quality. Microbial diversity revealed no significant differences among the three milk production practices. However, Pseudomonas was dominant across all milk types, with organic milk demonstrating significantly higher relative abundances of Lactococcus, Acinetobacter, and Carnobacterium. Fatty acid profiling revealed significantly higher levels of essential polyunsaturated fatty acids (PUFAs) in organic milk, probably due to easier access to pasture-based diets. Correlation and network analyses demonstrated associations between PUFAs and microbial genera predominantly present in organic milk, such as Serratia with C18:2n-6 and Lactococcus with C20:4n-6, suggesting a potential relationship between microbial composition and fatty acid metabolism influenced by production practices. These data emphasize the impact of production practices on milk quality and microbial dynamics.},
}

*Milk/microbiology/chemistry
Animals
*Fatty Acids/analysis/metabolism/chemistry
*Bacteria/classification/isolation & purification/genetics/metabolism
Cattle
Microbiota

@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
mesh = {*Wastewater/microbiology ; *Petroleum/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Metagenome ; Phylogeny ; Genome, Bacterial ; Nitrogen/metabolism ; Microbiota/genetics ; Biodegradation, Environmental ; Carbon/metabolism ; Metabolic Networks and Pathways/genetics ; CRISPR-Cas Systems ; },
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}

*Wastewater/microbiology
*Petroleum/metabolism
*Bacteria/genetics/classification/metabolism/isolation & purification
China
Metagenome
Phylogeny
Genome, Bacterial
Nitrogen/metabolism
Microbiota/genetics
Biodegradation, Environmental
Carbon/metabolism
Metabolic Networks and Pathways/genetics
CRISPR-Cas Systems

@article {pmid40752126,
year = {2025},
author = {Hong, W and Yang, S and Shu, W and Price, G and Song, L},
title = {Spatiotemporal dynamics of multi-kingdom microbiome interactions drive CNPS cycling in landfills.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115048},
doi = {10.1016/j.wasman.2025.115048},
pmid = {40752126},
issn = {1879-2456},
mesh = {*Microbiota ; *Waste Disposal Facilities ; Phosphorus/metabolism/analysis ; Soil Microbiology ; Nitrogen/metabolism/analysis ; *Refuse Disposal ; Bacteria/metabolism ; Carbon/metabolism/analysis ; Solid Waste/analysis ; Sulfur/metabolism ; },
abstract = {Landfill ecosystems represent significant terrestrial carbon sinks, where municipal solid waste (MSW) undergoes decomposition and transformation through biochemical reactions mediated by multi-kingdom microbiome. However, the spatial and temporal characterization of microbial interactions and collaboration within these multi-kingdom microbiomes remain largely unknown. In this study, we reveal the hierarchical and collaborative mechanisms by which multi-kingdom microbiomes drive carbon, nitrogen, phosphorus, and sulfur cycling across a 30-meter landfilling depth, corresponding to a landfilling age of 1 to 4 years. Through integration of metagenomics and network analyses, we elucidated vertical succession patterns in microbial community structure and function. The surface layer (1-2 years) was centered on bacterial-dominated primary metabolism, with Enterococcus aquimarinus and Brevundimonas bullata inferred to mediate metabolic coupling through fermentation, nitrogen fixation andphosphorus solubilization. Concurrently, phage-driven host lysis may contribute to the suppression of acidification. In the middle layer (2-3 years), co-occurrence patterns between archaea and fungi suggest mutualistic interaction supporting methanogenesis, wherein fungi such as Anaeromyces robustus would supply key substrates for methanogens such as Methanofollis ethanolicus. In the bottom layer (3-4 years), fungi, bacteria, and viruses collaborate under nutrient-limited conditions, with phages employing a "kill-the-winner" approach to sustain ecosystem function and stability. Collectively, our findings indicate that key microbial connectors across kingdoms contribute to elemental cycling through cross-kingdom interaction, including substrate exchange and nutrient supply. This study advances our understanding of multi-kingdom microbial dynamics during MSW decomposition and offers a conceptual framework for enhancing biogeochemical cycling efficiency within landfill ecosystems.},
}

*Microbiota
*Waste Disposal Facilities
Phosphorus/metabolism/analysis
Soil Microbiology
Nitrogen/metabolism/analysis
*Refuse Disposal
Bacteria/metabolism
Carbon/metabolism/analysis
Solid Waste/analysis
Sulfur/metabolism

@article {pmid40669611,
year = {2025},
author = {Song, S and Li, F and Zhao, B and Xu, Y and Liu, Z and Liu, J and Hou, Q and Chen, J and Chen, M and Liu, Z and Zhou, M and Wu, X and Wang, X},
title = {Sparfloxacin ameliorates DSS-induced ulcerative colitis by suppressing cellular senescence, JAK/NF-κB signaling pathway and modulation of the gut microbiota-metabolite axis.},
journal = {Biochemical pharmacology},
volume = {241},
number = {},
pages = {117167},
doi = {10.1016/j.bcp.2025.117167},
pmid = {40669611},
issn = {1873-2968},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice ; *NF-kappa B/metabolism/antagonists & inhibitors ; *Cellular Senescence/drug effects/physiology ; *Fluoroquinolones/pharmacology/therapeutic use ; Signal Transduction/drug effects/physiology ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Mice, Inbred C57BL ; *Dextran Sulfate/toxicity ; Male ; Humans ; },
abstract = {The progression of ulcerative colitis (UC) involves immune dysregulation, intestinal barrier dysfunction, and microbial dysbiosis while existing targeted therapies present challenges, including adverse effects and economic burdens. UC is characterized by persistent intestinal inflammation, manifesting as abdominal pain, hematochezia, and malnutrition. Prolonged uncontrolled inflammation may lead to colorectal cancer or severe complications, significantly impairing quality of life. Recent studies have revealed a significant correlation between pathological accumulation of senescent cells and UC pathogenesis, suggesting anti-senescence therapeutics as potential interventions. In this study, we identified sparfloxacin (SPA), a fluoroquinolone antibiotic, through high-throughput screening as an effective senolytic agent that markedly alleviates DSS-induced murine colitis. Mechanistically, combining cellular and animal experiments with transcriptomic, untargeted metabolomic, and metagenomic analyses, we demonstrated sparfloxacin's tripartite therapeutic effects: ① Senescence inhibition via downregulation of p16/p21 expression; ② Effective suppression of aberrant JAK/NF-κB signaling activation with a concomitant reduction in pro-inflammatory cytokines (TNF-α, IL-6); ③ Gut microbiota remodeling characterized by increased probiotic abundance and elevated levels of beneficial metabolites. This study for the first time elucidates the molecular mechanism whereby SPA ameliorates UC through coordinated multi-target actions involving senescence inhibition, anti-inflammatory effects, and microbiome restoration. Our findings not only expand the clinical applications of fluoroquinolones but also provide a theoretical foundation for developing integrated UC treatment strategies targeting cellular senescence.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Mice
*NF-kappa B/metabolism/antagonists & inhibitors
*Cellular Senescence/drug effects/physiology
*Fluoroquinolones/pharmacology/therapeutic use
Signal Transduction/drug effects/physiology
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism
Mice, Inbred C57BL
*Dextran Sulfate/toxicity
Male
Humans

@article {pmid40652650,
year = {2025},
author = {Meng, X and Chen, S and Liu, Z and Cheng, L and Hu, Y and Huang, X},
title = {Mechanism of electro-acclimation shaped microbiota facilitating phosphorus release from iron-containing sludge: microbial reduction and induced dissolution.},
journal = {Water research},
volume = {286},
number = {},
pages = {124197},
doi = {10.1016/j.watres.2025.124197},
pmid = {40652650},
issn = {1879-2448},
mesh = {*Sewage/chemistry/microbiology ; *Phosphorus ; *Iron/chemistry ; *Microbiota ; Waste Disposal, Fluid ; Electrodes ; },
abstract = {Iron-based Chemically Enhanced Primary Treatment (Fe-CEPT) can efficiently concentrate phosphorus (P) from municipal wastewater into sludge; however, unfavorable P release efficiency impedes P recovery from Iron-based Chemically Enhanced Primary Sludge (Fe-CEPS). This study developed an electro-digester by applying controlled potentials to bio-electrodes. The electro-acclimated microorganisms on bio-electrodes achieved efficient P release due to microbial Fe(III) reduction and microbial metabolism-induced P-Fe complexes dissolution. In P release potential tests, 53.2 % of total P was released within 60 h after +1.0 V acclimation, 2.2-fold of the control. P fractionation analysis revealed that the proportion of Fe(II)-P, Fe(III)-P, and Reductant-P in Fe-CEPS (substrate) decreased by 9.7 %, 44.8 %, and 37.5 % after P release, respectively, combined with X-ray diffraction analysis, indicating P-release process followed Fe(III)-P and reductant-P first being reduced to Fe(II)-P and then dissolved into P(liquid), while inherent Fe(II)-P directly dissolved into P(liquid). The enhanced electron transfer capacity of electro-acclimated microorganisms, demonstrated by cyclic voltammetry analysis, promoted Fe(III)-P reduction. The lower pH (a minimum of 5.7) in mixed liquor, achieved by the enhanced metabolism of electro-acclimated microorganisms and elevated enzyme activities relating to hydrolysis-acidification, facilitated the dissolution of Fe(II)-P into the liquid phase. These two steps were dominated by enriched iron-reducing bacteria as Deferribacteraceae and fermentative bacteria as Clostridiaceae in electro-acclimation shaped microbiota. Metagenomic analysis showed consistent results as genes encoding cellular respiratory, metabolism and electron transportation upregulated significantly. These findings provided an eco-friendly, cost-effective solution for treating iron-containing chemical sludge and recovering valuable P resources.},
}

*Sewage/chemistry/microbiology
*Phosphorus
*Iron/chemistry
*Microbiota
Waste Disposal, Fluid
Electrodes

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
mesh = {*Plastics ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Rivers/chemistry ; Biodegradation, Environmental ; Water Pollutants, Chemical ; Metals, Heavy ; },
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}

*Plastics
*Microbiota
*Geologic Sediments/microbiology/chemistry
*Rivers/chemistry
Biodegradation, Environmental
Water Pollutants, Chemical
Metals, Heavy

@article {pmid40645053,
year = {2025},
author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M},
title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145464},
doi = {10.1016/j.foodchem.2025.145464},
pmid = {40645053},
issn = {1873-7072},
mesh = {Fermentation ; *Flavoring Agents/metabolism/chemistry/analysis ; *Brassica/microbiology/chemistry/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Taste ; *Fungi/metabolism/genetics/classification/isolation & purification ; *Fermented Foods/microbiology/analysis ; Republic of Korea ; Volatile Organic Compounds/metabolism ; },
abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.},
}

Fermentation
*Flavoring Agents/metabolism/chemistry/analysis
*Brassica/microbiology/chemistry/metabolism
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
Microbiota
Taste
*Fungi/metabolism/genetics/classification/isolation & purification
*Fermented Foods/microbiology/analysis
Republic of Korea
Volatile Organic Compounds/metabolism

@article {pmid40528807,
year = {2025},
author = {Ding, X and Wang, J and Zhu, W},
title = {The hydrogenation metabolism process of rosmarinic acid by microbial enzymes in chickens.},
journal = {Journal of the science of food and agriculture},
volume = {105},
number = {13},
pages = {7340-7349},
doi = {10.1002/jsfa.70000},
pmid = {40528807},
issn = {1097-0010},
support = {2017YFE0135200//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Rosmarinic Acid ; *Chickens/microbiology/metabolism ; *Cinnamates/metabolism/chemistry ; *Depsides/metabolism/chemistry ; Gastrointestinal Microbiome ; Hydrogenation ; *Bacteria/genetics/enzymology/isolation & purification/classification/metabolism ; Tandem Mass Spectrometry ; *Bacterial Proteins/metabolism/genetics ; Gastrointestinal Tract/microbiology/metabolism ; },
abstract = {BACKGROUND: The gut microbiota plays a critical role in the metabolism of rosmarinic acid (RA) through converting RA to caffeic acid (CA), danshensu (DSS), and m-coumaric acid. However, the gut environment and microbiota may have complicated metabolic converting RA processes. This study aimed to investigate the metabolism of RA in gastrointestinal tract of chickens through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and metagenomic analysis.

RESULTS: Through in vivo and in vitro studies, RA was found to be hydrogenated into dihydrorosmarinic acid, then hydrolyzed into DSS and dihydrocaffeic acid (DHCA). DSS and DHCA could be further converted to 3-hydroxyphenylpropionic acid. But RA remained stable in the stomach, duodenum, jejunum, and ileum, as well as in the cecum of antibiotic-treated chickens. This indicated that the degradation of RA was mainly mediated by cecal microbiota. Furthermore, the metagenomic analysis of cecal microbiota revealed that reductases and hydrolases from Clostridium spp., Alistipes spp., and other microbiota were involved in these processes. NADH:flavin oxidoreductase and 3-oxoacyl-[acyl-carrier-protein] reductase participated in the hydrogenation reaction of RA, and BaiCD involved in dehydroxylation reaction of RA.

CONCLUSION: The hydrogenation process by microbial enzymes was an important metabolic pathway of RA. These hydrogenation products contribute to improving the biological function of RA. © 2025 Society of Chemical Industry.},
}

Animals
Rosmarinic Acid
*Chickens/microbiology/metabolism
*Cinnamates/metabolism/chemistry
*Depsides/metabolism/chemistry
Gastrointestinal Microbiome
Hydrogenation
*Bacteria/genetics/enzymology/isolation & purification/classification/metabolism
Tandem Mass Spectrometry
*Bacterial Proteins/metabolism/genetics
Gastrointestinal Tract/microbiology/metabolism

@article {pmid40460824,
year = {2025},
author = {Gogokhia, L and Tran, N and Grier, A and Nagayama, M and Xiang, G and Funez-dePagnier, G and Lavergne, A and Ericsson, C and Ben Maamar, S and Zhang, M and Battat, R and Scherl, E and Lukin, DJ and Longman, RS},
title = {Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis.},
journal = {Med (New York, N.Y.)},
volume = {6},
number = {9},
pages = {100707},
pmid = {40460824},
issn = {2666-6340},
support = {R01 DK128257/DK/NIDDK NIH HHS/United States ; T32 DK116970/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/microbiology ; Male ; Female ; Double-Blind Method ; *Dietary Fiber/administration & dosage ; Adult ; Middle Aged ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome ; Prebiotics ; Tissue Donors ; Psyllium/administration & dosage ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging treatment for ulcerative colitis (UC), but the impact of prebiotic fiber on FMT efficacy for UC is unclear. We performed a randomized, double-blind, placebo-controlled clinical trial to examine the efficacy of FMT with and without dietary fiber supplementation in patients with UC.

METHODS: 27 patients with mild to moderate UC were randomized to receive a single FMT or placebo with or without psyllium fiber supplementation for 8 weeks. The primary outcome was clinical response at week 8, and secondary outcomes included endoscopic improvement and clinical remission. Metagenomic sequencing of fecal DNA was analyzed to determine taxonomic profiles and donor strain engraftment.

FINDINGS: The trial was terminated early due to manufacturer discontinuation of FMT product. FMT induced clinical response, remission, and endoscopic improvement in UC patients compared to placebo (p < 0.05), but fiber did not improve clinical outcomes of FMT. Recipient microbiome composition post-FMT shifted toward donor composition in responders and non-responders, but the durability of this change was stronger in responders. Clinical response and durable change in microbiome composition following FMT was donor dependent. Strain tracking analysis also demonstrated a donor-dependent variability in the rate of successful engraftment and identified a consortium of engrafted bacteria associated with treatment response or fiber supplementation.

CONCLUSIONS: Single-dose FMT demonstrated clinical efficacy for mild to moderate UC compared to placebo but revealed no benefit of fiber supplementation. These results highlight proof of concept that donor selection and prebiotic fiber can shape strain-level engraftment. This study was registered at ClinicalTrials.gov: NCT03998488.

FUNDING: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK128257, to R.S.L.).},
}

Humans
*Fecal Microbiota Transplantation/methods
*Colitis, Ulcerative/therapy/microbiology
Male
Female
Double-Blind Method
*Dietary Fiber/administration & dosage
Adult
Middle Aged
Feces/microbiology
Treatment Outcome
Gastrointestinal Microbiome
Prebiotics
Tissue Donors
Psyllium/administration & dosage

@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}

@article {pmid40950593,
year = {2025},
author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D},
title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649514},
pmid = {40950593},
issn = {1664-302X},
abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.},
}

@article {pmid40943646,
year = {2025},
author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A},
title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943646},
issn = {1422-0067},
support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Bacteroides fragilis/genetics/isolation & purification ; Adult ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; *Hashimoto Disease/microbiology ; Young Adult ; Adolescent ; Aged ; Feces/microbiology ; Metagenomics/methods ; *Actinobacteria/genetics ; Case-Control Studies ; },
abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.},
}

Humans
*Bacteroides fragilis/genetics/isolation & purification
Adult
Middle Aged
Female
Male
*Gastrointestinal Microbiome
*Hashimoto Disease/microbiology
Young Adult
Adolescent
Aged
Feces/microbiology
Metagenomics/methods
*Actinobacteria/genetics
Case-Control Studies

@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
mesh = {*Wastewater/microbiology/chemistry ; *Rivers/microbiology ; *Bacteria/genetics/classification ; India ; *Environmental Monitoring ; *Drug Resistance, Bacterial ; Metagenomics ; Anti-Bacterial Agents/analysis ; Water Pollutants, Chemical/analysis ; *Water Microbiology ; *Microbiota ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}

*Wastewater/microbiology/chemistry
*Rivers/microbiology
*Bacteria/genetics/classification
India
*Environmental Monitoring
*Drug Resistance, Bacterial
Metagenomics
Anti-Bacterial Agents/analysis
Water Pollutants, Chemical/analysis
*Water Microbiology
*Microbiota

@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {67},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2%) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5%), followed by Giardia duodenalis (12.6%), Dientamoeba fragilis (7.5%), Cryptosporidium parvum (6.5%), and Entamoeba histolytica (4%). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}

@article {pmid40812303,
year = {2025},
author = {Huang, Y and Zhang, X and Yu, C and Liu, Y and Kang, H and Liu, Y and Ni, Y and Xia, Y and Jiang, Z and Chen, J and Zhao, K and Han, L and Zou, X and Wang, J and Lei, T and Gan, C and Zhang, H},
title = {Lactobacillus acidophilus promotes cognitive function recovery via regulating microglial peroxisomal function in cerebral ischemia.},
journal = {Cell host & microbe},
volume = {33},
number = {9},
pages = {1484-1501.e12},
doi = {10.1016/j.chom.2025.07.018},
pmid = {40812303},
issn = {1934-6069},
mesh = {*Microglia/metabolism ; Animals ; *Lactobacillus acidophilus/physiology ; Mice ; Humans ; *Brain Ischemia/therapy/microbiology ; Gastrointestinal Microbiome ; *Peroxisomes/metabolism ; *Cognition/physiology ; Male ; Disease Models, Animal ; Probiotics ; Mice, Inbred C57BL ; Female ; Reactive Oxygen Species/metabolism ; Cognitive Dysfunction ; Middle Aged ; },
abstract = {Cerebral ischemia causes significant mortality and is accompanied by inflammatory reactions that exacerbate damage. While the gut microbiota is linked to clinical outcomes, specific treatments and mechanisms remain unclear. Our metagenomics linked low Lactobacillus abundance to cognitive decline in patients with cerebral ischemia. L. acidophilus supplementation alleviated post-ischemic deficits in murine middle cerebral artery occlusion and bilateral carotid artery stenosis models. The neuroprotective effects of L. acidophilus were driven by enhanced gut absorption of linoleic acid (LinA). L. acidophilus-induced LinA activates peroxisomes in microglia, triggering microglial reprogramming to an anti-inflammatory state via reactive oxygen species (ROS) scavenging and β-oxidation-mediated epigenetic changes. These L. acidophilus-driven effects are lost upon dietary deficits in LinA, microglia depletion, or peroxisome disruption. A randomized clinical trial showed that L. acidophilus improved cognition and cerebral blood flow in ischemic patients. This study was registered at ClinicalTrials.gov (NCT05845983). Collectively, these findings reveal a therapeutic axis whereby L. acidophilus drives microglial reprogramming, providing a basis for microbiome-targeted neurotherapies.},
}

*Microglia/metabolism
Animals
*Lactobacillus acidophilus/physiology
Mice
Humans
*Brain Ischemia/therapy/microbiology
Gastrointestinal Microbiome
*Peroxisomes/metabolism
*Cognition/physiology
Male
Disease Models, Animal
Probiotics
Mice, Inbred C57BL
Female
Reactive Oxygen Species/metabolism
Cognitive Dysfunction
Middle Aged

@article {pmid40669466,
year = {2025},
author = {Ghiotto, G and Xirostylidou, A and Gaspari, M and Kougias, PG and Campanaro, S and Treu, L},
title = {Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.},
journal = {Cell genomics},
volume = {5},
number = {9},
pages = {100949},
doi = {10.1016/j.xgen.2025.100949},
pmid = {40669466},
issn = {2666-979X},
mesh = {*Metagenomics/methods ; Anaerobiosis ; *Ecosystem ; *Adaptation, Physiological/genetics ; *Microbiota/genetics ; *Methanobacteriaceae/genetics/metabolism ; Methane/metabolism ; Carbon Dioxide/metabolism ; Mutation ; },
abstract = {Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.},
}

*Metagenomics/methods
Anaerobiosis
*Ecosystem
*Adaptation, Physiological/genetics
*Microbiota/genetics
*Methanobacteriaceae/genetics/metabolism
Methane/metabolism
Carbon Dioxide/metabolism
Mutation

@article {pmid39672231,
year = {2025},
author = {Luo, HY and Fang, J and Zhang, WH and Chan, KC and Chan, YM and Dong, CX and Li, SL and Lyu, AP and Xu, J},
title = {Dissecting the anti-obesity components of ginseng: How ginseng polysaccharides and ginsenosides target gut microbiota to suppress high-fat diet-induced obesity.},
journal = {Journal of advanced research},
volume = {75},
number = {},
pages = {811-828},
doi = {10.1016/j.jare.2024.12.002},
pmid = {39672231},
issn = {2090-1224},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Panax/chemistry ; *Ginsenosides/pharmacology/chemistry ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/etiology/microbiology/metabolism ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Anti-Obesity Agents/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Metagenomics ; },
abstract = {INTRODUCTION: Ginseng demonstrates therapeutic potential in treating obesity, with both experimental and clinical studies suggesting its anti-obesity effects are mediated by gut microbiota. Nonetheless, the specific chemical components responsible for this effect remain largely unidentified.

OBJECTIVES: This study aims to investigate the anti-obesity effects and mechanisms of ginseng polysaccharides (GP) and ginsenosides (GS), the primary chemical components of ginseng, with a focus on their impact on gut microbiota.

METHODS: The impact of GP and GS on high-fat diet (HFD)-induced obesity was assessed using a mouse model. Molecular mechanisms were explored through a combination of chemical analysis, metagenomics, RT-qPCR, ELISA, and biochemical assays.

RESULTS: GP or GS administration effectively prevented adiposity in HFD-fed mice, and both effects were mediated by gut microbiota. Chemical analysis revealed diverse glycosyl groups in GP and GS. Metagenomics data suggested that GP-enriched species, e.g., Bacteroides stercorirosoris and Clostridiales bacterium encoded carbohydrate-active enzymes GH35, GH43 and PL9_1, while GS-enriched Sulfurospirillum halorespirans encoded GH16_5. These enzymes facilitated the utilization of glycosyl groups in GP and GS, selectively stimulating bacterial growth and reshaping the gut microbiota. Furthermore, bacterial species enriched by GP or GS encoded specific functional genes involved in short-chain fatty acid (SCFA) synthesis (K00625 and K00925 for GP; K18118, K00100, and K18122 for GS) and intestinal gluconeogenesis (IGN) (K01678, K00024, and K01596 for GP; K18118 and K00278 for GS). Consequently, the SCFA-GLP-1/PYY signaling and IGN were activated by both GP and GS to ameliorate obesity phenotypes.

CONCLUSION: GP and GS, containing diverse glycosyl groups, selectively stimulate specific gut bacteria, triggering mechanisms involved in SCFA-GLP-1/PYY signaling and IGN activation to reduce adiposity in HFD-fed mice. The study enhances understanding of the chemical components crucial for the gut microbiota-mediated anti-obesity effect of ginseng. The mechanistic understanding provides valuable insights for developing ginseng-based drugs or health products to combat obesity.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Panax/chemistry
*Ginsenosides/pharmacology/chemistry
Diet, High-Fat/adverse effects
*Obesity/drug therapy/etiology/microbiology/metabolism
*Polysaccharides/pharmacology/chemistry
Mice
*Anti-Obesity Agents/pharmacology
Male
Mice, Inbred C57BL
Disease Models, Animal
Metagenomics

@article {pmid40827090,
year = {2025},
author = {Mulligan, C and Gold, DA},
title = {A Reassessment of the Coprostane Biomarker in the Ediacaran With Implications for Dickinsonia.},
journal = {Geobiology},
volume = {23},
number = {4},
pages = {e70029},
pmid = {40827090},
issn = {1472-4669},
support = {2044871//National Science Foundation/ ; },
mesh = {Animals ; *Fossils/microbiology ; Biomarkers/analysis ; *Cholestanes/analysis ; *Bacteria/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {The discovery of cholestane in animal fossils from the Ediacaran (571-541 million years ago) has generated much excitement, but it is not the only interesting biomarker recovered. Coprostane, a geologically stable form of coprostanol, has also been found in Ediacaran rocks. This is surprising, since coprostanol is typically used in modern settings as an environmental biomarker for humans and other mammals, who produce the compound with help from bacteria in their gut. The prevailing hypothesis is that an abundance of coprostane in some Ediacaran fossils-particularly Dickinsonia-represents the degradation of the organism's cholesterol by bacteria in the microbial mat, comparable to what is seen in modern vertebrate corpses as they decompose. However, this hypothesis assumes coprostanol-producing bacteria were absent in the guts of Ediacaran organisms, and to date no one has tested whether such bacteria exist in modern invertebrates. In this study, we assembled 115 metagenomes to look for evidence of coprostanol-producing enzymes in invertebrate microbiomes. Ultimately, we did not find any evidence for the enzyme in any invertebrate microbiomes, supporting the hypothesis that coprostane is not a gut biomarker for Ediacaran animals. However, a reassessment of coprostane/cholestane ratios shows Dickinsonia was unique in coprostanol enrichment, with ratio levels comparable to waste polluted marine waters and modern vertebrate feces. While we cannot rule out the possibility of contamination, we prefer a novel interpretation of the coprostane signature in dickinsoniomorph fossils, where the elevated level of coprostanol comes from digestion of the microbial mat and concentration of the biologically inert compound. If correct, the elevated coprostanol signal provides new insights into the feeding strategy of these enigmatic animals.},
}

Animals
*Fossils/microbiology
Biomarkers/analysis
*Cholestanes/analysis
*Bacteria/genetics/metabolism
Gastrointestinal Microbiome

@article {pmid40826150,
year = {2025},
author = {Dang, HT and Phung, TTB and Tran, DM and Bui, ATP and Vu, YH and Luong, MT and Nguyen, HM and Trinh, HT and Vo, HTN and Nguyen, TTT and Nguyen, AH and Tung, PD and Tran, LH and Van Nguyen, AT},
title = {High-dose multi-strain Bacillus probiotics enhance treatment and reduce antibiotic usage in children with persistent diarrhea through immune and microbiota modulation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30231},
pmid = {40826150},
issn = {2045-2322},
support = {ANABIO/RG-2022-06//ANABIO R&D Ltd. Company, Viet Nam/ ; },
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Diarrhea/microbiology/immunology/therapy/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Male ; Female ; Child, Preschool ; *Gastrointestinal Microbiome/drug effects ; *Bacillus ; Infant ; Double-Blind Method ; Child ; Treatment Outcome ; Cytokines/blood ; },
abstract = {Persistent diarrhea remains medical challenge to date regarding both its etiology and therapeutic interventions. Here, we conducted a randomized, double-blind, controlled clinical trial to evaluate the effectiveness of high-dose multi-strain Bacillus spore probiotics (LiveSpo DIA30) containing B. subtilis, B. clausii, and B. coagulans at 5 billion CFU/5 mL ampoule, in the supportive treatment of persistent diarrhea in children. Our findings revealed a significant 3-day shorter recovery period, 1.60-fold enhanced efficacy, and a 9.47-fold increase in odds (all p-values < 0.0001) for effectively resolving diarrhea by day 5 with the Bacillus spores. Notably, the group receiving LiveSpo DIA30 (Dia30 group) experienced a reduction in antibiotic treatment duration by 2 days compared to the Control group, equivalent to a 25% decrease in antibiotic usage. After 5 days of treatment, LiveSpo DIA30 demonstrated significant reductions in elevated blood pro-inflammatory cytokines, including IL-17 (26.62%; p = 0.0178), IL-23 (25.13%; p = 0.0256), TNF-α (19.09%; p = 0.038), and in fecal sIgA (24.24%; p = 0.0433). Analysis of 16S rRNA metagenome revealed that Dia30 group exhibited a notable increase in density of Actinomycetota and Bacillota phylum, along with Actinomycetaceae, Lactobacillaceae, and Streptococaceae families. Lacticaseibacillus rhamnosus, a beneficial gut species, was not detectable at day 0 but reached a density of 0.91% (p = 0.015) in Dia30 group by day 5. Additionally, Dia30 group showed a significant reduction in density of the Proteobacteria phylum, Enterobacteriaceae family, and harmful species Escherichia fergusoni (682.8-fold; p = 0.011). In conclusion, this clinical trial presents robust clinical evidence, supported by laboratory testing data, demonstrating the efficacy of multi-strain and high-concentration Bacillus spore probiotics in rapidly alleviating symptoms and reducing antibiotic usage in children with persistent diarrhea. This is archived by improving the native gut microbiota and modulating immunological responses.Trial registration: ClinicalTrials.gov, Identifier No: NCT05812820, 14/4/2023.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Diarrhea/microbiology/immunology/therapy/drug therapy
*Anti-Bacterial Agents/therapeutic use
Male
Female
Child, Preschool
*Gastrointestinal Microbiome/drug effects
*Bacillus
Infant
Double-Blind Method
Child
Treatment Outcome
Cytokines/blood

@article {pmid40825877,
year = {2025},
author = {Xu, Y and Liu, Y and Leng, Y and Qian, J and Yang, Q and Zhu, J and Li, G and Peng, Y},
title = {Signature of oral microbial dysbiosis in different periodontitis risk levels.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {186},
pmid = {40825877},
issn = {1432-0614},
support = {XDYC-YLWS-2023-0048//Xingdian Talents Support Program/ ; 202401AU070088//Natural Science Foundation of Yunnan Province/ ; EYQ2024001//National Key Clinical Specialty Development Project of Pediatric Dentistry Division of China/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202401AY070001-365//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; },
mesh = {Humans ; *Periodontitis/microbiology ; *Dysbiosis/microbiology ; Metagenomics ; Female ; *Microbiota ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation & purification ; Saliva/microbiology ; Adult ; *Mouth/microbiology ; },
abstract = {Individuals categorized into distinct periodontitis risk levels often demonstrate substantial disparities not only in the likelihood of developing periodontitis but also in the rate at which the disease progresses. However, the oral microbial communities and their functional characteristics corresponding to different periodontitis risk levels remain to be further explored. Therefore, 52 subjects with periodontitis were selected and categorized into different periodontitis risk groups based on the periodontal risk calculator (PRC). Unstimulated saliva was collected, and metagenomics sequencing was performed to compare microbial diversity, taxonomy, and functional annotation among groups. There was no significant difference in species richness and evenness between the very high risk group and the high risk group, but beta diversity increased in the former group. A higher abundance of Filifactor alocis, Streptococcus cristatus, Klebsiella pneumoniae, and Streptococcus anginosus was attributed to the very high risk group, while Pseudopropionibacterium propionicum and Abiotrophia defectiva were found in higher abundance in the high risk group. Functional annotation revealed that biosynthesis of amino acids (lysine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; valine, leucine, and isoleucine biosynthesis), citrate cycle (TCA cycle), carbon fixation pathways in prokaryotes, oxidative phosphorylation, lipopolysaccharide biosynthesis, fatty acid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, pantothenate and CoA biosynthesis, and glutathione metabolism were enriched in the very high risk group. The combined results indicate that the periodontal pathogens associated with a higher risk of periodontitis and the regulation of their related functional pathways increase the risk and likelihood of periodontitis development. KEY POINTS : • There were differences in microbial diversity among different periodontitis risk-level groups. • Some previously overlooked species and pathogenic pathways were linked to periodontitis risk differences. • Combining PRC with metagenomic sequencing revealed more potential pathogens.},
}

Humans
*Periodontitis/microbiology
*Dysbiosis/microbiology
Metagenomics
Female
*Microbiota
Middle Aged
Male
*Bacteria/classification/genetics/isolation & purification
Saliva/microbiology
Adult
*Mouth/microbiology

@article {pmid40823805,
year = {2025},
author = {Kim, L and Lavrinienko, A and Sebechlebska, Z and Stoltenberg, S and Bokulich, NA},
title = {Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.},
journal = {Nucleic acids research},
volume = {53},
number = {15},
pages = {},
pmid = {40823805},
issn = {1362-4962},
support = {2020-2024//ETH Domain's Open Research Data (ORD)/ ; 2021-362//ETH Domain's Open Research Data (ORD)/ ; //Strategic Focus Area "Personalized Health and Related Technologies (PHRT)/ ; //ETH Zurich/ ; //ETH Read and Publish OA/ ; },
mesh = {*Metadata/standards ; Humans ; *Information Dissemination/methods ; *Microbiota/genetics ; Metagenome/genetics ; *Metagenomics/standards/methods ; Gastrointestinal Microbiome/genetics ; Software ; },
abstract = {Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (i) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (ii) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and case studies of soil and gut microbiota (n = 370), we found nearly half do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements and (ii) the lack of consistent metadata reporting. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate data reuse, supporting best practices that make microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).},
}

*Metadata/standards
Humans
*Information Dissemination/methods
*Microbiota/genetics
Metagenome/genetics
*Metagenomics/standards/methods
Gastrointestinal Microbiome/genetics
Software

@article {pmid40768422,
year = {2025},
author = {Pan, S and Li, W and Zhao, X and Wang, H and Liu, J and Zhang, W and Zhou, C and Xie, Y},
title = {Blood virome profiling reveals subtype-specific viral signatures and reduced diversity in non-Hodgkin lymphoma.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2542457},
pmid = {40768422},
issn = {2150-5608},
mesh = {Humans ; *Virome ; *Lymphoma, Non-Hodgkin/virology/blood ; Middle Aged ; Male ; Female ; Aged ; Adult ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Aged, 80 and over ; },
abstract = {Non-Hodgkin lymphoma (NHL), a heterogeneous lymphoid malignancy, demonstrates molecular diversity linked to genetic and immune factors, with emerging roles for viral infections in pathogenesis. Yet, the blood virome's composition and dynamics in NHL remain poorly characterized. This study characterizes the blood virome in NHL subtypes using viral metagenomic sequencing of serum from 217 patients (B-cell: BCL, T-cell: TCL, NK-cell: NKCL) and 40 healthy controls. Bioinformatic analysis identified 45 viral families, revealing subtype-specific viromic signatures. BCL exhibited a dominance of Anelloviridae, which accounted for 86% of eukaryotic viruses, compared with only 3% in controls, correlating with immunosuppression. Additionally, picobirnavirus, an opportunistic pathogen particularly in hosts with compromised immune systems, also showed a significant difference compared to controls. NKCL showed Flaviviridae enrichment, accounting for 82% of eukaryotic viruses, with nearly all of them being human pegivirus-1 (HPgV-1). Compared with healthy controls, patients with NHL exhibited significantly lower blood virome α-diversity at the genus level, and T-cell lymphomas showed the lowest species-level richness (140 vs. 332 in controls). Beta diversity highlighted BCL-specific viral heterogeneity, contrasting conserved T/NKCL viral profiles. Anelloviridae and Picobirnavirus expansion aligns with immune dysfunction, whereas NKCL-restricted HPgV-1 prevalence underscores biomarker potential. These findings implicate blood virome alterations marked by viral family predominance and diversity loss in NHL pathogenesis via immune modulation or oncogenesis. This first comprehensive NHL virome profile identifies subtype-specific signatures (Anelloviridae/Picobirnavirus/HPgV-1) for potential diagnostic and therapeutic targeting. Validation of these biomarkers may refine NHL subtyping and elucidate virome-lymphomagenesis mechanisms.},
}

Humans
*Virome
*Lymphoma, Non-Hodgkin/virology/blood
Middle Aged
Male
Female
Aged
Adult
*Viruses/classification/genetics/isolation & purification
Metagenomics
Aged, 80 and over

@article {pmid40738105,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1381-1395.e7},
pmid = {40738105},
issn = {1934-6069},
support = {DP2 AI154402/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Bacteriophages/physiology ; *Metagenomics ; Escherichia coli/virology/genetics ; *Bacteria/genetics/virology/classification ; Soil Microbiology ; *Metagenome ; },
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.},
}

Humans
*Microbiota
*Bacteriophages/physiology
*Metagenomics
Escherichia coli/virology/genetics
*Bacteria/genetics/virology/classification
Soil Microbiology
*Metagenome

@article {pmid40742180,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0098425},
pmid = {40742180},
issn = {2379-5077},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 DK133468/DK/NIDDK NIH HHS/United States ; R01DK133468//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; Biomass ; *Bacteria/genetics/isolation & purification ; *Metagenome ; Animals ; Host Microbial Interactions/genetics ; },
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Feces/microbiology
Biomass
*Bacteria/genetics/isolation & purification
*Metagenome
Animals
Host Microbial Interactions/genetics

@article {pmid40742167,
year = {2025},
author = {Fan, P and Ma, J and Shen, Q and Ouyang, Y and Zhang, T and Shen, J and Luo, Z-C and Liu, Z and Ouyang, F},
title = {Gut microbiota development, antibiotic resistome, and related perinatal factors in early infancy.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0050225},
pmid = {40742167},
issn = {2379-5077},
support = {81961128023,81673178//National Natural Science Foundation of China/ ; 2017YFE0124700//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Male ; Infant ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Bacteria/genetics/classification/drug effects ; Delivery, Obstetric ; Pregnancy ; *Drug Resistance, Microbial/genetics ; Cesarean Section ; },
abstract = {Early life is a critical window for gut microbiota development and antibiotic resistome. We aimed to investigate the microbiota longitudinal change during the first 6 months of life and the differences associated with assisted reproductive technology (ART) treatment, mode of delivery, and infant sex. Gut microbiota was measured by metagenomic sequencing of fecal samples repeatedly collected within 3 days after birth, at 42 days, 3 months, and 6 months in 155 Chinese infants. Among infants born by vaginal delivery, the ACE, Chao, and Sobs indexes increased with age. Accordingly, the relative abundance of Actinobacteria phylum increased from 43% ± 37% (mean ± SD) to 57% ± 36% and Proteobacteria phylum decreased from 48% ± 36% to 17% ± 25%; and Bifidobacterium and Klebsiella genus increased and Escherichia genus decreased, from the first 3 days to 6 months. The dominant antibiotic resistance genes were macB and msbA. Boys and girls had similar features. Infants born by cesarean section exhibited a similar gut microbiota developmental trajectory, but with a slower increase in alpha diversity over time, and lower Bacteroidetes phylum and Bacteroides genus at each age point. Compared with non-ART infants, ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. Our findings confirm increasing diversity and composition evolution of gut microbiota in the first 6 months of life. Both modes of delivery and ART conception are associated with early gut microbiota alteration.IMPORTANCEGut microbiota plays an important role in various aspects of human health. Early life is a critical period for the development of gut microbiota. In this prospective study, we observed that the diversity and antibiotic resistance genes of gut microbiota increased gradually with age in the first 6 months of life. Boys and girls had similar features of gut microbiota. Cesarean section was associated with a lower abundance of Bacteroidetes phylum and Bacteroides genus. Compared with non-ART infants (spontaneous conception), ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. This study presents gut microbiota development with age, antibiotic resistome, and related perinatal factors in early infancy.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Male
Infant
Infant, Newborn
Anti-Bacterial Agents/pharmacology
Feces/microbiology
Bacteria/genetics/classification/drug effects
Delivery, Obstetric
Pregnancy
*Drug Resistance, Microbial/genetics
Cesarean Section

@article {pmid40698936,
year = {2025},
author = {Maghini, DG and Kiguchi, Y and Darling, AE and Monahan, LG and Halpern, AL and Burke, CM and Jaeger, E and Statham, A and Truong, T and Ying, K and Bruinsma, SP and Schroth, GP and Bhatt, AS},
title = {Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0153124},
pmid = {40698936},
issn = {2379-5077},
support = {//Stand Up To Cancer/ ; //Allen Foundation/ ; //Stanford Medicine Children's Health Center for IBD and Celiac Disease/ ; R01 AI143757/AI/NIAID NIH HHS/United States ; //Chan Zuckerberg Initiative/ ; P30 CA124435, R01 AI143757, 1S10OD02014101, R01 AI148623/NH/NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; //Alfred P. Sloan Foundation/ ; R01 AI148623/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial/genetics ; *Metagenomics/methods ; *Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; Nanopore Sequencing ; },
abstract = {Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches require high DNA input and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics for the first time. We sequenced a microbial mock community and 10 human gut microbiome samples with standard, shotgun 2 × 150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 ± 24.8 kilobases) than short read assemblies (9.9 ± 4.5 kilobases; P = 0.002), and comparable N50 to nanopore assemblies (91.0 ± 43.8 kilobases; P = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% ± 20.6%) than nanopore draft genomes (85.9% ± 23.0%; P ≤ 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 ± 114.7 base pairs) relative to ICLR genomes (954.6 ± 71.5 base pairs; P ≤ 0.001). Overall, we find that ICLR sequencing is a promising method for the accurate assembly of microbial genomes from gut metagenomes.IMPORTANCEMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to high input requirements. A new method, the Illumina Complete Long Read (ICLR) assay, is capable of generating highly accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents an additional option for assembling complete genomes from complex metagenomes.},
}

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

@article {pmid40643235,
year = {2025},
author = {Wang, X and Lv, Y and Zhao, W and Xiao, X and Wang, J},
title = {D-amino acid metabolic versatility as a common adaptive strategy in the Mariana Trench microbiome.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0058125},
pmid = {40643235},
issn = {2379-5077},
mesh = {*Amino Acids/metabolism ; *Microbiota/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Geologic Sediments/microbiology ; Seawater/microbiology ; Ammonia/metabolism ; Carbon/metabolism ; Metagenomics ; },
abstract = {UNLABELLED: Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.

IMPORTANCE: Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.},
}

*Amino Acids/metabolism
*Microbiota/genetics
*Archaea/genetics/metabolism
*Bacteria/metabolism/genetics/classification
Geologic Sediments/microbiology
Seawater/microbiology
Ammonia/metabolism
Carbon/metabolism
Metagenomics

@article {pmid40631858,
year = {2025},
author = {Qu, S and Gu, Y and Hou, X and Wei, M and Wang, M and Su, Y and Miao, Y and Yang, J and Sun, Y and Zeng, Z},
title = {Dual associations of gut and oral microbial networks with kidney transplantation.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0025225},
pmid = {40631858},
issn = {2379-5077},
support = {82200679, 8246030754//National Natural Science Foundation of China/ ; 202201AW070019//Applied Basic Research Foundation of Yunnan Province/ ; },
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Saliva/microbiology ; Female ; Male ; Feces/microbiology ; Middle Aged ; Metagenomics/methods ; *Mouth/microbiology ; Adult ; Kidney Failure, Chronic/microbiology/surgery ; *Microbiota ; },
abstract = {UNLABELLED: Gut and oral microbiomes play an essential role in the occurrence and development of kidney disease, but their changes after kidney transplantation in patients with end-stage renal disease and their relationships with host health remain unclear. Through shotgun metagenomic sequencing of fecal and saliva samples, we found that for both gut and oral microbiome, the initial loss of species diversity after kidney transplantation led to a reduction in network nodes and interactions, but strengthened the connections among the remaining species, which started to get a recovery approximately 7-14 days later. Different network modules tended to exhibit unique functions and showed different responses to transplantation. These network changes were significantly correlated with clinical indicators, especially with estimated glomerular filtration rate, suggesting that microbial networks contributed to regulating kidney function and host health from dual dimensions. Our study provides novel insights into associating microbiomes with patient recovery after kidney transplantation and offers new diagnostic strategies.

IMPORTANCE: Understanding the dynamics of gut and oral microbiomes after kidney transplantation is crucial for improving post-transplant outcomes and managing potential complications. Through shotgun metagenomic sequencing of fecal and saliva samples from patients following kidney transplantation, our study emphasizes that, in addition to focusing on the various microbial species themselves, the topological properties of gut and oral microbial networks are also critically important for kidney function. We aim to explore the relationship between host health and the oral and gut microbiomes following kidney transplantation from an ecological perspective and extend to other diseases to advance the study of the microbiome and its clinical impact.},
}

Humans
*Kidney Transplantation/adverse effects
*Gastrointestinal Microbiome
Saliva/microbiology
Female
Male
Feces/microbiology
Middle Aged
Metagenomics/methods
*Mouth/microbiology
Adult
Kidney Failure, Chronic/microbiology/surgery
*Microbiota

@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0174424},
pmid = {40626735},
issn = {2379-5077},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {*Microbiota/genetics ; *Metagenome/genetics ; Metagenomics/methods ; Ecosystem ; },
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}

*Microbiota/genetics
*Metagenome/genetics
Metagenomics/methods
Ecosystem

@article {pmid40489796,
year = {2025},
author = {Andersen, S and Kennedy, G and Banks, M and Flanagan, B and Henden, A},
title = {Prebiotic fiber enteral supplementation after allogeneic transplantation: feasibility and impact on the microbiome.},
journal = {Blood advances},
volume = {9},
number = {16},
pages = {4167-4179},
pmid = {40489796},
issn = {2473-9537},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Female ; Male ; Middle Aged ; *Enteral Nutrition/methods ; Transplantation, Homologous ; *Gastrointestinal Microbiome ; Adult ; *Dietary Fiber/administration & dosage ; Pilot Projects ; },
abstract = {The decline in diversity of the gastrointestinal microbiome during hematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. Although provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fiber-containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome, and metabolomic outcomes between patients who received standard EN (n = 10) vs prebiotic fiber EN (n = 20) after allogeneic HSCT. Stool samples were collected at baseline and at periengraftment and were analyzed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fiber intake after transplant to an average 22 g/d compared with 4 g/d in the standard-care group. High tolerance of both EN formulas was observed with only 20% (n = 2) of the standard and 15% of the prebiotic group (n = 3) requiring parenteral nutrition (P = 1.0). There was no difference in the amount of EN provided, EN duration, or clinical outcomes. Microbial diversity declined in both groups with no difference post-EN provision (P = .93), however, there was a significant difference in relative abundance of Lactobacillus_C rhamnosus, with an increase in the prebiotic group only (P = .022). The relative abundance of Faecalicatena gnavus increased in the standard group and declined in the prebiotic group (P = .0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only after EN provision (P = .00035). A longer fiber intervention should be trialed to optimize clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as #ACTRN12621000832875.},
}

Humans
*Prebiotics/administration & dosage
*Hematopoietic Stem Cell Transplantation/adverse effects
Female
Male
Middle Aged
*Enteral Nutrition/methods
Transplantation, Homologous
*Gastrointestinal Microbiome
Adult
*Dietary Fiber/administration & dosage
Pilot Projects

@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
doi = {10.1093/pnasnexus/pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40929115,
year = {2025},
author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE},
title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331736},
pmid = {40929115},
issn = {1932-6203},
mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; },
abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.},
}

*Chiroptera/virology
Animals
Madagascar
Phylogeny
*Zoonoses/virology
*Genome, Viral
*Evolution, Molecular
*Viral Zoonoses/virology
Humans
Genomics
High-Throughput Nucleotide Sequencing
*Picornaviridae Infections/virology/veterinary/epidemiology

@article {pmid40765405,
year = {2025},
author = {Dai, G and Zhang, Y and Shen, C and Jiao, Y and Shen, W and Yu, F and Liu, R and Wang, D and Yuan, G and Jia, J},
title = {Luteolin Treats Obese Rats With Polycystic Ovary Syndrome by Improving Liver Lipid Metabolism and Regulating the Gut Microbiota.},
journal = {Phytotherapy research : PTR},
volume = {39},
number = {9},
pages = {4171-4180},
doi = {10.1002/ptr.70043},
pmid = {40765405},
issn = {1099-1573},
support = {JLY2021209//Clinical Medical Science and Technology Development Foundation of Jiangsu University/ ; BK20231251//Natural Science Foundation of Jiangsu Province/ ; JDY2022005//Key project for Medical Education Collaborative Innovation Fund of Jiangsu University/ ; BE2023757//Social Development Project of Jiangsu Province/ ; BRA2022008//the sixth phase 333 second level talent training project of Jiangsu Province (tackling bottleneck technology)/ ; jdfyRC2020010//Doctoral Research Initiation Fund/ ; BGYCA202207//Beigu Talent Cultivation Program of Affiliated Hospital of Jiangsu University/ ; SS202204-KFB05//open project of clinical medical research center of Gynecology and Traditional Chinese Medicine of Zhenjiang/ ; MS2024142//Science and Technology Development Program for Traditional Chinese Medicine of Jiangsu Province/ ; },
mesh = {Animals ; *Luteolin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Polycystic Ovary Syndrome/drug therapy/complications/metabolism ; *Obesity/drug therapy/complications ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Rats ; Rats, Sprague-Dawley ; Body Weight/drug effects ; Disease Models, Animal ; },
abstract = {Polycystic ovary syndrome (PCOS) and obesity share a bidirectional relationship. While previous studies have indicated the anti-obesity effects of luteolin, its role in PCOS exacerbated by obesity remains unclear. This study aimed to investigate the ameliorative effects of luteolin on obese rats with PCOS and explore its underlying mechanisms. We established a rat model of PCOS with obesity and administered luteolin to evaluate its mitigating effects on the metabolic phenotype. Liver transcriptomics and fecal metagenomics were employed to analyze potential targets and alterations in the gut microbiota composition associated with luteolin's effects. Results showed that luteolin reduced body weight, improved estrous cycles, polycystic ovarian morphology, and glucose tolerance, and lowered serum levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-c) in the model rats. Importantly, luteolin significantly alleviated hepatic steatosis and reversed the expression of 138 key differentially expressed genes (DEGs) in the liver, including UQCRC2, IRS2, NFIX, and ALDH6A1. In addition, luteolin significantly increased the alpha diversity of the gut microbiota and modulated its composition, specifically increasing the relative abundance of Bacteroidota and decreasing that of Firmicutes. Our findings suggest that luteolin exerts beneficial effects on PCOS with obesity, potentially mediated through the improvement of hepatic lipid metabolism and the restoration of gut microbiota homeostasis. Luteolin emerges as a promising therapeutic candidate for managing PCOS with obesity.},
}

Animals
*Luteolin/pharmacology
*Gastrointestinal Microbiome/drug effects
Female
*Polycystic Ovary Syndrome/drug therapy/complications/metabolism
*Obesity/drug therapy/complications
*Lipid Metabolism/drug effects
*Liver/metabolism/drug effects
Rats
Rats, Sprague-Dawley
Body Weight/drug effects
Disease Models, Animal

@article {pmid40689619,
year = {2025},
author = {Tambovtseva, RS and Arslan, LA and Grigoryeva, TA and Abdulkhakov, SR and Doludin, YV and Stoma, IO and Rizvanov, AA and Miftakhova, RR and Gabdoulkhakova, AG},
title = {Narrative review on bacteria-derived metabolites in the pathogenesis of ulcerative colitis.},
journal = {Clinical microbiology reviews},
volume = {38},
number = {3},
pages = {e0021024},
pmid = {40689619},
issn = {1098-6618},
support = {FZSM-2023-0011//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Colitis, Ulcerative/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/metabolism ; },
abstract = {SUMMARYThe pathogenesis of ulcerative colitis (UC) is heterogeneous; the causes are considered to be external factors such as stress, infections, antibiotics, and other medications, diet, and intrinsic factors such as genetic predisposition. The aim of this narrative review is to analyze data on intestinal flora and bacteria-derived metabolites in inflammatory bowel diseases and ulcerative colitis in particular. The main focus is on proteolytic, saccharolytic, mucin-degrading, and bile acid-metabolizing bacteria. What types of metabolites are beneficial for intestinal integrity and the patient's health? How can dietary preferences trigger disease and cause complications? What kind of changes in the microbiome promote the disease? We consider what targets/receptors metabolites act on and their physiological role. The knowledge accumulated over the past years on the gut metagenome, metabolome, and signaling mechanisms may allow, in the future, modulating the composition of the intestinal microbiome and suppressing the growth of pathogenic flora without the use of antibiotics, but due to pro- and prebiotics, products of bacterial metabolism, including quorum sensing molecules.},
}

*Colitis, Ulcerative/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Bacteria/metabolism

@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}

@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}

Humans
*Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals
*Drug Resistance, Neoplasm
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Tumor Microenvironment/immunology

@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
doi = {10.1111/1758-2229.70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}

*Solanum lycopersicum/microbiology/parasitology/immunology
Animals
*Microbiota
*Soil Microbiology
*Diptera/physiology
Ecuador
Plant Roots/microbiology/parasitology
Introduced Species
Bacteria/classification/genetics/isolation & purification
Plant Leaves/parasitology

@article {pmid40924621,
year = {2025},
author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C},
title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09633},
pmid = {40924621},
issn = {1520-5851},
abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.},
}

@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {16},
number = {9},
pages = {e0113425},
doi = {10.1128/mbio.01134-25},
pmid = {40793781},
issn = {2150-7511},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; },
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*DNA Transposable Elements
Feces/microbiology
Ecuador
Metagenomics
Child
Child, Preschool
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Female
Gene Transfer, Horizontal
Male
Plasmids/genetics

@article {pmid40779866,
year = {2025},
author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ},
title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139382},
doi = {10.1016/j.jhazmat.2025.139382},
pmid = {40779866},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics & numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics & numerical data ; Wetlands ; Electrochemical Techniques ; },
abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.},
}

Biodegradation, Environmental
*Bioreactors/microbiology/statistics & numerical data
Desulfovibrio/metabolism
Geobacter/metabolism
Metagenome
*Microbiota
Nitrates/metabolism
*Polybrominated Biphenyls/metabolism
*Water Pollutants, Chemical/metabolism
*Water Purification/methods/statistics & numerical data
Wetlands
Electrochemical Techniques

@article {pmid40671669,
year = {2025},
author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Estévez, M},
title = {Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {36},
pages = {22698-22713},
doi = {10.1021/acs.jafc.5c02799},
pmid = {40671669},
issn = {1520-5118},
mesh = {Animals ; Rats, Wistar ; Rats ; *Gastrointestinal Microbiome ; Male ; *Biomarkers/urine/blood ; Bacteria/classification/isolation & purification/genetics/metabolism ; Triticum/metabolism ; *Meat/analysis ; Cattle ; Humans ; Urine/chemistry ; Glycine max/metabolism ; },
abstract = {Growing concerns about the alleged negative outcomes of the consumption of animal-based foods (ABF) lead a number of consumers to demand so-called plant-based meat analogues (PBMAs), which are designed to replicate the sensory and nutritional characteristics of genuine meat. This study aimed to characterize the physiological effects of long-term PBMA consumption by comparing their specific influence on both gut microbiota and fluids (i.e., plasma and urine) with those of conventional beef in a rodent model by using metagenomic and metabolomic tools. Twenty-one Wistar rats were divided into groups and consumed diets made with either wheat- and soy-based meat analogues or beef. The microbiota of PBMA-fed animals showed increased amounts of the harmful genus of gut bacteria, while their metabolomes reflected disturbances in the nitrogen-containing compound metabolism and the presence of potentially harmful metabolites. These results should raise concern and prompt further research into the long-term impact of consumption of PBMAs on health.},
}

Animals
Rats, Wistar
Rats
*Gastrointestinal Microbiome
Male
*Biomarkers/urine/blood
Bacteria/classification/isolation & purification/genetics/metabolism
Triticum/metabolism
*Meat/analysis
Cattle
Humans
Urine/chemistry
Glycine max/metabolism

@article {pmid40923121,
year = {2025},
author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L},
title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.},
journal = {Brain and behavior},
volume = {15},
number = {9},
pages = {e70843},
doi = {10.1002/brb3.70843},
pmid = {40923121},
issn = {2162-3279},
support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.

METHODS: We conducted metagenomic sequencing on stool samples from 42 patients diagnosed with glioma after operation and 30 non-intracranial tumor patients and developed a Gradient Boosting Machine (GBM) machine learning model to predict the glioma patients based on the gut microbiome data.

RESULTS: The AUC-ROC for the GBM model was 0.79, indicating a good level of discriminative ability.

CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.},
}

Humans
*Machine Learning
*Gastrointestinal Microbiome/physiology/genetics
*Glioma/microbiology/diagnosis
*Brain Neoplasms/microbiology/diagnosis
Male
Female
Middle Aged
Adult
Feces/microbiology

@article {pmid40922218,
year = {2025},
author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K},
title = {Survey of a grapevine microbiome through functional metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {117000},
doi = {10.1016/j.foodres.2025.117000},
pmid = {40922218},
issn = {1873-7145},
mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; },
abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.},
}

*Vitis/microbiology
*Metagenomics/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
Rhizosphere
Fruit/microbiology
Plant Leaves/microbiology

@article {pmid40922213,
year = {2025},
author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y},
title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {116992},
doi = {10.1016/j.foodres.2025.116992},
pmid = {40922213},
issn = {1873-7145},
mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; },
abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.},
}

*Taste
*Fruit/microbiology/chemistry
Odorants/analysis
*Food Microbiology
*Microbiota
Bacteria/classification/genetics
Humans
Amino Acids/analysis
Metagenomics

@article {pmid40922105,
year = {2025},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70178},
doi = {10.1111/1758-2229.70178},
pmid = {40922105},
issn = {1758-2229},
mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; },
abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.},
}

Biodegradation, Environmental
*Plastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
Soil Microbiology
Metagenome
Genomics
Multiomics

@article {pmid40920777,
year = {2025},
author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A},
title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331692},
pmid = {40920777},
issn = {1932-6203},
mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; },
abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.

METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) ≤40%, and healthy controls (plasma: n = 51, stool samples: n = 69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.

RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.

CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.},
}

Humans
*Dysbiosis/blood/microbiology/metabolism
*Heart Failure/blood/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Aged
Feces/microbiology
Chronic Disease
Case-Control Studies
Metabolomics
Metabolome

@article {pmid40795725,
year = {2025},
author = {Zhang, FL and Li, AY and Zhu, KX and Zhang, K and Tian, Z and Wang, T and Zhang, XH and Zang, J and Sun, XF and Shen, W and Li, L},
title = {Integrated multi-omics analysis uncovers Zearalenone-induced ovarian and intestinal inflammation is mediated by the tumor necrosis factor-α.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139476},
doi = {10.1016/j.jhazmat.2025.139476},
pmid = {40795725},
issn = {1873-3336},
mesh = {*Zearalenone/toxicity ; Animals ; Female ; *Tumor Necrosis Factor-alpha/genetics/metabolism ; *Inflammation/chemically induced/metabolism/genetics ; *Ovary/drug effects/pathology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/pathology ; Mice, Knockout ; Mice, Inbred C57BL ; Dysbiosis/chemically induced ; Cell Line ; Multiomics ; },
abstract = {As a widely encountered foodborne mycotoxin, Zearalenone (ZEN) has the potential to accumulate along the food chain, posing threats to public health and safety. However, the precise mechanisms by which ZEN causes tissue damage remain incompletely understood. Here, we established in vivo (40 μg/kg) and in vitro (30 μM) models to elucidate the underlying processes of ZEN-induced damage to the ovary and intestine. Our results demonstrated that, following ZEN exposure, pro-inflammatory signaling factors, including NLR family pyrin domain containing 3 (NLRP3) and Interleukin 6 (IL6), were significantly elevated in both ovarian and intestines. Metagenomic analysis revealed dysbiosis of the gut microbiota, which was closely associated with tumor necrosis factor (TNF)-α signaling pathway. Transcriptomic results further indicated that inflammatory response are intricately linked to TNF signaling pathway. Additionally, the Tnf-α knockout mouse model showed a marked resistance to ZEN-induced ovarian and intestinal injuries. In vitro, RNA interference targeting TNF-α attenuated the inflammatory response in IPEC-J2 cells. Moreover, dysregulated expression of the hormone synthesis genes, including KISS-1 metastasis suppressor (Kiss1) and gonadotropin releasing hormone 1 (Gnrh1), was observed, suggesting that ZEN-induced microbial dysbiosis and ovary damage may be interconnected through hormonal disruption. In summary, our results emphasize the role of TNF-α in causing ovarian and intestinal damage after ZEN exposure.},
}

*Zearalenone/toxicity
Animals
Female
*Tumor Necrosis Factor-alpha/genetics/metabolism
*Inflammation/chemically induced/metabolism/genetics
*Ovary/drug effects/pathology/metabolism
Mice
Gastrointestinal Microbiome/drug effects
*Intestines/drug effects/pathology
Mice, Knockout
Mice, Inbred C57BL
Dysbiosis/chemically induced
Cell Line
Multiomics

@article {pmid40752173,
year = {2025},
author = {Li, WJ and Ghaly, TM and Tetu, SG and Huang, FY and Li, HZ and Li, H},
title = {Effects of agricultural inputs on soil virome-associated antibiotic resistance and virulence: A focus on manure, microplastic and pesticide.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139380},
doi = {10.1016/j.jhazmat.2025.139380},
pmid = {40752173},
issn = {1873-3336},
mesh = {*Manure ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Pesticides/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Virome/drug effects ; Agriculture ; Virulence/genetics ; Virulence Factors/genetics ; Bacteria/genetics ; Soil/chemistry ; },
abstract = {Soil viruses are increasingly recognized as crucial mediators of horizontal gene transfer, yet their role in disseminating antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) under agricultural disturbances remains poorly understood. Here, we characterized the viromes and associated ARGs and VFGs in agricultural soils treated with low- and high-dose manures, microplastics, and pesticides. Using metagenomic sequencing coupled with advanced viral identification tools, we found that manure fertilization markedly altered viral community composition and increased viral diversity. Manure also enhanced the abundance of ARGs and VFGs in viromes by 2.0-9.8-fold and 2.0-8.1-fold, respectively, while microplastics and pesticides had limited impacts. Additionally, gene pathways related to human diseases and environmental adaptation were enriched in soil viromes treated with manures and high-dose pesticides. Virus-host prediction revealed that Actinomycetia dominated bacterial hosts of both ARG- and VFG-carrying viruses, with some VFG-carrying viruses linked to potential human pathogens, e.g., Escherichia albertii and Klebsiella pneumoniae. Co-occurrence network analysis indicated that these disturbances strengthened connections between bacteria, viruses, and ARGs (or VFGs). Our study provides a comprehensive profile of viromes and associated risks in agricultural soil under three disturbances, highlighting the role of viruses in spread of antibiotic resistance and pathogenic risks in agricultural soil.},
}

*Manure
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Pesticides/toxicity
*Soil Pollutants/toxicity
*Microplastics/toxicity
*Virome/drug effects
Agriculture
Virulence/genetics
Virulence Factors/genetics
Bacteria/genetics
Soil/chemistry

@article {pmid40749656,
year = {2025},
author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC},
title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139384},
doi = {10.1016/j.jhazmat.2025.139384},
pmid = {40749656},
issn = {1873-3336},
mesh = {Pakistan ; *Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Humans ; Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/transmission ; Microbiota ; },
abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.},
}

Pakistan
*Metagenomics
*Drug Resistance, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Humans
Bacteria/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
*Cross Infection/microbiology/transmission
Microbiota

@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
mesh = {*Archaea/drug effects/genetics ; *Microplastics/toxicity ; *Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity ; *Rivers/microbiology ; Biodegradation, Environmental ; Polyvinyl Chloride/toxicity ; Microbiota/drug effects ; Polyesters ; Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}

*Archaea/drug effects/genetics
*Microplastics/toxicity
*Bacteria/drug effects/genetics
*Water Pollutants, Chemical/toxicity
*Rivers/microbiology
Biodegradation, Environmental
Polyvinyl Chloride/toxicity
Microbiota/drug effects
Polyesters
Drug Resistance, Microbial/genetics

@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
mesh = {Animals ; *Gene Transfer, Horizontal ; Swine ; *Gastrointestinal Microbiome/genetics ; *Plasmids/genetics ; Humans ; Farms ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

Animals
*Gene Transfer, Horizontal
Swine
*Gastrointestinal Microbiome/genetics
*Plasmids/genetics
Humans
Farms
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40682875,
year = {2025},
author = {Beltrán de Heredia, I and Sbaffi, T and González-Gaya, B and Di Cesare, A and Sabatino, R and Alkorta, I and Ruiz-Romera, E},
title = {Comparative analysis of planktonic and sessile microbiomes and associated resistomes in a freshwater ecosystem impacted by municipal wastewater treatment plant discharge.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139250},
doi = {10.1016/j.jhazmat.2025.139250},
pmid = {40682875},
issn = {1873-3336},
mesh = {*Microbiota/drug effects ; *Wastewater ; Biofilms ; *Plankton/drug effects ; *Fresh Water/microbiology ; Rivers/microbiology ; Ecosystem ; Waste Disposal, Fluid ; Water Microbiology ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical ; },
abstract = {Wastewater treatment plants (WWTPs) disrupt freshwater ecosystems and are recognised as hotspots for antimicrobial resistance. This study assessed the effect of treated municipal wastewater discharge on both planktonic and sessile freshwater microbial communities. A monitoring network was established in a Spanish urban river basin during 2022 dry season, with sampling points upstream and downstream of a WWTP. Artificial glass-based substrates enabled biofilm colonisation, while river water and effluent samples were collected during biofilm harvesting. Chemical exposure was assessed by characterising nutrients and antimicrobial concentrations in water, while shotgun metagenomics revealed taxonomic composition and resistome pools in both matrices. River water exhibited greater genus richness and pathobiome diversity than biofilms. Wastewater discharge shaped microbial composition, leading to shifts in less dominant groups, with partial attenuation of this effect downstream. Resistome richness was higher in river water compared to biofilm, though the latter displayed greater total abundances and distinct resistance profiles suggesting their role as genetic reservoirs. While no consistent resistome trends were linked to sampling location, higher total resistance abundances occurred in river water at sites impacted by wastewaters. Background resistance levels found upstream likely persisted downstream due to pollutant-driven selection. Lower resistome richness in effluent water suggests downstream abundances may also result from microbiome shifts and environmental factors. Assembly-based analysis revealed resistance genetic contexts and indicators of gene dissemination.},
}

*Microbiota/drug effects
*Wastewater
Biofilms
*Plankton/drug effects
*Fresh Water/microbiology
Rivers/microbiology
Ecosystem
Waste Disposal, Fluid
Water Microbiology
Bacteria/genetics/drug effects
*Water Pollutants, Chemical

@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, aging, and the gut microbiome: Intersections of immunity, barrier dysfunction, and disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {128},
number = {},
pages = {1-12},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology/physiology ; *Aging/immunology ; *Alcohol Drinking/immunology/adverse effects ; Intestinal Mucosa/drug effects/immunology ; *Ethanol/adverse effects ; Animals ; Inflammation ; },
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2∗2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology/physiology
*Aging/immunology
*Alcohol Drinking/immunology/adverse effects
Intestinal Mucosa/drug effects/immunology
*Ethanol/adverse effects
Animals
Inflammation

@article {pmid40643197,
year = {2025},
author = {Xu, T and Wu, X and Zhang, Y and Cai, Y and Zhang, X and Zeng, Q and Luo, J and Wei, J and Chen, T},
title = {L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway.},
journal = {Aging cell},
volume = {24},
number = {9},
pages = {e70166},
doi = {10.1111/acel.70166},
pmid = {40643197},
issn = {1474-9726},
support = {32201250//National Natural Science Foundation of China/ ; 2024YFA1307103//National Key R&D Program of China/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; 20242BAB25464//Jiangxi Provincial Natural Science Foundation/ ; },
mesh = {Animals ; Mice ; *Sirtuin 1/metabolism ; *Tryptophan/pharmacology/biosynthesis/metabolism ; *Signal Transduction/drug effects ; *Aging/drug effects ; *Bifidobacterium/metabolism ; *Tumor Suppressor Protein p53/metabolism ; Probiotics/pharmacology ; Male ; Gastrointestinal Microbiome ; Hippocampus ; },
abstract = {Gut microbiota delays aging by regulating the immune, metabolic, and neurological functions of the host. However, current research on novel probiotics with antiaging properties significantly lags, impacting their application in clinical treatments. In this study, metagenomics, culturomics, and probiotic property screening were used to identify Bifidobacterium pseudocatenulatum NCU-08 as a potential probiotic with anti-aging properties. In addition, B. pseudocatenulatum NCU-08 effectively improved the behavioral characteristics, significantly reduced the levels of the age-related protein β-galactosidase (β-gal) (BP: M = 0.81 vs. 1.13, p < 0.05), attenuated neuronal damage in the hippocampus, and improved the composition of the gut microbiota of senescence-accelerated mouse tendency-8 (SAMP8) mice. The targeted metabolomics suggested that L-tryptophan (L-Trp) may be a key substance for B. pseudocatenulatum NCU-08 to exert anti-aging effects (BP: M = 14878.6 ng/mL vs. 5464.99 ng/mL, p < 0.01). Mechanistically, using the aging model of SAMP8 mice and HT22 mouse hippocampal neuronal cells, it was found that B. pseudocatenulatum NCU-08 might enter the intestine to regulate L-Trp, and then transport it to the brain. In the brain, L-Trp was metabolized to NAD[+], which activated the Sirt1/P53/P21/Rb signaling pathway, thereby exerting antiaging effects. Interestingly, this antiaging effect was inhibited after the intervention of the Sirt1 inhibitor EX-527. This study is the first to confirm the antiaging properties of NCU-08 isolated from the fecal samples of seven centenarians in Jiangxi Province, providing data support for the future development of probiotic preparations with antiaging effects.},
}

Animals
Mice
*Sirtuin 1/metabolism
*Tryptophan/pharmacology/biosynthesis/metabolism
*Signal Transduction/drug effects
*Aging/drug effects
*Bifidobacterium/metabolism
*Tumor Suppressor Protein p53/metabolism
Probiotics/pharmacology
Male
Gastrointestinal Microbiome
Hippocampus

@article {pmid40461059,
year = {2025},
author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Huys, GR and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , },
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.},
journal = {Gut},
volume = {74},
number = {10},
pages = {1624-1637},
doi = {10.1136/gutjnl-2024-334634},
pmid = {40461059},
issn = {1468-3288},
mesh = {*Renal Insufficiency, Chronic/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Disease Progression ; Male ; Female ; Middle Aged ; Animals ; Mice ; Fecal Microbiota Transplantation ; Longitudinal Studies ; *Uremic Toxins/metabolism/blood ; Aged ; Metagenomics ; Adult ; Diet ; },
abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.

OBJECTIVE: To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).

DESIGN: This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Intérieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.

RESULTS: Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.

CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.},
}

*Renal Insufficiency, Chronic/microbiology
*Gastrointestinal Microbiome/physiology
Humans
Disease Progression
Male
Female
Middle Aged
Animals
Mice
Fecal Microbiota Transplantation
Longitudinal Studies
*Uremic Toxins/metabolism/blood
Aged
Metagenomics
Adult
Diet

@article {pmid40918253,
year = {2025},
author = {McMahon, S and Franklin, S and Galloway-Peña, J},
title = {Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629422},
pmid = {40918253},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Leukemia, Myeloid, Acute/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Induction Chemotherapy/adverse effects ; Bacteria/drug effects/genetics/classification ; Aged ; Adult ; Feces/microbiology ; Metagenomics ; *Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Acute myeloid leukemia (AML) patients are highly susceptible to infection. Moreover, prophylactic and empirical antibiotic treatment during chemotherapy disrupts the gut microbiome, raising the risk for antibiotic-resistant (AR) opportunistic pathogens. There is limited data on risk factors for AR infections or colonization events in treated cancer patients, and no predictive models exist. This study aims to combine metagenomic and antibiotic administration data to develop a model predicting AR event outcomes.

METHODS: Baseline stool microbiome, antibiotic administration, resistome, and clinical metadata from 95 patients were utilized to build a Random Forest model to predict AR infection and colonization events by serious AR threats. Additionally, sparse canonical correlation analysis assessed correlations between microbiome and resistome data, while Spearman correlation networks identified direct associations with AR event outcomes and secondary variables.

RESULTS: AR-events were identified in 14 of the 95 included patients, with 8 developing AR infections and 9 identified as AR colonized. A Random Forest model predicted AR event outcomes (AUC = 0.73), identifying bacterial taxa and antibiotic resistance gene (ARG) classes as key variables of importance. Methanobrevibacter smithii, Clostridium leptum, and Bacteroides dorei were identified as key taxa associated with reduced risk of AR events, suggesting the potential roles of commensals in maintaining gut microbial resilience during chemotherapy. ARG classes, particularly those conferring resistance to lincosamides, macrolides, and streptogramins, were negatively associated with AR events.

CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.},
}

Humans
*Machine Learning
*Leukemia, Myeloid, Acute/drug therapy/microbiology/complications
*Anti-Bacterial Agents/therapeutic use/pharmacology
Gastrointestinal Microbiome/drug effects
Male
Female
Middle Aged
*Induction Chemotherapy/adverse effects
Bacteria/drug effects/genetics/classification
Aged
Adult
Feces/microbiology
Metagenomics
*Drug Resistance, Bacterial

@article {pmid40914968,
year = {2025},
author = {Cho, Y and Kim, E and Kim, M and Rho, M},
title = {DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
pmid = {40914968},
issn = {1477-4054},
support = {RS-2023-00217123//MSIT/ ; RS-2023-KH135226//Ministry of Health/ ; 2023ER210902/GF/NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Metagenome ; Metagenomics/methods ; Humans ; Neural Networks, Computer ; Sequence Analysis, DNA ; Drug Resistance, Microbial/genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {MOTIVATION: Mobile genetic elements (MGEs) play an important role in facilitating the acquisition of antibiotic resistance genes (ARGs) within microbial communities, significantly impacting the evolution of antibiotic resistance. Understanding the mechanism and trajectory of ARG acquisition requires a comprehensive analysis of the ARG-carrying mobilome-a collective set of MGEs carrying ARGs. However, identifying the mobilome within complex microbiomes poses considerable challenges. Existing MGE prediction methods, designed primarily for single genomes, exhibit substantial limitations when applied to metagenomic data, often producing high false positive rates in identifying target MGEs from metagenome sequencing data.

RESULTS: To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.},
}

*Microbiota/genetics
*Interspersed Repetitive Sequences
Metagenome
Metagenomics/methods
Humans
Neural Networks, Computer
Sequence Analysis, DNA
Drug Resistance, Microbial/genetics
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid40780374,
year = {2025},
author = {Mao, Z and Liu, C and Ni, J and Huang, M and Qu, W and Chen, W and Shen, Y and Qin, T and Gao, M and Zheng, S and Chen, Y},
title = {Gut derived (S)-Equol mitigates influenza viral pneumonia by modulating macrophage polarization via Nrf2 mediated AKT/ERK/NF-κb signaling pathways.},
journal = {Free radical biology & medicine},
volume = {239},
number = {},
pages = {457-471},
doi = {10.1016/j.freeradbiomed.2025.08.004},
pmid = {40780374},
issn = {1873-4596},
mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; NF-kappa B/metabolism/genetics ; Proto-Oncogene Proteins c-akt/metabolism/genetics ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/immunology/metabolism ; Signal Transduction/drug effects ; Humans ; *Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology ; *Orthomyxoviridae Infections/drug therapy/virology/pathology ; *Influenza, Human/virology/drug therapy ; Male ; Influenza A virus/pathogenicity ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; },
abstract = {Respiratory virus including influenza A virus (IAV) infection induces alterations in gut microbiota structure and function, which in turn plays an essential role in the pathogenic process. Alterations in gut microbiota are usually accompanied with changes in metabolites. The specific relationship between dynamic changes in gut microbiota and serum metabolites in influenza remains unclear. In this study, we depicted dynamic changes in composition of gut microbiota by using metagenomic sequencing in an influenza mouse model. Through mass spectrometry based metabolomic, we identified (S)-Equol as a notable protective metabolite derived from intestinal flora. Serum (S)-Equol level decreased from the initial infection phase and increased gradually during the convalescence phase, which was positively associated with the changes in some Eggerthella and Bifidobacterium species. Antibiotic treatment reduced serum (S)-Equol level and exacerbated lung pathological damage. Oral administration of (S)-Equol relieved disease severity and controlled inflammatory infiltration. Mechanistically, (S)-Equol activated Nrf2 in macrophages, thereby inhibited AKT, ERK and NF-κB phosphorylation. The inhibition of these signaling pathways ultimately restrained pro-inflammatory cytokines release and repressed pro-inflammatory macrophage polarization. Moreover, serum (S)-Equol level was lower in influenza patients at progressed phase and was negatively correlated with serum levels of IL-6, IL-1β, and TNF-α. Collectively, our data highlighted gut derived (S)-Equol a promising postbiotic for alleviating influenza pneumonia.},
}

Animals
*NF-E2-Related Factor 2/metabolism/genetics
Mice
NF-kappa B/metabolism/genetics
Proto-Oncogene Proteins c-akt/metabolism/genetics
*Gastrointestinal Microbiome/drug effects
*Macrophages/drug effects/immunology/metabolism
Signal Transduction/drug effects
Humans
*Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology
*Orthomyxoviridae Infections/drug therapy/virology/pathology
*Influenza, Human/virology/drug therapy
Male
Influenza A virus/pathogenicity
Disease Models, Animal
Mice, Inbred C57BL
Female

@article {pmid40773868,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HR and Kim, NY and Kim, HL and Chang, Y and Ryu, S and Kim, HN},
title = {Shotgun metagenomics reveals alteration of gut microbiota and metabolic pathways in adults with poor sleep quality.},
journal = {Psychoneuroendocrinology},
volume = {180},
number = {},
pages = {107565},
doi = {10.1016/j.psyneuen.2025.107565},
pmid = {40773868},
issn = {1873-3360},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; Adult ; Middle Aged ; *Metabolic Networks and Pathways/genetics/physiology ; Feces/microbiology ; Metagenomics/methods ; *Sleep Quality ; *Sleep Wake Disorders/microbiology/metabolism ; Metagenome/genetics ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the gut microbiome plays a role in sleep disturbance. This study explored the characteristics of the gut microbiome and the functional metabolic pathways related to sleep quality.

METHODS: A total of 588 participants were recruited. Sleep quality was assessed using the Pittsburgh Sleep Quality Index, employing a cutoff score of 8.5. Based on this criterion, 42 individuals with poor sleep quality (PSQ) and 546 healthy controls with good sleep quality (GSQ) were identified. The fecal microbiome was analyzed using shotgun whole-metagenome sequencing, and groups were compared based on diversity metrics, differentially abundant species, metabolic pathways and metabolites.

RESULTS: No significant differences in alpha and beta diversity indices were observed between individuals experiencing subjective sleep disturbances and those who did not. Klebsiella pneumoniae was more abundant in the PSQ group (β = 0.476; q = 0.017). Additionally, the following metabolic pathways were enriched in the PSQ group: octane oxidation (coefficient = 0.495, q = 0.033), the superpathway of acetyl-CoA biosynthesis (coefficient = 0.377, q = 0.025), superpathway of (Kdo)2-lipid A biosynthesis (coefficient = 0.367, q = 0.026), petroselinate biosynthesis (coefficient = 0.353, q = 0.034), and superpathway of histidine, purine, and pyrimidine biosynthesis (coefficient = 0.349, q = 0.042). When metabolites levels associated with poor sleep quality were inferred using MelonnPan, higher xanthine levels were observed in the PSQ group (coefficient = 0.018; q = 0.025).

CONCLUSION: In summary, this study poses significant questions regarding the relationship between the gut microbiome and poor sleep quality.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Male
Female
Adult
Middle Aged
*Metabolic Networks and Pathways/genetics/physiology
Feces/microbiology
Metagenomics/methods
*Sleep Quality
*Sleep Wake Disorders/microbiology/metabolism
Metagenome/genetics

@article {pmid40719338,
year = {2025},
author = {Louca, S and Mullin, CE},
title = {Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70020},
pmid = {40719338},
issn = {1755-0998},
support = {2243038//US National Science Foundation/ ; },
mesh = {*Desiccation/methods ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Specimen Handling/methods ; Vacuum ; Feces/microbiology ; Hot Temperature ; Metagenomics/methods ; Soil Microbiology ; },
abstract = {Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.},
}

*Desiccation/methods
Animals
RNA, Ribosomal, 16S/genetics
*Microbiota
*Specimen Handling/methods
Vacuum
Feces/microbiology
Hot Temperature
Metagenomics/methods
Soil Microbiology

@article {pmid40671648,
year = {2025},
author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S},
title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70010},
pmid = {40671648},
issn = {1755-0998},
support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; },
abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.},
}

*DNA Barcoding, Taxonomic/methods
*Kelp
Ecosystem
California
Animals
*Biodiversity
*Aquatic Organisms/classification/genetics
*DNA, Environmental/genetics
*Metagenomics/methods
*Biota

@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
mesh = {Humans ; *Military Personnel ; *Saliva/microbiology ; *Microbiota ; Male ; Adult ; Phylogeny ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; Metagenomics ; },
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.

RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p > 0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p < 0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p < 0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p < 0.05). At the metabolic level, training resulted in a relative increase (p < 0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p < 0.05).

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}

Humans
*Military Personnel
*Saliva/microbiology
*Microbiota
Male
Adult
Phylogeny
*Mouth/microbiology
Young Adult
Bacteria/classification
Metagenomics

@article {pmid40577531,
year = {2025},
author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS},
title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40577531},
issn = {1751-7370},
support = {GBMF9200//Gordon and Betty Moore Foundation/ ; 1394//UK NERC NEOF Pilot Genomics Competition/ ; MR/S037195/1//MRC Methodology Grant "Strain resolved metagenomics for medical microbiology"/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme Grant (Decoding Biodiversity)/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; },
mesh = {*Cyanobacteria/metabolism/genetics/classification/growth & development ; *Biodiversity ; Metagenomics ; Gene Expression Profiling ; Oxygen/metabolism ; },
abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via metatranscriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.},
}

*Cyanobacteria/metabolism/genetics/classification/growth & development
*Biodiversity
Metagenomics
Gene Expression Profiling
Oxygen/metabolism

@article {pmid40499635,
year = {2025},
author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F},
title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122108},
doi = {10.1016/j.envres.2025.122108},
pmid = {40499635},
issn = {1096-0953},
mesh = {Animals ; Hong Kong ; Rats/microbiology ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA, as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.},
}

Animals
Hong Kong
Rats/microbiology
*Gastrointestinal Microbiome
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Bacteria/genetics
*Drug Resistance, Microbial/genetics

@article {pmid40459094,
year = {2025},
author = {Dahl, MB and Brachmann, S and Söllinger, A and Schnell, M and Ahlers, L and Wutkowska, M and Hoff, KJ and Nath, N and Groß, V and Wang, H and Weil, M and Piecha, M and Schaffer, M and Jensen, C and Kuss, AW and Gall, C and Wimmer, E and Pribasnig, T and Tveit, AT and Sigurdsson, BD and Schleper, C and Richter, A and Urich, T},
title = {Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques-Cross-Validation and Perspectives.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14130},
pmid = {40459094},
issn = {1755-0998},
support = {21-17322M//The Czech Science Foundation/ ; BO 5559/1-1//Deutsche Forschungsgemeinschaft/ ; INST 292/146-1 FUGB//Deutsche Forschungsgemeinschaft/ ; UR198/7-1//Deutsche Forschungsgemeinschaft/ ; 813114//HORIZON EUROPE European Innovation Council/ ; //Research Council of Norway/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gene Expression Profiling/methods ; *Bacteria/genetics/classification ; Transcriptome ; Soil/chemistry ; },
abstract = {Linking meta-omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAEstd). RNA reads originating from NAEstd were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray-Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between-sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT-PCR experiments, NAEstd and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAEstd and MBC extracts. We discuss how simultaneous changes in community size and the soils nucleic acid retention strength might hamper accurate biomass estimation. Adding NAEstd has the potential to shed important light on nucleic acid retention in the substance matrix (e.g., soil) during extraction.},
}

*Soil Microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gene Expression Profiling/methods
*Bacteria/genetics/classification
Transcriptome
Soil/chemistry

@article {pmid40243260,
year = {2025},
author = {Bayer, PE and Bennett, A and Nester, G and Corrigan, S and Raes, EJ and Cooper, M and Ayad, ME and McVey, P and Kardailsky, A and Pearce, J and Fraser, MW and Goncalves, P and Burnell, S and Rauschert, S},
title = {A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14107},
pmid = {40243260},
issn = {1755-0998},
support = {//Minderoo Foundation/ ; },
mesh = {Animals ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/genetics ; Computational Biology/methods ; Australia ; *Metagenomics/methods ; Biodiversity ; RNA, Ribosomal/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic approaches are used for eDNA-based community composition analysis. Simulation studies and careful evaluation of taxonomic classifiers are essential to establish reliable benchmarks to improve the accuracy and reproducibility of eDNA-based findings. Here we present a comprehensive evaluation of nine taxonomic classifiers exploring three widely used mitochondrial markers (12S rDNA, 16S rDNA and COI) in Australian marine vertebrates. Curated reference databases and exclusion database tests were used to simulate diverse species compositions, including three positive control and two negative control datasets. Using these simulated datasets ranging from 36 to 302 marker genes, we were able to identify between 19% and 89% of marine vertebrate species using mitochondrial markers. We show that MMSeqs2 and Metabuli generally outperform BLAST with 10% and 11% higher F1 scores for 12S and 16S rDNA markers, respectively, and that Naive Bayes Classifiers such as Mothur outperform sequence-based classifiers except MMSeqs2 for COI markers by 11%. Database exclusion tests reveal that MMSeqs2 and BLAST are less susceptible to false positives compared to Kraken2 with default parameters. Based on these findings, we recommend that MMSeqs2 is used for taxonomic classification of marine vertebrates given its ability to improve species-level assignments while reducing the number of false positives. Our work contributes to the establishment of best practices in eDNA-based biodiversity analysis to ultimately increase the reliability of this monitoring tool in the context of marine vertebrate conservation.},
}

Animals
*Vertebrates/classification/genetics
*Aquatic Organisms/classification/genetics
*DNA Barcoding, Taxonomic/methods
RNA, Ribosomal, 16S/genetics
*DNA, Environmental/genetics
Computational Biology/methods
Australia
*Metagenomics/methods
Biodiversity
RNA, Ribosomal/genetics

@article {pmid40081359,
year = {2025},
author = {Ali, MJ},
title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.},
journal = {Ophthalmic plastic and reconstructive surgery},
volume = {41},
number = {5},
pages = {584-588},
pmid = {40081359},
issn = {1537-2677},
mesh = {Humans ; Prospective Studies ; *Lacrimal Duct Obstruction/congenital/microbiology ; *Metagenomics/methods ; *Nasolacrimal Duct/microbiology ; Male ; Female ; *Bacteria/genetics/isolation & purification ; *Microbiota ; Dacryocystorhinostomy ; *Fungi/genetics/isolation & purification ; Child ; Child, Preschool ; *Metagenome ; Infant ; *Lacrimal Apparatus/microbiology ; },
abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).

METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from the patients with CNLDO who underwent endoscopic dacryocystorhinostomy at a tertiary care dacryology service. Immediately after a full-length lacrimal sac marsupialization, the samples were collected and transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina platform following DNA extraction and library preparation. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in the SqueezeMeta pipeline, and the functional annotation was performed using the MetaCerberus, v1.3.1.

RESULTS: The taxonomic hit distribution across the samples showed that bacteria were the most common isolates, followed by fungi and viruses. The major bacterial phyla identified across the samples of CNLDO were proteobacteria, firmicutes, actinobacteria, and bacteroidetes. The prevalent organisms include Haemophilus influenzae , Streptococcus pneumoniae , Stenotrophomonas maltophilia , Achromobacter xylosoxidans, Staphylococcus aureus , and Ochrobactrum anthropi , among others. The predominant fungal species identified include Botrytis cinerea , Aspergillus oryzae , and Fusarium fujikuroi . Several species of pandoravirus were the common viruses recognized.

CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.},
}

Humans
Prospective Studies
*Lacrimal Duct Obstruction/congenital/microbiology
*Metagenomics/methods
*Nasolacrimal Duct/microbiology
Male
Female
*Bacteria/genetics/isolation & purification
*Microbiota
Dacryocystorhinostomy
*Fungi/genetics/isolation & purification
Child
Child, Preschool
*Metagenome
Infant
*Lacrimal Apparatus/microbiology

@article {pmid40910796,
year = {2025},
author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R},
title = {The Earth Hologenome Initiative: Data Release 1.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação/ ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; },
abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.

RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.

CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}

Animals
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
Earth, Planet
*Vertebrates/genetics/microbiology
Databases, Genetic

@article {pmid40749888,
year = {2025},
author = {Carella, F and Correggia, M and Cordone, A and Iacovino, O and Maresca, F and Villari, G and Roque, A and Vico, G},
title = {Bald disease in a natural population of the purple sea urchin Paracentrotus lividus of the Mediterranean Sea: From spines to tissues.},
journal = {Journal of invertebrate pathology},
volume = {213},
number = {},
pages = {108415},
doi = {10.1016/j.jip.2025.108415},
pmid = {40749888},
issn = {1096-0805},
mesh = {Animals ; *Paracentrotus/microbiology ; Mediterranean Sea ; Microbiota ; },
abstract = {Recently, unusual mortality outbreaks have been reported in the echinoderm populations over broad geographic regions. The present work used different diagnostic approaches to unravel the Bald Sea Urchin Disease (BSUD) causes in a natural population of Paracentrotus lividus from the Gulf of Naples sampled in 2021. Symptomatic individuals displayed the typical signs such as test discoloration and ulceration, loss of spines and pedicellariae and visceral hyperpigmentation. Scanning electron microscopy of diseased individuals (stage 2 and stage 3) revealed a bare exoskeleton with multiplying bacteria penetrating the damaged test, and histopathology revealed inflammatory lesions and phagocytosis only in stages 2 and 3, with Gram negative and positive bacteria at stage 3. Metagenomics revealed an increase in DNA virus and Proteobacteria during disease progression. Microbial community analyses failed to reveal a single putative pathogen associated with symptoms, but microbiome analysis showed higher diversity in asymptomatic individuals compared to the symptomatic. Different Vibrio spp. belonging to the Splendidus clade were also isolated, with V. crassostreae as the most represented in advanced stages of disease. We cannot confirm that the observed microorganisms were associated with tissue damage and their contribution to the disease outcome remains unclear as they could be just opportunistic in the lesions. This preliminary study on a wild population highlights the importance of morphological analysis (histopathology and SEM) coupled with microbiome and metagenome analyses in sea urchin disease investigations. Moreover, we suggest also performing transmission electron microscopy (TEM), experimental challenges and in situ hybridization methods (ISH) to provide morphological evidence of potential infective agents. Future studies should also include histopathology of the test.},
}

Animals
*Paracentrotus/microbiology
Mediterranean Sea
Microbiota

@article {pmid40909338,
year = {2025},
author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA},
title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629901},
pmid = {40909338},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; HIV-1/drug effects ; },
abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).

METHODS: Data from fecal shotgun metagenomics, plasma metabolome, cognitive (standardized neuropsychological test score covering 6 cognitive domains, NPZ-6), functional (neuropsychiatric symptoms) and neuroimaging assessments were obtained and evaluated in 18 participants before and after RMD administration, and at the study end (post-MAP follow-up) in the BCN02 trial.

RESULTS: Participants with neurocognitive impairment (Lower vs. Higher NPZ-6 score group) were enriched in bacterial species, including Desulfovibrio desulfuricans, Sutterella wadsworthensis and Streptococcus thermophilus, and showed higher 1,2-propanediol degradation microbial pathway levels, before RMD administration. A multi-omics profiling showed significant and positive correlations between these microbial features and lipid-related metabolic pathways, previously linked to neurological disorders (i.e., sphingolipid, ether lipid, and glycerophospholipid metabolism), in participants with neurocognitive impairment, before RMD administration. Three indices (microbial-, metabolite-based and combined) obtained from the discriminant features were assessed longitudinally, showing progressive similarities between NPZ-6 score groups over time. Furthermore, the three indices and related discriminant features correlated negatively with functional outcomes, such as quality of life and daily functioning, and positively with depression, stress and CNS-related symptoms before RMD administration, while these associations became less discernible at the subsequent timepoints.

CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolome
*HIV Infections/drug therapy/complications/microbiology
Male
Female
*Brain/physiopathology/physiology
Adult
Biomarkers/blood
Middle Aged
Feces/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
HIV-1/drug effects

@article {pmid40908554,
year = {2025},
author = {Susilowati, A and Christita, M and Larekeng, SH and Lateef, AA and Ren, W and Azeez, AA and Simarmata, R and Khairina, Y and Khumairah, FH and Elfiati, D and Asiegbu, FO},
title = {Forest Type, Bark Wounding, and Tapping: Their Combined Influence on Bacteria Biota of Styrax Paralleloneurus in Natural and Community Forest.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70184},
doi = {10.1111/1758-2229.70184},
pmid = {40908554},
issn = {1758-2229},
support = {353365//Research Council of Finland/ ; 13/UN5.2.3.1/PPM/KP-WCU/2022//Universitas Sumatera Utara/ ; },
mesh = {*Forests ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Plant Bark/microbiology ; Biodiversity ; Indonesia ; Phylogeny ; *Trees/microbiology ; DNA, Bacterial/genetics ; *Biota ; },
abstract = {Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.},
}

*Forests
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Plant Bark/microbiology
Biodiversity
Indonesia
Phylogeny
*Trees/microbiology
DNA, Bacterial/genetics
*Biota

@article {pmid40816430,
year = {2025},
author = {Kong, Z and Wang, H and Man, S and Yan, Q},
title = {Magnetite modulates bacterial cooperation during cathodic nitrogen removal in bioelectrochemical systems under trace dissolved oxygen.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133147},
doi = {10.1016/j.biortech.2025.133147},
pmid = {40816430},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources/microbiology ; *Denitrification/drug effects ; Electrodes ; *Ferrosoferric Oxide/pharmacology ; Oxygen ; *Water Purification/methods ; Metagenome ; Ammonium Compounds/metabolism ; *Microbiota ; },
abstract = {Nitrate and ammonium co-contamination poses a major challenge for sustainable nitrogen removal, especially under microoxic conditions. This study investigated the effect of magnetite on microbial nitrogen metabolism and nitrite accumulation in biocathodes of bioelectrochemical systems under 0.25 mg/L dissolved oxygen. Magnetite improved total nitrogen removal by 22.8 %, reduced peak nitrite levels by 22.6 %, and lowered residual ammonium by 49.2 %. Magnetite promoted interspecies cooperation, driving modular specialization in nitrite reduction while suppressing dissimilatory nitrate reduction to ammonium. Concurrently, it stimulated ammonia-oxidizing bacteria activity, accelerating ammonium conversion and mitigating nitrite accumulation through enhanced denitrification. A cooperative microbial pattern emerged, with dominant species such as Hanamia sp. and Moheibacter sp. carrying out nitrite reduction, while less abundant species performed single nitrogen metabolic processes. This study highlights the role of magnetite in integrating aerobic and anaerobic nitrogen pathways, offering a sustainable strategy for controlling complex nitrogen pollution.},
}

*Bioelectric Energy Sources/microbiology
*Denitrification/drug effects
Electrodes
*Ferrosoferric Oxide/pharmacology
Oxygen
*Water Purification/methods
Metagenome
Ammonium Compounds/metabolism
*Microbiota

@article {pmid40763378,
year = {2025},
author = {Mollick, SA},
title = {Genetic sex prediction from human gut shotgun metagenomic data: An ethical appraisal.},
journal = {Forensic science international},
volume = {376},
number = {},
pages = {112585},
doi = {10.1016/j.forsciint.2025.112585},
pmid = {40763378},
issn = {1872-6283},
mesh = {Humans ; Male ; Female ; *Metagenomics ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; *Metagenome ; Sequence Analysis, DNA ; Chromosomes, Human, Y ; High-Throughput Nucleotide Sequencing ; Forensic Genetics ; },
abstract = {Human DNA inadvertently captured during gut shotgun metagenomic sequencing is typically treated as background contamination, yet it can reveal sensitive personal traits, raising ethical and forensic concerns. In this study, fecal metagenomes from 626 individuals were processed using four DNA extraction protocols and both paired and single-end sequencing, to evaluate the extent of identifiable human information. Host-derived reads exhibited uniform chromosomal coverage, enabling the accurate prediction of genetic sex based on the Y-to-X read-depth ratio. A machine learning model trained on this metric achieved over 92 % accuracy with the detection threshold (-β0/β1) = 0.34 across different protocols and sequencing configurations, demonstrating the method's robustness and general applicability. These findings highlight that even low levels of residual human DNA in microbiome datasets are sufficient to infer individual traits, such as sex, which can compromise participant anonymity. Given that such reads are often retained in public repositories, the risk of re-identification persists despite microbiome-focused study designs. This work serves as both a technical demonstration and an ethical imperative. Host-DNA masking should become standard before data sharing; ethics boards and data custodians must recognize the potential for unintentional disclosure; and informed consent procedures must reflect the realities of high-throughput sequencing. While the Y-to-X depth ratio offers a scalable quality control and forensic tool, its application must be balanced with rigorous privacy safeguards to uphold research integrity and participant trust.},
}

Humans
Male
Female
*Metagenomics
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/genetics
Machine Learning
*Metagenome
Sequence Analysis, DNA
Chromosomes, Human, Y
High-Throughput Nucleotide Sequencing
Forensic Genetics

@article {pmid40738886,
year = {2025},
author = {Wang, S and Zhang, Z and Zhao, J and Yang, K and Zhang, W and Wang, Z and Liang, Z and Zhang, Y and Zhang, Y and Liu, J and Zhang, L},
title = {Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea.},
journal = {Journal of proteome research},
volume = {24},
number = {9},
pages = {4780-4791},
doi = {10.1021/acs.jproteome.5c00551},
pmid = {40738886},
issn = {1535-3907},
mesh = {China ; *Proteomics/methods ; *Seawater/microbiology ; *Microbiota ; Energy Metabolism ; Metagenomics ; Metagenome ; Archaea/enzymology/genetics ; Oceans and Seas ; Bacteria/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Carbon Cycle ; },
abstract = {Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.},
}

China
*Proteomics/methods
*Seawater/microbiology
*Microbiota
Energy Metabolism
Metagenomics
Metagenome
Archaea/enzymology/genetics
Oceans and Seas
Bacteria/enzymology/genetics
*Bacterial Proteins/metabolism/genetics
Carbon Cycle

@article {pmid40738384,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Chen, Y and Chen, T and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Lactiplantibacillus plantarum strain 84-3-derived l-glutamine ameliorates glucose homeostasis via AMPK/PPARγ signaling pathway activation in type 2 diabetes.},
journal = {Metabolism: clinical and experimental},
volume = {172},
number = {},
pages = {156357},
doi = {10.1016/j.metabol.2025.156357},
pmid = {40738384},
issn = {1532-8600},
mesh = {*Glutamine/metabolism/pharmacology ; *Diabetes Mellitus, Type 2/metabolism ; Animals ; Rats ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Humans ; Male ; *AMP-Activated Protein Kinases/metabolism ; Case-Control Studies ; *PPAR gamma/metabolism ; *Lactobacillus plantarum/metabolism ; *Glucose/metabolism ; Gastrointestinal Microbiome ; Probiotics ; Diabetes Mellitus, Experimental/metabolism ; Blood Glucose/metabolism ; Rats, Sprague-Dawley ; Middle Aged ; Adult ; Female ; },
abstract = {BACKGROUND: Gut microbiota and their metabolites play an essential role in type 2 diabetes (T2D). However, contributions of individual bacterial strains and their metabolites to T2D pathogenesis remain poorly understood. We investigated T2D regulation by Lactobacillus in various animal models to understand its therapeutic effects.

METHODS AND RESULTS: We performed a case-control study of Chinese adults using metabolome profiling and identified an inverse correlation between l-glutamine and T2D serum concentrations. The glnA and GLUL genes encoding glutamine synthetase (GS) in L. plantarum 84-3 were also identified. L. plantarum 84-3 treatment significantly decreased serum inflammation and improved metabolic phenotypes in streptozotocin- or tetraoxypyrimidine-induced T2D rats, including blood glucose, glucose tolerance, insulin resistance, and lipids. We confirmed elevated serum l-glutamine levels in the L. plantarum 84-3 group. RNA sequencing analysis demonstrated that L. plantarum 84-3-derived l-glutamine is a vital bioactive molecule, improving glucose homeostasis by activating the liver AMPK/PPAR signaling pathway and ameliorating T2D. We conducted co-culture fermentation experiments in vitro and in vivo, and metagenomic and metabolomic analyses revealed that resistance starch combined with L. plantarum 84-3 significantly enriched of Lactobacillus abundance and increased the l-glutamine level, affecting of alanine, aspartate, and glutamate metabolism pathways, which was confirmed in vivo in rats. The reduced L. plantarum and l-glutamine levels were validated in a human T2D cohort.

CONCLUSIONS: These findings revealed a novel therapeutic effect of L. plantarum in alleviating T2D-related glucose homeostasis by increasing circulating l-glutamine, which suggests viable preventive and therapeutic strategies for metabolic disorders.},
}

*Glutamine/metabolism/pharmacology
*Diabetes Mellitus, Type 2/metabolism
Animals
Rats
Homeostasis/drug effects
Signal Transduction/drug effects
Humans
Male
*AMP-Activated Protein Kinases/metabolism
Case-Control Studies
*PPAR gamma/metabolism
*Lactobacillus plantarum/metabolism
*Glucose/metabolism
Gastrointestinal Microbiome
Probiotics
Diabetes Mellitus, Experimental/metabolism
Blood Glucose/metabolism
Rats, Sprague-Dawley
Middle Aged
Adult
Female

@article {pmid40645526,
year = {2025},
author = {Xu, J and Zhang, Y and Wang, X and Xu, W and Chen, S and Pan, L and Gao, J},
title = {A P2X7 receptor antagonist alleviates PTSD-like behaviors in adolescent rats through gut microbiota modulation and hippocampal transcriptomic remodeling.},
journal = {Journal of affective disorders},
volume = {390},
number = {},
pages = {119859},
doi = {10.1016/j.jad.2025.119859},
pmid = {40645526},
issn = {1573-2517},
mesh = {Animals ; *Stress Disorders, Post-Traumatic/drug therapy/microbiology/genetics ; *Gastrointestinal Microbiome/drug effects ; *Hippocampus/drug effects/metabolism ; Rats ; Male ; *Transcriptome/drug effects ; *Purinergic P2X Receptor Antagonists/pharmacology ; Rats, Sprague-Dawley ; Disease Models, Animal ; Behavior, Animal/drug effects ; Receptors, Purinergic P2X7 ; *Rosaniline Dyes/pharmacology ; Dysbiosis/drug therapy ; },
abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric disorder that frequently manifests during adolescence, a critical neurodevelopmental period. Although the P2X7 receptor is implicated in the pathophysiology of PTSD, its role in adolescent-onset PTSD, particularly concerning gut microbiota dysbiosis and hippocampal transcriptomic alterations, remains unclear. This study investigated the effects of the P2X7 receptor antagonist Brilliant Blue G (BBG) on PTSD-like behaviors, gut microbiota, and hippocampal transcriptomic profiles in adolescent rats subjected to single prolonged stress and electric foot shock (SPS&S). BBG treatment significantly ameliorated SPS&S-induced fear- and anxiety-like behaviors and spatial working memory deficits. Metagenomic analysis revealed that BBG partially reversed SPS&S-induced gut microbiota dysbiosis, significantly enriching key bacterial taxa (e.g., Bacteroidota) and modulating functional pathways related to immunity and metabolism. Hippocampal transcriptomic analysis demonstrated that BBG normalized a majority of SPS&S-induced differentially expressed genes; these corrected genes were significantly enriched in pathways for extracellular matrix organization, neural differentiation, and PI3K-Akt signaling pathway. Integrated multi-omics correlation analyses revealed significant correlations among key microbial abundances, hippocampal gene expression, and behavioral outcomes, supporting a gut-brain axis mechanism underlying the therapeutic effects of BBG. These findings position the P2X7 receptor as a promising therapeutic target for adolescent PTSD and highlight the crucial role of gut microbiota in modulating stress-related neuropathology via the gut-brain axis.},
}

Animals
*Stress Disorders, Post-Traumatic/drug therapy/microbiology/genetics
*Gastrointestinal Microbiome/drug effects
*Hippocampus/drug effects/metabolism
Rats
Male
*Transcriptome/drug effects
*Purinergic P2X Receptor Antagonists/pharmacology
Rats, Sprague-Dawley
Disease Models, Animal
Behavior, Animal/drug effects
Receptors, Purinergic P2X7
*Rosaniline Dyes/pharmacology
Dysbiosis/drug therapy

@article {pmid40908508,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J},
title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70173},
doi = {10.1111/1462-2920.70173},
pmid = {40908508},
issn = {1462-2920},
support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; },
abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.},
}

@article {pmid40904108,
year = {2025},
author = {Meaden, S and Westra, ER and Fineran, PC},
title = {Phage defence-system abundances vary across environments and increase with viral density.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240069},
pmid = {40904108},
issn = {1471-2970},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //James Cook Research Fellowship (RSNZ, Te Apārangi)/ ; //Philip Leverhulme/ ; //Bioprotection Aotearoa (Tertiary Education Commission, NZ)/ ; //UK Horizon Funding Guarantee/ ; },
mesh = {*Bacteriophages/physiology ; *Bacteria/virology/immunology ; *Microbiota ; *Metagenome ; *Virome ; },
abstract = {The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence-system ecology.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}

*Bacteriophages/physiology
*Bacteria/virology/immunology
*Microbiota
*Metagenome
*Virome

@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, J and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.},
journal = {Molecular biology and evolution},
volume = {42},
number = {9},
pages = {},
pmid = {40856172},
issn = {1537-1719},
mesh = {Animals ; *Geologic Sediments/chemistry ; Humans ; *Bone and Bones/chemistry ; Rats ; *DNA, Ancient/analysis ; Archaeology ; Metagenomics ; Fossils ; Gastrointestinal Microbiome/genetics ; },
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.},
}

Animals
*Geologic Sediments/chemistry
Humans
*Bone and Bones/chemistry
Rats
*DNA, Ancient/analysis
Archaeology
Metagenomics
Fossils
Gastrointestinal Microbiome/genetics

@article {pmid40848630,
year = {2025},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111399},
doi = {10.1016/j.ijfoodmicro.2025.111399},
pmid = {40848630},
issn = {1879-3460},
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Biogenic Amines/metabolism/analysis ; *Zygosaccharomyces/metabolism ; Temperature ; *Flavoring Agents/metabolism ; Food Microbiology ; Taste ; *Microbial Interactions ; Bacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; Amino Acids/metabolism ; Odorants/analysis ; Saccharomycetales ; },
abstract = {This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.},
}

Fermentation
*Soy Foods/microbiology/analysis
*Biogenic Amines/metabolism/analysis
*Zygosaccharomyces/metabolism
Temperature
*Flavoring Agents/metabolism
Food Microbiology
Taste
*Microbial Interactions
Bacteria/metabolism/genetics/classification/isolation & purification
Microbiota
Amino Acids/metabolism
Odorants/analysis
Saccharomycetales

@article {pmid40840192,
year = {2025},
author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH},
title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111392},
doi = {10.1016/j.ijfoodmicro.2025.111392},
pmid = {40840192},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; Fermentation ; *Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Bacteria/metabolism/genetics/classification/isolation & purification ; Humans ; Temperature ; Metagenomics ; Metabolic Networks and Pathways ; Edible Grain/microbiology/chemistry ; Taste ; Multiomics ; },
abstract = {Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.},
}

*Volatile Organic Compounds/analysis/metabolism/chemistry
Fermentation
*Odorants/analysis
Gas Chromatography-Mass Spectrometry
Microbiota
Bacteria/metabolism/genetics/classification/isolation & purification
Humans
Temperature
Metagenomics
Metabolic Networks and Pathways
Edible Grain/microbiology/chemistry
Taste
Multiomics

@article {pmid40780971,
year = {2025},
author = {Boulanger, N},
title = {Tick and host microbiotas: immunomodulators in tick-borne diseases?.},
journal = {Trends in parasitology},
volume = {41},
number = {9},
pages = {796-805},
doi = {10.1016/j.pt.2025.07.009},
pmid = {40780971},
issn = {1471-5007},
mesh = {Animals ; *Tick-Borne Diseases/microbiology/immunology/prevention & control ; *Microbiota/immunology ; *Ticks/microbiology/immunology ; Humans ; },
abstract = {Vector-borne diseases have a growing impact on human and animal health. Metagenomics has been largely used to characterize the microbiome and has highlighted the key role of the microbiota in modulating the vector competence of insects. Currently, an integrated approach combining vector control, vaccine prevention, and drug treatment is being developed to limit the transmission of insect-borne pathogens. This is more complex for tick-associated diseases, considering the biology of the tick and the possibility of modifications of its microbiota in vector control. Conversely, because the skin is an essential interface in tick-borne diseases, an in-depth study of the precise role of the tick and host microbiota during tick bite and pathogen inoculation opens up new prospects for controlling these diseases.},
}

Animals
*Tick-Borne Diseases/microbiology/immunology/prevention & control
*Microbiota/immunology
*Ticks/microbiology/immunology
Humans

@article {pmid40735808,
year = {2025},
author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET},
title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).},
journal = {Diabetes, obesity & metabolism},
volume = {27},
number = {10},
pages = {5444-5454},
doi = {10.1111/dom.16578},
pmid = {40735808},
issn = {1463-1326},
support = {P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/physiology ; Longitudinal Studies ; Cross-Sectional Studies ; *Insulin Resistance/physiology ; *Menopause/physiology/metabolism ; Homeostasis/physiology ; *Insulin/metabolism/blood ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; Glucose Tolerance Test ; },
abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.

MATERIALS AND METHODS: Baseline data (n = 175 women) from the Microbiome and Insulin Longitudinal Evaluation Study (MILES) were used, including insulin and dysglycaemia indices calculated from a 2-h oral glucose tolerance test, untargeted peripheral metabolomics, targeted peripheral short chain fatty-acid levels and faecal bacterial microbiota surveyed by whole-metagenomic sequencing.

RESULTS: After adjustment for covariates, menopause age <50 years and use of hormone replacement therapy (HRT) were associated with lower Matsuda et al. insulin sensitivity index levels (β = -0.232, confidence interval (CI) = [-0.450, -0.014] and β = -0.275, CI = [-0.444, -0.107], respectively) but not pre-menopausal gynaecologic surgery. Pre-menopausal gynaecologic surgery was significantly associated with faecal microbiota beta diversity driven by a relative increase in diabetogenic Ruminococcus gnavus and Clostridium species and a decrease in protective Alistipes species and Akkermansia muciniphila relative abundances. A reduction in two glycerophospholipids in the plasmalogen class significantly statistically mediated an inverse association between gynaecologic surgery before menopause and insulin sensitivity.

CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.},
}

Humans
Female
Middle Aged
*Gastrointestinal Microbiome/physiology
Longitudinal Studies
Cross-Sectional Studies
*Insulin Resistance/physiology
*Menopause/physiology/metabolism
Homeostasis/physiology
*Insulin/metabolism/blood
*Dysbiosis/microbiology/metabolism
Adult
Feces/microbiology
Glucose Tolerance Test

@article {pmid40619005,
year = {2025},
author = {Hullar, MA and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW},
title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.},
journal = {The American journal of clinical nutrition},
volume = {122},
number = {3},
pages = {780-792},
doi = {10.1016/j.ajcnut.2025.06.026},
pmid = {40619005},
issn = {1938-3207},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Cross-Over Studies ; Female ; Adult ; *Glycemic Load ; *Diet ; Feces/microbiology ; *Bacteria/classification/genetics/metabolism ; Young Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Dietary patterns characterized by low glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.

OBJECTIVES: Evaluate the effects of a low glycemic load (LGL) compared with a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.

METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n = 69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.

RESULTS: Overall community structure measured by alpha and beta diversity was not significantly different across the diets, although diet did significantly increase the abundance of 13 of 161 genera (Padj < 0.05) and 5 species in the LGL diet and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (β = -1.15; SE = 0.24; 95% confidence interval [CI]: -1.63, -0.67; Padj = 0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (β = 0.20; SE = 0.05; 95% CI: 0.09, 0.30; Padj = 0.03) was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, P < 0.001). CAZymes enriched in the HGL diet reflected dietary additives, whereas CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between homeostasis model assessment of insulin resistance (HOMA-IR) and the coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (Padj = 0.035), which was positive in the HGL diet (b = 0.20; SE = 0.09; 95% CI: 0.02, 0.39) and negative in the LGL diet (β = -0.23; SE = 0.09; 95% CI: -0.40, -0.06).

CONCLUSIONS: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}