@article {pmid40302838,
year = {2025},
author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL},
title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.},
journal = {Access microbiology},
volume = {7},
number = {4},
pages = {},
pmid = {40302838},
issn = {2516-8290},
abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.},
}

@article {pmid40295121,
year = {2025},
author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ},
title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {5},
pages = {},
doi = {10.1093/femsec/fiaf041},
pmid = {40295121},
issn = {1574-6941},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //University of Calgary/ ; },
mesh = {*Nitrates/metabolism ; *Ponds/microbiology/chemistry ; *Oil and Gas Fields/microbiology ; Sulfates/metabolism ; *Bacteria/metabolism/genetics/classification ; *Water Microbiology ; Oxidation-Reduction ; Sulfides/metabolism ; Nitrites/metabolism ; Microbiota ; },
abstract = {Nitrate addition for mitigating sulfide production in oil field systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and reuse associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, and Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.},
}

*Nitrates/metabolism
*Ponds/microbiology/chemistry
*Oil and Gas Fields/microbiology
Sulfates/metabolism
*Bacteria/metabolism/genetics/classification
*Water Microbiology
Oxidation-Reduction
Sulfides/metabolism
Nitrites/metabolism
Microbiota

@article {pmid40209382,
year = {2025},
author = {Su, C and Kang, J and Liu, S and Li, C},
title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144192},
doi = {10.1016/j.foodchem.2025.144192},
pmid = {40209382},
issn = {1873-7072},
mesh = {*Morinda/microbiology/chemistry/growth & development/metabolism ; *Fruit/microbiology/chemistry/growth & development/metabolism ; *Fruit and Vegetable Juices/analysis/microbiology ; *Microbiota ; Fermentation ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Volatile Organic Compounds/metabolism/chemistry ; Taste ; },
abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.},
}

*Morinda/microbiology/chemistry/growth & development/metabolism
*Fruit/microbiology/chemistry/growth & development/metabolism
*Fruit and Vegetable Juices/analysis/microbiology
*Microbiota
Fermentation
*Flavoring Agents/metabolism/chemistry
*Bacteria/classification/genetics/isolation & purification/metabolism
Volatile Organic Compounds/metabolism/chemistry
Taste

@article {pmid40209373,
year = {2025},
author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J},
title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144178},
doi = {10.1016/j.foodchem.2025.144178},
pmid = {40209373},
issn = {1873-7072},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Stichopus/metabolism/microbiology/chemistry ; *Sea Cucumbers/metabolism/microbiology ; Polysaccharides/metabolism/analysis ; Collagen/metabolism ; },
abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.},
}

Animals
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/metabolism/isolation & purification
*Stichopus/metabolism/microbiology/chemistry
*Sea Cucumbers/metabolism/microbiology
Polysaccharides/metabolism/analysis
Collagen/metabolism

@article {pmid39919372,
year = {2025},
author = {Swain, S and Sahoo, P and Biswal, S and Sethy, K and Panda, AN and Sahoo, N},
title = {Fecal bacterial microbiota diversity characterized for dogs with atopic dermatitis: its alteration and clinical recovery after meat-exclusion diet.},
journal = {American journal of veterinary research},
volume = {86},
number = {5},
pages = {},
doi = {10.2460/ajvr.24.09.0274},
pmid = {39919372},
issn = {1943-5681},
mesh = {Animals ; *Dermatitis, Atopic/veterinary/microbiology/diet therapy ; Dogs ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; *Dog Diseases/microbiology/diet therapy ; Animal Feed/analysis ; Female ; Meat ; Male ; RNA, Ribosomal, 16S ; Bacteria/classification/isolation & purification ; India ; },
abstract = {OBJECTIVE: To achieve clinical recovery in canine atopic dermatitis affected pet dogs via alteration of the gut microbiome, following a meat and egg exclusion diet for 60 days.

METHODS: 24 atopic dermatitis-affected pet dogs, all fed poultry meat and egg, and another 48 apparently healthy controls fed both poultry meat and egg (n = 24) or vegetable diet (24) were included in the study. The study was undertaken in the Bhubaneswar Smart City, Odisha, India, from July to December 2023. Fecal samples were collected at 2 points for DNA analysis, ie, on day 0 and day 60 of the change from a meat/egg-based diet to a vegetable-based diet. Extracted DNA samples were pooled category-wise and subjected to the gut microbiome analysis in the Nanopore sequencer targeting the 16S rRNA gene. Burrows-Wheeler Transform, Ferragina-Manzini index, and Krona charts were used for taxonomical classification and visualization of relative abundances of bacterial species within the metagenome. Alpha- and beta-diversity analyses were performed.

RESULTS: Atopic pets at day 0 showed elevation in the gut microbiome population with an adequate concentration of pathogens like Escherichia coli and Clostridiodes difficile with lower amounts of the beneficial bacteria like Lactobacillus sp, while the pets at 60 days after dietary intervention showed a significant decline in bacterial species like E coli and C difficile with higher amount of Lactobacillus sp. Both control groups showed variations of microbiome between them as well as from the atopic pets.

CONCLUSIONS: We found a close association of poultry meat/egg diet with gut microbiome population and atopic symptoms as well in dogs, and elimination of such diet could be helpful in clinical recovery.

CLINICAL RELEVANCE: Dietary intervention with the exclusion of potential allergens from poultry meat and egg sources can be an effective approach for the management of canine atopic dermatitis.},
}

Animals
*Dermatitis, Atopic/veterinary/microbiology/diet therapy
Dogs
*Feces/microbiology
*Gastrointestinal Microbiome
*Diet/veterinary
*Dog Diseases/microbiology/diet therapy
Animal Feed/analysis
Female
Meat
Male
RNA, Ribosomal, 16S
Bacteria/classification/isolation & purification
India

@article {pmid39838455,
year = {2025},
author = {Liao, H and Li, J and Wang, YZ and Li, H and An, XL and Wang, T and Chang, RY and Zhu, YG and Su, JQ},
title = {Evolutionary diversification and succession of soil huge phages in glacier foreland.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {18},
pmid = {39838455},
issn = {2049-2618},
support = {4237070301//National Natural Science Foundation of China/ ; 42161134002//National Natural Science Foundation of China/ ; STEP, 2021QZKK0103//Second Tibetan Plateau Scientific Expedition and Research Program/ ; },
mesh = {*Bacteriophages/genetics/classification/isolation & purification ; *Soil Microbiology ; Phylogeny ; *Ice Cover/virology/microbiology ; Metagenomics/methods ; Tibet ; Genome, Viral ; Biodiversity ; Evolution, Molecular ; Soil ; },
abstract = {BACKGROUND: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.

RESULTS: Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.

CONCLUSIONS: Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.},
}

*Bacteriophages/genetics/classification/isolation & purification
*Soil Microbiology
Phylogeny
*Ice Cover/virology/microbiology
Metagenomics/methods
Tibet
Genome, Viral
Biodiversity
Evolution, Molecular
Soil

@article {pmid40301729,
year = {2025},
author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S},
title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {39},
pmid = {40301729},
issn = {2730-7182},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.

RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200 m, with a slight increase observed above 1400 m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.

CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.},
}

Bees/microbiology
Animals
*Gastrointestinal Microbiome
India
RNA, Ribosomal, 16S/genetics/analysis
*Altitude
*Bacteria/classification/genetics/isolation & purification

@article {pmid40301728,
year = {2025},
author = {Munoz Briones, J and Brubaker, DK},
title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {115},
pmid = {40301728},
issn = {1471-2105},
support = {2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; },
mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; },
abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.

RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.

CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.},
}

Humans
*Microbiota
*Metabolomics/methods
Gastrointestinal Microbiome
Metagenomics/methods
*Computational Biology/methods
Principal Component Analysis
Crohn Disease/microbiology
Multiomics

@article {pmid40301726,
year = {2025},
author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J},
title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {258},
pmid = {40301726},
issn = {1471-2180},
support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; },
mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.},
}

Humans
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification/growth & development
*Metagenomics/methods
*Gastrointestinal Microbiome
Culture Media/chemistry
*Biodiversity
*Bacteriological Techniques/methods
Sequence Analysis, DNA
DNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid40298543,
year = {2025},
author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E},
title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {40298543},
issn = {2079-6382},
support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie & Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; },
abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.},
}

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

*Metagenomics/methods
Computational Biology/methods
*Software
*Gene Expression Profiling/methods
*Microbiota
Data Collection
Quality Control
Workflow
RNA, Untranslated
Molecular Sequence Annotation
Rhizosphere
Automation

@article {pmid40250228,
year = {2025},
author = {Wang, H and Yang, Q and Wang, S},
title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179427},
doi = {10.1016/j.scitotenv.2025.179427},
pmid = {40250228},
issn = {1879-1026},
mesh = {*Triticum/growth & development ; *Soil Microbiology ; Soil/chemistry ; *Agriculture/methods ; Phosphorus/analysis ; Nitrogen/analysis ; Metagenomics ; Microbiota ; Carbon/analysis ; Nitrogen Cycle ; },
abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.},
}

*Triticum/growth & development
*Soil Microbiology
Soil/chemistry
*Agriculture/methods
Phosphorus/analysis
Nitrogen/analysis
Metagenomics
Microbiota
Carbon/analysis
Nitrogen Cycle

@article {pmid40098591,
year = {2025},
author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J},
title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.},
journal = {HIV medicine},
volume = {26},
number = {5},
pages = {785-799},
doi = {10.1111/hiv.70014},
pmid = {40098591},
issn = {1468-1293},
support = {2022218//Universidad Antonio Nariño/ ; },
mesh = {Humans ; Male ; Adult ; *Homosexuality, Male ; Metagenomics ; *HIV Infections/microbiology ; *Anal Canal/microbiology ; Middle Aged ; *Rectum/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; },
abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.

MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.

RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200 ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p = 0.45) and beta diversity (PERMANOVA R = -0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.

CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.},
}

Humans
Male
Adult
*Homosexuality, Male
Metagenomics
*HIV Infections/microbiology
*Anal Canal/microbiology
Middle Aged
*Rectum/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome

@article {pmid39823337,
year = {2025},
author = {Wu, D and Seshadri, R and Kyrpides, NC and Ivanova, NN},
title = {A metagenomic perspective on the microbial prokaryotic genome census.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2166},
pmid = {39823337},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; Phylogeny ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Metagenome ; *Genome, Bacterial ; *Genome, Archaeal ; Humans ; Biodiversity ; },
abstract = {Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.},
}

*Metagenomics/methods
Phylogeny
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Metagenome
*Genome, Bacterial
*Genome, Archaeal
Humans
Biodiversity

@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology
Male
*Microbiota
*Gastrointestinal Microbiome
Tumor Microenvironment/immunology
Animals

@article {pmid40297587,
year = {2025},
author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z},
title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1543817},
pmid = {40297587},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.

METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (≤6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.

RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).

CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology
Male
Female
*Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology
Middle Aged
*Proteomics/methods
Aged
Immunotherapy/methods
Treatment Outcome
*Proteome
Biomarkers, Tumor/urine
Gastrointestinal Microbiome
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}

*Plant Leaves/metabolism/microbiology
*Bacteria/genetics/metabolism
*Fungi/genetics/metabolism
*Rivers/microbiology
Ecosystem
Alnus
Transcriptome
RNA, Ribosomal, 16S/genetics

@article {pmid40297464,
year = {2025},
author = {Zhang, Y and Ding, G and Gao, Y and Li, Y and Zhou, P and Wu, L and Zhou, M and Wang, J and Tang, J},
title = {Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19384},
pmid = {40297464},
issn = {2167-8359},
mesh = {*Lakes/microbiology/chemistry ; China ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: Chaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.

METHODS: To solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.

RESULTS: Our findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (-0.1975), and NH3-N (-0.0952).

CONCLUSIONS: These findings provide valuable insights into the distribution and influencing factors of ARGs in lakes.},
}

*Lakes/microbiology/chemistry
China
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Genes, Bacterial
Microbiota/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40296156,
year = {2025},
author = {Fan, Y and Wang, D and Yang, JX and Ning, D and He, Z and Zhang, P and Rocha, AM and Xiao, N and Michael, JP and Walker, KF and Joyner, DC and Pan, C and Adams, MWW and Fields, MW and Alm, EJ and Stahl, DA and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J},
title = {Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {106},
pmid = {40296156},
issn = {2049-2618},
support = {DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; },
mesh = {*Groundwater/microbiology/chemistry ; Phylogeny ; *Microbiota/genetics ; Tennessee ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Nitrates/analysis ; Water Pollutants, Chemical/analysis ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; },
abstract = {BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).

RESULTS: Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.

CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.},
}

*Groundwater/microbiology/chemistry
Phylogeny
*Microbiota/genetics
Tennessee
*Bacteria/classification/genetics/isolation & purification/metabolism
Nitrates/analysis
Water Pollutants, Chemical/analysis
Biodiversity
RNA, Ribosomal, 16S/genetics
Metals, Heavy/analysis

@article {pmid40197113,
year = {2025},
author = {Karabekmez, ME},
title = {Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications.},
journal = {Omics : a journal of integrative biology},
volume = {29},
number = {5},
pages = {179-182},
doi = {10.1089/omi.2025.0024},
pmid = {40197113},
issn = {1557-8100},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; Proteomics/methods ; Precision Medicine ; High-Throughput Nucleotide Sequencing ; Multiomics ; },
abstract = {Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.},
}

Humans
*Metagenomics/methods
*Microbiota
Proteomics/methods
Precision Medicine
High-Throughput Nucleotide Sequencing
Multiomics

@article {pmid40293591,
year = {2025},
author = {Orlova, EA and Sinkov, VV and Ogarkov, OB and Suzdalnitsky, AE and Kondratov, IG and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI},
title = {Metagenomic Analysis of Caseum of Tuberculosis Foci.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {40293591},
issn = {1573-8221},
abstract = {The microbiota of the deep lung regions significantly differs from that of the upper respiratory tract by much lower biomass and dynamic diversity. In our previous studies we found that the biodiversity of the satellite microbiota of tuberculosis foci is sharply reduced in comparison with intact lung tissues. These findings allowed us to classify microbial communities in the caseous necrosis of tuberculomas into two types: (i) mycobacterial caseoma (tuberculoma), where 70% or more of the genomes correspond to Mycobacterium tuberculosis, and (ii) a polymicrobial community, where the concentration of M. tuberculosis varies from 0 to 10%. Using shotgun metagenomic sequencing, 14 tuberculomas from 13 patients were analyzed on a NextSeq 550 platform (Illumina). Taxonomic classification of short reads was performed using Kraken 2. The results show that, on average, 99.95% of the short reads belonged to human DNA or were unclassified. However, the classified reads related to bacterial genomes confirmed the concept that in many cases, tuberculomas contained polymicrobial communities that either replaced or supplemented the original mycobacterial microbiota of the caseous material.},
}

@article {pmid40289251,
year = {2025},
author = {Slager, J and Simpson, HL and Gacesa, R and Chen, L and Tan, IL and Gelderloos, J and Maatman, A and Wijmenga, C and Zhernakova, A and Fu, J and Weersma, RK and Gonera, G and Jonkers, IH and Withoff, S},
title = {High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489071},
pmid = {40289251},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/diet therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Middle Aged ; Adult ; Netherlands ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; },
abstract = {BACKGROUND: Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterized by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.

METHODS: To address these limitations, we analyzed fecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analyzed in tCeD patients and controls.

RESULTS: Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.

CONCLUSION: Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role in intestinal health and disease.},
}

Humans
*Celiac Disease/microbiology/diet therapy
*Gastrointestinal Microbiome/genetics
Male
Female
Feces/microbiology
Middle Aged
Adult
Netherlands
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Aged

@article {pmid40154057,
year = {2025},
author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y},
title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.},
journal = {Food chemistry},
volume = {481},
number = {},
pages = {143980},
doi = {10.1016/j.foodchem.2025.143980},
pmid = {40154057},
issn = {1873-7072},
mesh = {Fermentation ; *Microbiota ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolomics ; },
abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.},
}

Fermentation
*Microbiota
*Bacteria/metabolism/genetics/classification/isolation & purification
Metabolomics

@article {pmid39528106,
year = {2025},
author = {Nyawo, G and Naidoo, CC and Wu, BG and Kwok, B and Clemente, JC and Li, Y and Minnies, S and Reeve, B and Moodley, S and John, TJ and Karamchand, S and Singh, S and Pecararo, A and Doubell, A and Kyriakakis, C and Warren, R and Segal, LN and Theron, G},
title = {Bad company? The pericardium microbiome in people investigated for tuberculous pericarditis in an HIV-prevalent setting.},
journal = {Microbes and infection},
volume = {27},
number = {3},
pages = {105434},
doi = {10.1016/j.micinf.2024.105434},
pmid = {39528106},
issn = {1769-714X},
mesh = {Humans ; *HIV Infections/complications/microbiology/epidemiology/drug therapy ; Female ; Male ; Cross-Sectional Studies ; *Pericarditis, Tuberculous/microbiology ; *Pericardium/microbiology ; Middle Aged ; Adult ; *Microbiota ; C-Reactive Protein/analysis ; *Pericardial Fluid/microbiology ; Bacteria/classification/genetics/isolation & purification ; Prevalence ; Aged ; },
abstract = {BACKGROUND: The site-of-disease microbiome and predicted metagenome were evaluated in a cross-sectional study involving people with presumptive tuberculous pericarditis. We also explored the interaction between C-reactive protein (CRP) and the microbiome.

METHODS: People with effusions requiring diagnostic pericardiocentesis (n=139) provided pericardial fluid for sequencing and blood for CRP measurement.

RESULTS: Pericardial fluid microbiota differed in β-diversity among people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis. dTBs were Mycobacterium-, Lacticigenium-, and Kocuria-enriched vs. nTBs. HIV-positive dTBs were Mycobacterium-, Bifidobacterium-, Methylobacterium-, and Leptothrix-enriched vs. HIV-negative dTBs. HIV-positive dTBs on ART were Mycobacterium- and Bifidobacterium-depleted vs. those not on ART. dTBs exhibited enrichment in short-chain fatty acid (SCFA) and mycobacterial metabolism pathways vs. nTBs. Additional non-pericardial involvement (pulmonary infiltrates) was associated with Mycobacterium-enrichment and Streptococcus-depletion. Mycobacterium reads were in 34 % (31/91) of dTBs, 8 % (2/25) of pTBs and 17 % (4/23) nTBs. People with CRP above (vs. below) the median value had different β-diversity (Pseudomonas-depleted). No correlation was found between enriched taxa in dTBs and CRP.

CONCLUSIONS: Pericardial fluid microbial composition varies by tuberculosis status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance, including mycobacterial reads in nTBs and pTBs, requires evaluation.},
}

Humans
*HIV Infections/complications/microbiology/epidemiology/drug therapy
Female
Male
Cross-Sectional Studies
*Pericarditis, Tuberculous/microbiology
*Pericardium/microbiology
Middle Aged
Adult
*Microbiota
C-Reactive Protein/analysis
*Pericardial Fluid/microbiology
Bacteria/classification/genetics/isolation & purification
Prevalence
Aged

@article {pmid39428055,
year = {2025},
author = {Hazra, D and Chawla, K and S M, F and Sintchenko, V and Magazine, R and Martinez, E and Pandey, A},
title = {The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis.},
journal = {Microbes and infection},
volume = {27},
number = {3},
pages = {105432},
doi = {10.1016/j.micinf.2024.105432},
pmid = {39428055},
issn = {1769-714X},
mesh = {Humans ; *Microbiota/drug effects ; *Tuberculosis, Pulmonary/drug therapy/microbiology ; Sputum/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; Adult ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Antitubercular Agents/therapeutic use ; *Respiratory System/microbiology ; Dysbiosis/microbiology ; DNA, Bacterial/genetics ; },
abstract = {The growing evidence has underscored the significance of interactions between the host and microbiota in respiratory health, presenting a novel perspective on disease management. Yet, comprehension of the respiratory microbiome shifts before and after anti-tuberculosis treatment is limited. This study compares respiratory microbiome profiles in untreated tuberculosis (UTB) and completed TB treatment (CTB) cases with healthy controls, using 16S rRNA sequencing on sputum samples. Significant reduction in sputum microbial alpha diversity was observed in both TB groups when compared to healthy controls (P < 0.05). Beta diversity analysis showed distinct clustering (P < 0.05). Linear discriminant analysis revealed an abundance of potentially pathogenic bacterial genera like Haemophilus, Pseudomonas, and Mycobacterium in the UTB group, while Streptococcus, Rothia, and Neisseria dominated in CTB samples. Healthy sputum microbiomes were enriched with Prevotella, Fusobacterium, Porphyromonadaceae_unclassified,andPeptostreptococcus. Moreover, predicted bacterial functional pathways showed significant differences among the three groups, mainly related to nutrient metabolism. These findings indicated significant microbial dysbiosis in sputum samples recovered from patients with pulmonary TB with an elevated presence of potentially pathogenic bacteria, depletion of beneficial genera, and downregulation of several essential metabolic pathways. Further exploration of respiratory microbiome-based diagnostic biomarkers and their role in targeted treatment strategies in tuberculosis is warranted.},
}

Humans
*Microbiota/drug effects
*Tuberculosis, Pulmonary/drug therapy/microbiology
Sputum/microbiology
RNA, Ribosomal, 16S/genetics
Male
Female
Adult
Middle Aged
*Bacteria/classification/genetics/isolation & purification/drug effects
*Antitubercular Agents/therapeutic use
*Respiratory System/microbiology
Dysbiosis/microbiology
DNA, Bacterial/genetics

@article {pmid40289152,
year = {2025},
author = {Jarrige, D and Tardy, V and Loux, V and Rué, O and Chabbi, A and Terrat, S and Maron, PA},
title = {Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14723},
pmid = {40289152},
issn = {2045-2322},
support = {ANR-20-PAMR-0004//Agence Nationale de la Recherche/ ; },
mesh = {*Soil Microbiology ; *Triticum ; *Metagenomics/methods ; *Microbiota/genetics ; *Grassland ; Bacteria/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; },
abstract = {Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions. Metagenomics allows studying taxa that are often overlooked in microbiota studies, such as protists or viruses. Here, we employed metagenomics to characterise microbial successions after wheat straw input in a 4-month in-situ field study. We compared microbial successions patterns with those obtained by high throughput amplicon sequencing on the same soil samples to validate metagenomics as a tool for the fine analysis of microbial population dynamics in situ. Taxonomic patterns were concordant between the two methodologies but metagenomics allowed studying all the microbial groups simultaneously. Notably, our results evidenced that each domain displayed a specific dynamic pattern after wheat straw amendment. For instance, viral sequences multiplied in the early phase of straw decomposition, in parallel to copiotrophic bacteria, suggesting a "kill-the-winner" pattern that, to our knowledge, had not been observed before in soil. Altogether, our results highlighted that both inter and intra-domain trophic interactions were impacted by wheat amendment and these patterns depended on the land use history. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.},
}

*Soil Microbiology
*Triticum
*Metagenomics/methods
*Microbiota/genetics
*Grassland
Bacteria/genetics/classification
Soil/chemistry
Crops, Agricultural
High-Throughput Nucleotide Sequencing

@article {pmid40289138,
year = {2025},
author = {Weathers, SP and Li, X and Zhu, H and Damania, AV and Knafl, M and McKinley, B and Lin, H and Harrison, RA and Majd, NK and O'Brien, BJ and Penas-Prado, M and Loghin, M and Kamiya-Matsuoka, C and Yung, WKA and Solis Soto, LM and Maru, DM and Wistuba, I and Parra Cuentas, ER and Hernandez, S and Futreal, A and Wargo, JA and Schulze, K and Darbonne, WC and Ajami, NJ and Woodman, SE and de Groot, JF},
title = {Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3950},
pmid = {40289138},
issn = {2041-1723},
mesh = {Humans ; *Glioblastoma/genetics/immunology/mortality/therapy/drug therapy ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy ; Temozolomide/therapeutic use/administration & dosage ; Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Mutation ; Aged ; Adult ; *B7-H1 Antigen/antagonists & inhibitors ; Tumor Microenvironment ; Prospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; },
abstract = {This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.},
}

Humans
*Glioblastoma/genetics/immunology/mortality/therapy/drug therapy
*Gastrointestinal Microbiome/genetics/drug effects
Male
Female
Middle Aged
*Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy
Temozolomide/therapeutic use/administration & dosage
Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage
Mutation
Aged
Adult
*B7-H1 Antigen/antagonists & inhibitors
Tumor Microenvironment
Prospective Studies
*Immune Checkpoint Inhibitors/therapeutic use
Treatment Outcome

@article {pmid40289100,
year = {2025},
author = {Mok, K and Tomtong, P and Ogawa, T and Nagai, K and Torrungruang, P and Charoensiddhi, S and Nakayama, J and Wanikorn, B and Nitisinprasert, S and Vongsangnak, W and Nakphaichit, M},
title = {Synbiotic-driven modulation of the gut microbiota and metabolic functions related to obesity: insights from a human gastrointestinal model.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {250},
pmid = {40289100},
issn = {1471-2180},
support = {FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; *Obesity/microbiology/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; Feces/microbiology ; Limosilactobacillus reuteri/growth & development ; Bacteria/classification/genetics/isolation & purification/metabolism ; Microbial Viability ; Adult ; Male ; *Gastrointestinal Microbiome ; Female ; },
abstract = {Synbiotic interventions have gained increasing attention for modulating gut microbiota and metabolic functions in obesity-related disorders. This study evaluated the effects of Limosilactobacillus reuteri KUB-AC5 (10[8] CFU) and Wolffia globosa powder (6 g/day) using an in vitro continuous human gastrointestinal model. Fecal samples from obese donors were used to simulate the ascending and descending colon, with microbial viability, diversity, and metabolite production assessed over 14 days via culture-dependent and culture-independent methods. Synbiotic supplementation increased anaerobic bacterial counts by 2.6 log CFU/mL in the ascending colon and 2.2 log CFU/mL in the descending colon, with notable increases in lactic acid bacteria and reductions in Enterobacteriaceae. Metagenomic analysis revealed an increasing trend in microbial diversity and evenness after 7 days of treatment, though the changes were not statistically significant. PERMANOVA analysis confirmed significant shift in microbial community composition between stabilization, treatment, and washout periods (p < 0.05). Additionally, butyrate levels significantly increased (p < 0.05), while p-cresol, a deleterious metabolite, significantly decreased (p < 0.05). Bile acid composition was modulated, with increased tertiary bile acid 3-oxo-LCA and enhanced bile acid deconjugation, suggesting improved lipid metabolism and potential weight management benefits. These findings highlight the potential of synbiotic supplementation to enhance beneficial bacterial populations, improve microbial diversity, and support metabolic health in obesity management.},
}

Humans
*Synbiotics/administration & dosage
*Obesity/microbiology/metabolism
*Gastrointestinal Tract/microbiology/metabolism
Feces/microbiology
Limosilactobacillus reuteri/growth & development
Bacteria/classification/genetics/isolation & purification/metabolism
Microbial Viability
Adult
Male
*Gastrointestinal Microbiome
Female

@article {pmid40289092,
year = {2025},
author = {Qiu, J and Hu, P and Li, F and Huang, Y and Yang, Y and Sun, F and Wu, P and Lai, Y and Wang, Y and He, X and Dong, Y and Zhang, P and Zhang, S and Wu, N and Wang, T and Yang, S and Li, S and Yuan, J and Liu, X and Liu, G and Hu, Y and Wu, JHY and Chen, D and Pan, A and Pan, XF},
title = {Circulating linoleic acid and its interplay with gut microbiota during pregnancy for gestational diabetes mellitus.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {245},
pmid = {40289092},
issn = {1741-7015},
support = {2022YFC2702905//National Key R&D Program of China/ ; 82325043//the National Science Fund for Distinguished Young Scholars/ ; 82473646//Natural Science Foundation of China/ ; 2024NSFSC0578//Sichuan Provincial Natural Science Foundation/ ; YJ202346//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; Pregnancy ; Female ; *Diabetes, Gestational/blood/microbiology ; *Gastrointestinal Microbiome/physiology ; Adult ; Case-Control Studies ; *Linoleic Acid/blood ; China/epidemiology ; Mendelian Randomization Analysis ; },
abstract = {BACKGROUND: Circulating linoleic acid (LA) levels have been reported to be associated with various metabolic outcomes. However, the role of LA and its interplay with gut microbiota in gestational diabetes mellitus (GDM) remains unclear. This study aimed to investigate the longitudinal association between circulating LA levels during pregnancy and the risk of GDM, and the potential role of gut microbiota.

METHODS: A nested case-control study was conducted within the ongoing Tongji-Huaxi-Shuangliu Birth Cohort in Chengdu, China. Blood and fecal samples were collected during early and middle pregnancy from 807 participants. GDM was diagnosed in middle pregnancy using the International Association of Diabetes and Pregnancy Study Groups criteria. Plasma LA levels were measured using gas chromatography-mass spectrometry, and gut microbiota was analyzed through 16S rRNA gene sequencing and shotgun metagenomic sequencing. A two-sample Mendelian randomization study was conducted using data from the IEU OpenGWAS database and the FinnGen consortium.

RESULTS: Elevated plasma LA levels were associated with a lower risk of GDM in both early (P for trend = 0.002) and middle pregnancy (P for trend = 0.02). Consistently, Mendelian randomization analysis revealed that each unit increase in LA was associated with a 16% reduction in GDM risk (odds ratio: 0.84, 95% confidence interval: 0.72, 0.95). In early pregnancy, higher plasma LA levels were correlated with higher adiponectin levels (P < 0.001) and lower levels of triglycerides (P < 0.001), HbA1c (P = 0.04), and C-peptide (P = 0.04). The LA-accociated microbiota mediated the relationship between LA and C-peptide (P = 0.01). Additionally, the inverse association between LA and GDM was modified by Bilophila (P for interaction = 0.03), with a stronger association observed in participants with lower Bilophila levels in early pregnancy. Metagenomic analyses further showed that the LA-associated pathway (D-galacturonate degradation I) and its key enzyme (EC 4.2.1.7) were associated with metabolic traits.

CONCLUSIONS: Our study provides evidence for an inverse causal association between plasma LA levels during pregnancy and GDM risk, which is both mediated and modified by gut microbiota.},
}

Humans
Pregnancy
Female
*Diabetes, Gestational/blood/microbiology
*Gastrointestinal Microbiome/physiology
Adult
Case-Control Studies
*Linoleic Acid/blood
China/epidemiology
Mendelian Randomization Analysis

@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}

*Rhizosphere
*Metagenomics/methods
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Glycine max/microbiology/growth & development
*Microbiota/genetics
China
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40286059,
year = {2025},
author = {Men, C and Pan, Z and Liu, J and Miao, S and Yuan, X and Zhang, Y and Yang, N and Cheng, S and Li, Z and Zuo, J},
title = {Single and Combined Effects of Aged Polyethylene Microplastics and Cadmium on Nitrogen Species in Stormwater Filtration Systems: Perspectives from Treatment Efficiency, Key Microbial Communities, and Nitrogen Cycling Functional Genes.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {7},
pages = {},
pmid = {40286059},
issn = {1420-3049},
support = {52400245//National Natural Science Foundation of China/ ; 2017ZX07103-007//National Key Research and Development Program of China/ ; 5221101156//National Natural Science Foundation of China/ ; },
mesh = {*Cadmium/chemistry ; *Microplastics/chemistry ; *Nitrogen Cycle/genetics/drug effects ; *Water Pollutants, Chemical ; *Nitrogen ; Filtration ; *Polyethylene/chemistry ; *Microbiota/drug effects ; Denitrification ; Water Purification/methods ; },
abstract = {Microplastics and heavy metal contamination frequently co-occur in stormwater filtration systems, where their interactions may potentially compromise nitrogen removal. Current research on microplastics and Cd contamination predominantly focuses on soils and constructed wetlands, with limited attention given to stormwater filtration systems. In this study, the single and synergistic effects of aged polyethylene microplastics (PE) and cadmium (Cd) contamination in stormwater infiltration systems were investigated from perspectives of nitrogen removal, microbial community structures, and predicted functional genes in nitrogen cycling. Results showed that PE single contamination demonstrated stronger inhibition on NO3[-]-N removal than Cd. Low-level PE contamination (PE content: 0.1% w/w) in Cd-contaminated systems showed stronger inhibitory effect than high-level PE contamination (PE content: 5% w/w). The mean NO3[-]-N removal efficiency under combined Cd50 (Cd concentration: 50 μg/L) and PE5 contamination during the sixth rainstorm event was 1.04 to 34.68 times that under other contamination scenarios. Metagenomic analysis identified keystone genera (Saccharimonadales, Enterobacter, Aeromonas, etc.), and critical nitrogen transformation pathways (nitrate reduction to ammonium, denitrification, nitrogen fixation, and nitrification) govern system performance. PE and Cd contamination effects were most pronounced on nitrification/denitrification enzymes beyond nitrite oxidase and nitrate reductase. These mechanistic findings advance our understanding of co-contaminant interactions in stormwater filtration systems.},
}

*Cadmium/chemistry
*Microplastics/chemistry
*Nitrogen Cycle/genetics/drug effects
*Water Pollutants, Chemical
*Nitrogen
Filtration
*Polyethylene/chemistry
*Microbiota/drug effects
Denitrification
Water Purification/methods

@article {pmid40252307,
year = {2025},
author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S},
title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {283},
number = {},
pages = {107370},
doi = {10.1016/j.aquatox.2025.107370},
pmid = {40252307},
issn = {1879-1514},
mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Dysbiosis/chemically induced/veterinary ; Gills/drug effects ; RNA, Ribosomal, 16S/genetics ; Bacteria/drug effects ; },
abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.},
}

Animals
*Zebrafish/microbiology/physiology
*Gastrointestinal Microbiome/drug effects
*Water Pollutants, Chemical/toxicity
*Dysbiosis/chemically induced/veterinary
Gills/drug effects
RNA, Ribosomal, 16S/genetics
Bacteria/drug effects

@article {pmid39853270,
year = {2025},
author = {Cardones, AR and Emiola, A and Hall, RP and Sung, AD and Zhang, J and Petty, AJ and Puza, C and Bohannon, LM and Bush, AT and Lew, MV and Fleming, E and Jin, YJ and Nichols, KR and Jain, V and Gregory, SG and Sullivan, KM and Chao, NJ and Oh, J},
title = {Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.},
journal = {Blood advances},
volume = {9},
number = {9},
pages = {2173-2182},
doi = {10.1182/bloodadvances.2021004792},
pmid = {39853270},
issn = {2473-9537},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Dysbiosis/etiology ; Male ; Female ; Middle Aged ; Adult ; *Skin/microbiology/pathology ; Transplantation, Homologous/adverse effects ; Microbiota ; Graft vs Host Disease/etiology ; Aged ; },
abstract = {Gut dysbiosis is linked to mortality and the development of graft-versus-host disease after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study, obtained retroauricular and forearm skin swabs from 12 adult patients before conditioning chemotherapy/radiation and at 1 week, 1 month, and 3 months after allogeneic HSCT, and performed shotgun metagenomic sequencing. The cutaneous microbiome among HSCT patients was enriched for gram-negative bacteria such as Escherichia coli and Pseudomonas, fungi, and viruses. Enrichment with bacteriophages and Polyomavirus species was observed among patients who died within 1 year. We observed longitudinal stability of the cutaneous microbiome at the 3-month time point among those who survived beyond 1 year after HSCT, although these may simply be a reflection of the overall medical status of the patients. There was no association with fungal abundance and any of the outcomes observed. The cutaneous microbiome may be a reservoir of pathobionts among allogeneic HSCT patients. Our findings suggest that cutaneous dysbiosis exists after HSCT, but the ultimate implication of this to patient outcomes remains to be seen through larger studies.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Dysbiosis/etiology
Male
Female
Middle Aged
Adult
*Skin/microbiology/pathology
Transplantation, Homologous/adverse effects
Microbiota
Graft vs Host Disease/etiology
Aged

@article {pmid40285778,
year = {2025},
author = {Alotaib, AS and Anwar, W and Albalawi, HQ and Albalawi, HS and Alshehri, MA and Al-Atawi, FM and Al Joundi, IT and Y Al Samini, A and Alqarni, RZ and Alzahrani, NE and Huraysi, MA},
title = {Metagenomic analysis microbial biodiversity of Trojena' the Mountains of Neom.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {4},
pages = {100-110},
doi = {10.14715/cmb/2025.71.4.13},
pmid = {40285778},
issn = {1165-158X},
mesh = {*Metagenomics/methods ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Saudi Arabia ; Soil Microbiology ; *Metagenome/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; },
abstract = {About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance & distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. & Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.},
}

*Metagenomics/methods
*Biodiversity
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Saudi Arabia
Soil Microbiology
*Metagenome/genetics
Phylogeny
High-Throughput Nucleotide Sequencing
Microbiota/genetics

@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}

*Microbiota
*Plankton
China
*Rivers/microbiology
Bacteria/genetics/drug effects
Urbanization

@article {pmid40284601,
year = {2025},
author = {Song, Z and Zhang, T and Liang, Y and Mcminn, A and Wang, M and Jiao, N and Luo, T},
title = {Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040764},
pmid = {40284601},
issn = {2076-2607},
abstract = {Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus.},
}

@article {pmid40284188,
year = {2025},
author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G},
title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081323},
pmid = {40284188},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.},
}

Humans
*Arthritis, Psoriatic/microbiology/therapy/immunology
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040547},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}

@article {pmid40282295,
year = {2025},
author = {Laguerre, H and Noël, C and Jégou, C and Fleury, Y and Le Chevalier, P},
title = {The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040430},
pmid = {40282295},
issn = {2079-7737},
abstract = {In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential "specific" microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio.},
}

@article {pmid40280272,
year = {2025},
author = {Bačnik, K and Kranjc, L and Botella, L and Maguire, I and Pavić, D and Patoka, J and Dragičević, P and Bláha, M and Bielen, A and Kouba, A and Kutnjak, D and Hudina, S},
title = {Crayfish pet trade as a pathway for the introduction of known and novel viruses.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108345},
doi = {10.1016/j.jip.2025.108345},
pmid = {40280272},
issn = {1096-0805},
abstract = {Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.},
}

@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}

@article {pmid40180172,
year = {2025},
author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D},
title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.},
journal = {Molecular and cellular endocrinology},
volume = {603},
number = {},
pages = {112534},
doi = {10.1016/j.mce.2025.112534},
pmid = {40180172},
issn = {1872-8057},
mesh = {Humans ; Female ; *Estrogens/metabolism/blood ; Male ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Young Adult ; },
abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.},
}

Humans
Female
*Estrogens/metabolism/blood
Male
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome
Adult
Middle Aged
Tandem Mass Spectrometry
Chromatography, Liquid
Young Adult

@article {pmid40273394,
year = {2025},
author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH},
title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.},
journal = {Neurology},
volume = {104},
number = {10},
pages = {e213592},
doi = {10.1212/WNL.0000000000213592},
pmid = {40273394},
issn = {1526-632X},
mesh = {Humans ; *Caffeine/blood/metabolism ; *Parkinson Disease/blood/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Metabolomics ; Middle Aged ; Aged ; Coffee ; Cohort Studies ; Taiwan ; },
abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.},
}

Humans
*Caffeine/blood/metabolism
*Parkinson Disease/blood/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
Male
Female
Metabolomics
Middle Aged
Aged
Coffee
Cohort Studies
Taiwan

@article {pmid40184632,
year = {2025},
author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T},
title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf058},
pmid = {40184632},
issn = {1751-7370},
support = {17212124//Hong Kong GRF/ ; },
mesh = {*Eukaryota/classification/genetics/isolation & purification ; *Sewage/microbiology/virology/parasitology ; *Wastewater/microbiology ; Hong Kong ; Metagenomics ; Animals ; Biodiversity ; Phylogeny ; },
abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analysed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416 044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.},
}

*Eukaryota/classification/genetics/isolation & purification
*Sewage/microbiology/virology/parasitology
*Wastewater/microbiology
Hong Kong
Metagenomics
Animals
Biodiversity
Phylogeny

@article {pmid39488451,
year = {2025},
author = {Xiao, C and Ide, K and Matsunaga, H and Kogawa, M and Wagatsuma, R and Takeyama, H},
title = {Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan.},
journal = {Journal of bioscience and bioengineering},
volume = {139},
number = {2},
pages = {147-155},
doi = {10.1016/j.jbiosc.2024.09.006},
pmid = {39488451},
issn = {1347-4421},
mesh = {*Rivers/microbiology ; Japan ; *Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Cities ; Seasons ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.},
}

*Rivers/microbiology
Japan
*Metagenomics
*Bacteria/genetics/classification/drug effects/isolation & purification
RNA, Ribosomal, 16S/genetics
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
Cities
Seasons
Anti-Bacterial Agents/pharmacology
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Metagenome

@article {pmid40269516,
year = {2025},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf177},
pmid = {40269516},
issn = {1477-4054},
support = {U24HG006620/NH/NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; },
abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Metagenomics/methods
*Metagenome
*Microbiota
*Gastrointestinal Microbiome
Computational Biology/methods
Algorithms

@article {pmid40269515,
year = {2025},
author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH},
title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf176},
pmid = {40269515},
issn = {1477-4054},
support = {2430236//National Science Foundation/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; },
abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
High-Throughput Nucleotide Sequencing
Machine Learning
Biomarkers/blood

@article {pmid40269473,
year = {2025},
author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL},
title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70088},
doi = {10.1111/1758-2229.70088},
pmid = {40269473},
issn = {1758-2229},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; },
mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation & purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation & purification ; Machine Learning ; Brazil ; },
abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.},
}

*Rainforest
*Soil Microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Microbiota
Metagenomics/methods
Metagenome
*Archaea/genetics/metabolism/classification/isolation & purification
Soil/chemistry
Viruses/genetics/classification/metabolism/isolation & purification
Machine Learning
Brazil

@article {pmid40269059,
year = {2025},
author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M},
title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14204},
pmid = {40269059},
issn = {2045-2322},
support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration & dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; },
abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.},
}

Animals
*Gastrointestinal Microbiome/genetics
Camelus
Rats
*Obesity/microbiology/diet therapy
*Probiotics/administration & dosage
*Fasting
*Milk
Male
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Biodiversity
Cultured Milk Products
Intermittent Fasting

@article {pmid40268958,
year = {2025},
author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L},
title = {The dynamics of microbiome and virome in migratory birds of southwest China.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {64},
pmid = {40268958},
issn = {2055-5008},
mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; },
abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.},
}

Animals
China
*Virome
Feces/microbiology/virology
*Gastrointestinal Microbiome
*Charadriiformes/microbiology/virology
Animal Migration
*Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Birds/microbiology/virology
Metagenomics
Phylogeny

@article {pmid40263874,
year = {2025},
author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y},
title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {208},
number = {},
pages = {116061},
doi = {10.1016/j.foodres.2025.116061},
pmid = {40263874},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; },
abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.},
}

*Fermentation
*Microbiota
Fungi/metabolism/genetics
*Bacteria/metabolism/genetics
*Viruses/genetics/classification
Metagenomics
Food Microbiology
*Fermented Foods/microbiology/virology
Bacteriophages/genetics
*Metabolome
Multiomics

@article {pmid40239498,
year = {2025},
author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA},
title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179357},
doi = {10.1016/j.scitotenv.2025.179357},
pmid = {40239498},
issn = {1879-1026},
mesh = {*Arsenic/analysis/metabolism ; *Groundwater/microbiology/chemistry ; *Water Pollutants, Chemical/analysis/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Alberta ; Bacteria/metabolism ; Biodegradation, Environmental ; },
abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.},
}

*Arsenic/analysis/metabolism
*Groundwater/microbiology/chemistry
*Water Pollutants, Chemical/analysis/metabolism
*Microbiota
RNA, Ribosomal, 16S/analysis
Alberta
Bacteria/metabolism
Biodegradation, Environmental

@article {pmid40118219,
year = {2025},
author = {Yan, R and Zhang, L and Chen, Y and Zheng, Y and Xu, P and Xu, Z},
title = {Therapeutic potential of gut microbiota modulation in epilepsy: A focus on short-chain fatty acids.},
journal = {Neurobiology of disease},
volume = {209},
number = {},
pages = {106880},
doi = {10.1016/j.nbd.2025.106880},
pmid = {40118219},
issn = {1095-953X},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Fatty Acids, Volatile/metabolism ; *Epilepsy/metabolism/microbiology/therapy ; Blood-Brain Barrier/metabolism ; Animals ; Dysbiosis/metabolism ; },
abstract = {According to the criteria established by the International League Against Epilepsy (ILAE), epilepsy is defined as a disorder characterized by at least two unprovoked seizures occurring more than 24 h apart. Its pathogenesis is closely related to various physiological and pathological factors. Advances in high-throughput metagenomic sequencing have increasingly highlighted the role of gut microbiota dysbiosis in epilepsy. Short-chain fatty acids (SCFAs), the major metabolites of the gut microbiota and key regulators of the gut-brain axis, support physiological homeostasis through multiple mechanisms. Recent studies have indicated that SCFAs not only regulate seizures by maintaining intestinal barrier integrity and modulating intestinal immune responses, but also affect the structure and function of the blood-brain barrier (BBB) and regulate neuroinflammation. This review, based on current literatures, explores the relationship between SCFAs and epilepsy, emphasizing how SCFAs affect epilepsy by modulating the intestinal barrier and BBB. In-depth studies on SCFAs may reveal their therapeutic potential and inform the development of gut microbiota-targeted epilepsy treatments.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Fatty Acids, Volatile/metabolism
*Epilepsy/metabolism/microbiology/therapy
Blood-Brain Barrier/metabolism
Animals
Dysbiosis/metabolism

@article {pmid40263747,
year = {2025},
author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J},
title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.},
journal = {Thoracic cancer},
volume = {16},
number = {8},
pages = {e70068},
doi = {10.1111/1759-7714.70068},
pmid = {40263747},
issn = {1759-7714},
support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; },
abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.

METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n = 18) and those without distant metastasis (n = 12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.

RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.

CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology
*Gastrointestinal Microbiome
*Brain Neoplasms/secondary/metabolism
*Lung Neoplasms/pathology/metabolism/microbiology
*Metabolomics/methods
Female
Male
*Metagenomics/methods
Middle Aged
Aged
Prognosis

@article {pmid40263287,
year = {2025},
author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z},
title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {61},
pmid = {40263287},
issn = {2055-5008},
support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; },
mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.},
}

Animals
Cattle
*Oxidative Stress
*Antioxidants/metabolism
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Female
Mice
Fatty Acids, Volatile/metabolism
Metabolomics
Metagenomics
*Clostridiales/genetics/metabolism/isolation & purification
Multiomics

@article {pmid40263159,
year = {2025},
author = {Pandey, A and Israr, J and Pandey, J and Misra, S},
title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {258},
pmid = {40263159},
issn = {1432-0991},
mesh = {*Biological Products/metabolism/pharmacology/isolation & purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; },
abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.},
}

*Biological Products/metabolism/pharmacology/isolation & purification/chemistry
*Drug Discovery/methods
*Bacteria/metabolism/genetics
Multigene Family
Biosynthetic Pathways/genetics
Microbiota

@article {pmid40230307,
year = {2025},
author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S},
title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {16},
pages = {9637-9649},
doi = {10.1021/acs.jafc.5c00079},
pmid = {40230307},
issn = {1520-5118},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Pantothenic Acid/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism/microbiology/prevention & control/drug therapy ; Male ; Mice, Inbred C57BL ; Humans ; Diet, High-Fat/adverse effects ; Liver/metabolism ; *Trisaccharides/administration & dosage ; Prebiotics/administration & dosage/analysis ; Lipid Metabolism/drug effects ; Bacteria/isolation & purification/classification/genetics/metabolism ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Pantothenic Acid/metabolism
*Non-alcoholic Fatty Liver Disease/metabolism/microbiology/prevention & control/drug therapy
Male
Mice, Inbred C57BL
Humans
Diet, High-Fat/adverse effects
Liver/metabolism
*Trisaccharides/administration & dosage
Prebiotics/administration & dosage/analysis
Lipid Metabolism/drug effects
Bacteria/isolation & purification/classification/genetics/metabolism

@article {pmid40084893,
year = {2025},
author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F},
title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {4},
pages = {e0029625},
doi = {10.1128/aem.00296-25},
pmid = {40084893},
issn = {1098-5336},
support = {42277115, 42177113, 42277418//National Natural Science Foundation of China/ ; Modern Agriculture BE2022322//Key P&D Project of Jiangshu Province/ ; 2024M761435//China Postdoctoral Science Foundation/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Soil Microbiology ; Composting ; Manure/microbiology ; *Carbon Sequestration ; *Soil/chemistry ; Swine ; *Bacteria/metabolism/genetics/virology ; Animals ; *Microbiota ; Carbon/metabolism ; },
abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.},
}

*Bacteriophages/genetics/metabolism
*Soil Microbiology
Composting
Manure/microbiology
*Carbon Sequestration
*Soil/chemistry
Swine
*Bacteria/metabolism/genetics/virology
Animals
*Microbiota
Carbon/metabolism

@article {pmid40047424,
year = {2025},
author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D},
title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {4},
pages = {e0247724},
doi = {10.1128/aem.02477-24},
pmid = {40047424},
issn = {1098-5336},
support = {31770540//The Natural Science Foundation of China/ ; BE2018663//The Key Research Program of Jiangsu/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Immune Tolerance ; *Hygiene ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Male ; Bacteria/classification/genetics/isolation & purification ; Housing, Animal ; },
abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Immune Tolerance
*Hygiene
Specific Pathogen-Free Organisms
Feces/microbiology
Male
Bacteria/classification/genetics/isolation & purification
Housing, Animal

@article {pmid39443733,
year = {2025},
author = {Hudobenko, J and Di Gesù, CM and Mooz, PR and Petrosino, J and Putluri, N and Ganesh, BP and Rebeles, K and Blixt, FW and Venna, VR and McCullough, LD},
title = {Maternal dysbiosis produces long-lasting behavioral changes in offspring.},
journal = {Molecular psychiatry},
volume = {30},
number = {5},
pages = {1847-1858},
pmid = {39443733},
issn = {1476-5578},
support = {RF1AG058463//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R35NS132265//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; MERIT Award//American Heart Association (American Heart Association, Inc.)/ ; },
mesh = {Animals ; Female ; Gastrointestinal Microbiome/physiology ; Pregnancy ; *Dysbiosis/microbiology/metabolism/complications/physiopathology ; Mice ; Mice, Inbred C57BL ; Prenatal Exposure Delayed Effects ; Behavior, Animal/physiology ; Anxiety ; Brain/metabolism ; Male ; Animals, Newborn ; Depression ; },
abstract = {Advanced maternal age (AMA) is defined as a pregnancy in a woman older than 35 years of age. AMA increases the risk for both maternal and neonatal complications, including miscarriage and stillbirth. AMA has also been linked to neurodevelopmental and neuropsychiatric disorders in the offspring. Recent studies have found that age-associated compositional shifts in the gut microbiota contribute to altered microbial metabolism and enhanced inflammation in the host. We investigated the specific contribution of the maternal microbiome on pregnancy outcomes and offspring behavior by recolonizing young female mice with aged female microbiome prior to pregnancy. We discovered that pre-pregnancy colonization of young dams with microbiome from aged female donors significantly increased fetal loss. There were significant differences in the composition of the gut microbiome in pups born from dams recolonized with aged female biome that persisted through middle age. Offspring born from dams colonized with aged microbiome also had significant changes in levels of neurotransmitters and metabolites in the blood and the brain. Adult offspring from dams colonized with an aged microbiome displayed persistent depressive- and anxiety-like phenotypes. Collectively, these results demonstrate that age-related changes in the composition of the maternal gut microbiome contribute to chronic alterations in the behavior and physiology of offspring. This work highlights the potential of microbiome-targeted approaches, even prior to birth, may reduce the risk of neuropsychiatric disorders.},
}

Animals
Female
Gastrointestinal Microbiome/physiology
Pregnancy
*Dysbiosis/microbiology/metabolism/complications/physiopathology
Mice
Mice, Inbred C57BL
Prenatal Exposure Delayed Effects
Behavior, Animal/physiology
Anxiety
Brain/metabolism
Male
Animals, Newborn
Depression

@article {pmid40259731,
year = {2025},
author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q},
title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.},
journal = {Zoological research},
volume = {46},
number = {3},
pages = {505-517},
doi = {10.24272/j.issn.2095-8137.2025.094},
pmid = {40259731},
issn = {2095-8137},
mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; },
abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.},
}

Animals
*Deer/microbiology/metabolism
*Fatty Acids, Monounsaturated/metabolism
*Microbiota
Scent Glands/metabolism
*Arvicolinae/microbiology/metabolism

@article {pmid40259344,
year = {2025},
author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE},
title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {101},
pmid = {40259344},
issn = {2049-2618},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation & purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation & purification ; Cecum/microbiology ; },
abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Amylases/genetics/metabolism
Genome-Wide Association Study
Metagenomics/methods
Male
Bacteroidetes/genetics/classification/isolation & purification
Mendelian Randomization Analysis
Firmicutes/genetics/classification/isolation & purification
Cecum/microbiology

@article {pmid40223703,
year = {2025},
author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H},
title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.},
journal = {Environmental science & technology},
volume = {59},
number = {15},
pages = {7550-7560},
doi = {10.1021/acs.est.5c00306},
pmid = {40223703},
issn = {1520-5851},
mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; Soil/chemistry ; Soil Pollutants/metabolism ; Bacteria/metabolism ; Microbiota ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.},
}

*Polycyclic Aromatic Hydrocarbons/metabolism
*Soil Microbiology
Biodegradation, Environmental
Soil/chemistry
Soil Pollutants/metabolism
Bacteria/metabolism
Microbiota

@article {pmid40214404,
year = {2025},
author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, MØ and Rudi, K},
title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.},
journal = {Environmental science & technology},
volume = {59},
number = {15},
pages = {7517-7529},
doi = {10.1021/acs.est.4c12464},
pmid = {40214404},
issn = {1520-5851},
mesh = {Microbiota ; Norway ; Iceland ; Animals ; Ecosystem ; Archaea ; Aquaculture ; },
abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.},
}

Microbiota
Norway
Iceland
Animals
Ecosystem
Archaea
Aquaculture

@article {pmid40105325,
year = {2025},
author = {Zhang, H and Lu, T and Guo, S and He, T and Shin, M-K and Luo, C and Tong, J and Zhang, Y},
title = {Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism.},
journal = {mSystems},
volume = {10},
number = {4},
pages = {e0109324},
doi = {10.1128/msystems.01093-24},
pmid = {40105325},
issn = {2379-5077},
support = {32272904//National Natural Science Foundation of China/ ; 32373086//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; Milk/metabolism/cytology ; *Glutathione/metabolism ; Cell Count ; Cytokines/blood ; *Gastrointestinal Microbiome ; Microbiota ; Lactation ; Mastitis, Bovine/microbiology/metabolism ; Dysbiosis ; },
abstract = {Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
Female
Milk/metabolism/cytology
*Glutathione/metabolism
Cell Count
Cytokines/blood
*Gastrointestinal Microbiome
Microbiota
Lactation
Mastitis, Bovine/microbiology/metabolism
Dysbiosis

@article {pmid40258842,
year = {2025},
author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P},
title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13723},
pmid = {40258842},
issn = {2045-2322},
support = {NNF22OC0080109//Novo Nordisk Foundation/ ; },
mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation & purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; },
abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.},
}

Humans
*Parkinson Disease/microbiology/virology
*Gastrointestinal Microbiome/genetics
*Bacteriophages/genetics/isolation & purification
Aged
*Plasmids/genetics
Male
Female
Middle Aged
Feces/microbiology/virology
Case-Control Studies
Metagenomics/methods
Machine Learning

@article {pmid40255076,
year = {2025},
author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B},
title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487209},
doi = {10.1080/19490976.2025.2487209},
pmid = {40255076},
issn = {1949-0984},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation & purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; },
abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.},
}

Humans
Male
Female
Middle Aged
*Gastrointestinal Microbiome/drug effects
*Bacteria/classification/genetics/isolation & purification/drug effects
*Anti-Bacterial Agents/therapeutic use/adverse effects
Aged
Dysbiosis/microbiology
*Fungi/classification/isolation & purification/genetics
*Inflammation/microbiology
*Liver Cirrhosis/microbiology
*Mycobiome
Prospective Studies
Metagenomics
Intestinal Mucosa/microbiology
*End Stage Liver Disease/microbiology/drug therapy
Adult

@article {pmid40254830,
year = {2025},
author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ},
title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf173},
pmid = {40254830},
issn = {1477-4054},
support = {GNT1194325//National Health and Medical Research Council of Australia/ ; },
mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; },
abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.},
}

*Microbiota
Humans
*Software
*Metagenomics/methods
Diabetes Mellitus, Type 2/microbiology/genetics
*Databases, Genetic
*Computational Biology/methods
Inflammatory Bowel Diseases/microbiology/genetics
Metagenome

@article {pmid40254701,
year = {2025},
author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K},
title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40254701},
issn = {1867-1314},
abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.},
}

@article {pmid40211688,
year = {2025},
author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX},
title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.},
journal = {Molecular ecology},
volume = {34},
number = {9},
pages = {e17751},
doi = {10.1111/mec.17751},
pmid = {40211688},
issn = {1365-294X},
support = {2021YFD1400900//National Key R&D Program of China/ ; },
mesh = {Animals ; *Coleoptera/microbiology/genetics/growth & development ; *Microbiota/genetics ; Larva/microbiology ; Bacteria/genetics/classification ; Gastrointestinal Microbiome/genetics ; Wood ; Life Cycle Stages ; Fungi/genetics/classification ; },
abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.},
}

Animals
*Coleoptera/microbiology/genetics/growth & development
*Microbiota/genetics
Larva/microbiology
Bacteria/genetics/classification
Gastrointestinal Microbiome/genetics
Wood
Life Cycle Stages
Fungi/genetics/classification

@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn's disease.},
journal = {Journal of Crohn's & colitis},
volume = {19},
number = {4},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
support = {82170542//National Natural Science Foundation of China/ ; 2021YFF0703700/2021YFF0703702//National Key Research and Development Program of China/ ; 2014008//Sun Yat-sen University Clinical Research 5010 Program/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/diagnosis/genetics ; *Gastrointestinal Microbiome/genetics ; Child ; *Metagenomics/methods ; *INDEL Mutation ; Feces/microbiology ; Female ; Male ; Biomarkers/analysis ; Adolescent ; Machine Learning ; },
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1175 fecal metagenomic sequencing samples, predominantly from 3 cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1357 KEGG orthology genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1256 insertions/deletions (InDels), and 3567 single nucleotide variants, with a considerable portion of these variants located in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an area under the ROC curve (AUC) of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC = 0.996) and 5 other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of noninvasive diagnostic tools and targeted therapies.},
}

Humans
*Crohn Disease/microbiology/diagnosis/genetics
*Gastrointestinal Microbiome/genetics
Child
*Metagenomics/methods
*INDEL Mutation
Feces/microbiology
Female
Male
Biomarkers/analysis
Adolescent
Machine Learning

@article {pmid40253169,
year = {2025},
author = {Aryal, A and Nwachukwu, ID and Aryee, ANA},
title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.},
journal = {Food research international (Ottawa, Ont.)},
volume = {209},
number = {},
pages = {116189},
doi = {10.1016/j.foodres.2025.116189},
pmid = {40253169},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; },
abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.},
}

*Gastrointestinal Microbiome/physiology
*Micronutrients
Humans
*Crops, Agricultural
*Biofortification
*Food, Fortified
Animals

@article {pmid40252793,
year = {2025},
author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S},
title = {Impact of Watershed-Scale Land Restoration on Soil Microbial Communities and Their Functions: Insights from Metagenomic Analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121609},
doi = {10.1016/j.envres.2025.121609},
pmid = {40252793},
issn = {1096-0953},
abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45%-52.57%, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.},
}

@article {pmid40252553,
year = {2025},
author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K},
title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109436},
doi = {10.1016/j.envint.2025.109436},
pmid = {40252553},
issn = {1873-6750},
abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.},
}

@article {pmid40249033,
year = {2025},
author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S},
title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.},
journal = {Journal of medical virology},
volume = {97},
number = {4},
pages = {e70341},
doi = {10.1002/jmv.70341},
pmid = {40249033},
issn = {1096-9071},
support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation & purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*HIV Infections/microbiology/blood/drug therapy
*Microbiota
Metagenomics
*Blood Donors
*Bacteria/genetics/classification/isolation & purification
Male
Adult
Female
Middle Aged
Sequence Analysis, DNA
*Blood/microbiology
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry

@article {pmid40157594,
year = {2025},
author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D},
title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {200},
number = {},
pages = {115419},
doi = {10.1016/j.fct.2025.115419},
pmid = {40157594},
issn = {1873-6351},
mesh = {Animals ; *Zea mays/genetics/metabolism ; *Plants, Genetically Modified/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; Macaca fascicularis ; *Endotoxins/genetics/metabolism ; *Hemolysin Proteins/genetics/metabolism ; Bacillus thuringiensis Toxins ; *Animal Feed/analysis ; Male ; *Bacterial Proteins/genetics/metabolism ; Female ; },
abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70 % non-GM maize (Corn group), and diet formulation containing 70 % GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.},
}

Animals
*Zea mays/genetics/metabolism
*Plants, Genetically Modified/genetics/metabolism
*Gastrointestinal Microbiome/drug effects
Macaca fascicularis
*Endotoxins/genetics/metabolism
*Hemolysin Proteins/genetics/metabolism
Bacillus thuringiensis Toxins
*Animal Feed/analysis
Male
*Bacterial Proteins/genetics/metabolism
Female

@article {pmid40086585,
year = {2025},
author = {Rawat, N and Sivanesan, S and Kanade, GS and Bafana, A},
title = {Interaction of environmental fluoride exposure and gut microbes: Potential implication in the development of fluorosis in human subjects.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {200},
number = {},
pages = {115388},
doi = {10.1016/j.fct.2025.115388},
pmid = {40086585},
issn = {1873-6351},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Fluorides/toxicity ; Male ; Female ; *Fluorosis, Dental/microbiology/etiology ; *Environmental Exposure/adverse effects ; Adult ; Middle Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; },
abstract = {Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58 %), group II had predominance of Proteobacteria (61.25 %) while group III showed similar abundance of Proteobacteria (50.38 %) and Firmicutes (49.51 %). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Fluorides/toxicity
Male
Female
*Fluorosis, Dental/microbiology/etiology
*Environmental Exposure/adverse effects
Adult
Middle Aged
Bacteria/classification/isolation & purification/genetics/metabolism
Fatty Acids, Volatile/metabolism
Feces/microbiology

@article {pmid40248366,
year = {2025},
author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z},
title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582553},
pmid = {40248366},
issn = {2235-2988},
mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; },
abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.

METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.

RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.

DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.},
}

Female
Humans
*Virome/genetics
*Vagina/virology/microbiology
*Metagenomics
Phylogeny
*Vaginitis/virology/microbiology
Adult
Microbiota
Bacteriophages/genetics/classification
*Viruses/classification/genetics/isolation & purification
Middle Aged
Biodiversity
Young Adult
Bacteria/classification/genetics

@article {pmid40247828,
year = {2025},
author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R},
title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19158},
pmid = {40247828},
issn = {2167-8359},
mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.},
}

*Biodiversity
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
North Sea
Nanopores
Belgium
High-Throughput Nucleotide Sequencing/methods

@article {pmid40247632,
year = {2025},
author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP},
title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2490211},
doi = {10.1080/19490976.2025.2490211},
pmid = {40247632},
issn = {1949-0984},
mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; },
abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.},
}

Animals
*Escherichia coli/genetics/metabolism
*Wound Healing
Gastrointestinal Microbiome
Mice
*Purines/metabolism
*Colon/microbiology/metabolism/pathology
*Butyrates/metabolism
Mice, Inbred C57BL
Disease Models, Animal
*Colitis/chemically induced/microbiology
Intestinal Mucosa/metabolism/microbiology
Male

@article {pmid40244481,
year = {2025},
author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R},
title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {248},
pmid = {40244481},
issn = {1432-0991},
support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; },
mesh = {Thailand ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; },
abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.},
}

Thailand
*Bacteria/classification/genetics/isolation & purification
*Water Microbiology
*Rivers/microbiology
Metagenomics
*Microbiota
Water Quality
Environmental Monitoring

@article {pmid40193404,
year = {2025},
author = {Aroney, STN and Newell, RJP and Nissen, JN and Camargo, AP and Tyson, GW and Woodcroft, BJ},
title = {CoverM: read alignment statistics for metagenomics.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {4},
pages = {},
pmid = {40193404},
issn = {1367-4811},
support = {2022070//EMERGE National Science Foundation/ ; DE-SC0004632//Genomic Science Program of the United States Department of Energy/ ; },
mesh = {*Metabolomics/methods ; *Biostatistics/methods ; *Microbiota ; *Software Design ; Genome ; },
abstract = {SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.

CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.},
}

*Metabolomics/methods
*Biostatistics/methods
*Microbiota
*Software Design
Genome

@article {pmid40185186,
year = {2025},
author = {Liu, Y and Pei, Y and Wang, H and Yang, Z},
title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {373},
number = {},
pages = {126187},
doi = {10.1016/j.envpol.2025.126187},
pmid = {40185186},
issn = {1873-6424},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Larva/drug effects/metabolism ; *Amidohydrolases/metabolism ; *Lead/toxicity ; *Ranidae ; Bacteria ; },
abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Bile Acids and Salts/metabolism
Larva/drug effects/metabolism
*Amidohydrolases/metabolism
*Lead/toxicity
*Ranidae
Bacteria

@article {pmid40152095,
year = {2025},
author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q},
title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.},
journal = {Food & function},
volume = {16},
number = {8},
pages = {3101-3119},
doi = {10.1039/d4fo06308b},
pmid = {40152095},
issn = {2042-650X},
mesh = {Cell Line, Tumor ; Humans ; *Signal Transduction ; Lactic Acid/metabolism ; NF-kappa B/metabolism ; *Gastritis/metabolism/microbiology/pathology ; *Lactobacillaceae/physiology ; Helicobacter pylori ; *Helicobacter Infections/metabolism/microbiology/pathology ; Animals ; Mice ; Mice, Inbred C57BL ; Sulfones/pharmacology ; Nitriles/pharmacology ; Gastrointestinal Microbiome ; },
abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.},
}

Cell Line, Tumor
Humans
*Signal Transduction
Lactic Acid/metabolism
NF-kappa B/metabolism
*Gastritis/metabolism/microbiology/pathology
*Lactobacillaceae/physiology
Helicobacter pylori
*Helicobacter Infections/metabolism/microbiology/pathology
Animals
Mice
Mice, Inbred C57BL
Sulfones/pharmacology
Nitriles/pharmacology
Gastrointestinal Microbiome

@article {pmid40127751,
year = {2025},
author = {Lim, TW and Huang, S and Burrow, MF and McGrath, C},
title = {A randomised crossover clinical trial of the efficacy of an ultrasonic cleaner combined with a denture cleanser on the microbiome on removable dentures among community-dwelling older adults.},
journal = {Journal of dentistry},
volume = {156},
number = {},
pages = {105709},
doi = {10.1016/j.jdent.2025.105709},
pmid = {40127751},
issn = {1879-176X},
mesh = {Humans ; Cross-Over Studies ; *Denture Cleansers/therapeutic use/pharmacology ; Aged ; Female ; Male ; Single-Blind Method ; *Microbiota/drug effects ; Prospective Studies ; Biofilms/drug effects ; Aged, 80 and over ; *Denture, Partial, Removable/microbiology ; Independent Living ; Ultrasonics ; Toothbrushing ; },
abstract = {OBJECTIVE: To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).

MATERIALS AND METHODS: A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.

RESULTS: For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P = 0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R[2] = 0.01118, P = 0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.

CONCLUSIONS: The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.

CLINICAL SIGNIFICANCE: Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.},
}

Humans
Cross-Over Studies
*Denture Cleansers/therapeutic use/pharmacology
Aged
Female
Male
Single-Blind Method
*Microbiota/drug effects
Prospective Studies
Biofilms/drug effects
Aged, 80 and over
*Denture, Partial, Removable/microbiology
Independent Living
Ultrasonics
Toothbrushing

@article {pmid40244477,
year = {2025},
author = {Li, J and Zhang, Y and He, L},
title = {The role of urine microbiota in culture-negative patients with pyuria.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {227},
pmid = {40244477},
issn = {1433-8726},
mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; },
abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.},
}

Humans
*Pyuria/microbiology/virology/urine
Retrospective Studies
Male
Female
*Microbiota
Middle Aged
*Urine/microbiology/virology
Aged
Adult

@article {pmid40243577,
year = {2025},
author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J},
title = {Potential Role of Malassezia restricta in Pterygium Development.},
journal = {International journal of molecular sciences},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/ijms26072976},
pmid = {40243577},
issn = {1422-0067},
support = {IP-2020-02-8921//Croatian Science Foundation/ ; },
mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; },
abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.},
}

Humans
*Pterygium/microbiology/pathology/genetics
*Malassezia/genetics/isolation & purification
Male
Female
Middle Aged
Conjunctiva/microbiology/pathology
Microbiota
Aged
Gene Expression Profiling

@article {pmid40240641,
year = {2025},
author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR},
title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40240641},
issn = {1618-1905},
abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.},
}

@article {pmid40240456,
year = {2025},
author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S},
title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13179},
pmid = {40240456},
issn = {2045-2322},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; },
abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Bronchoalveolar Lavage Fluid/microbiology
Male
Female
Aged
Middle Aged
*Microbiota
Bacteria/classification/genetics/isolation & purification
*Lung/microbiology/physiopathology
Dysbiosis/microbiology

@article {pmid40240384,
year = {2025},
author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, JÉCT and Arruda, P and Dante, RA and Gerhardt, IR},
title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {636},
pmid = {40240384},
issn = {2052-4463},
support = {2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; },
mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.},
}

*Droughts
Seasons
*Soil Microbiology
Brazil
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
*Microbiota
Bacteria/genetics/classification

@article {pmid40238917,
year = {2025},
author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ},
title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.},
journal = {Science translational medicine},
volume = {17},
number = {794},
pages = {eadq8870},
doi = {10.1126/scitranslmed.adq8870},
pmid = {40238917},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; },
abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.},
}

Animals
Humans
*Operon/genetics
*Fluorouracil/therapeutic use/toxicity/adverse effects
Gastrointestinal Microbiome/drug effects/genetics
Mice
*Colorectal Neoplasms/drug therapy/microbiology
*Pyrimidines/toxicity
*Bacteria/genetics/drug effects
RNA, Ribosomal, 16S/genetics
Female
Male

@article {pmid40238748,
year = {2025},
author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C},
title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321389},
doi = {10.1371/journal.pone.0321389},
pmid = {40238748},
issn = {1932-6203},
mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; },
abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.},
}

Animals
Female
Horses/microbiology/immunology
*Uterus/microbiology/immunology/metabolism
Proteomics/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Vagina/microbiology/immunology
Bacteria/genetics/classification
Proteome

@article {pmid40238740,
year = {2025},
author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X},
title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013069},
doi = {10.1371/journal.ppat.1013069},
pmid = {40238740},
issn = {1553-7374},
mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; },
abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.},
}

Animals
*Succinic Acid/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/physiology
*Trichinellosis/complications/metabolism/pathology
*Trichinella spiralis
*Bacteroides/metabolism
Mice, Inbred C57BL
Receptors, G-Protein-Coupled/metabolism
Myocardium/pathology/metabolism
Male

@article {pmid40237336,
year = {2025},
author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR},
title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2493900},
doi = {10.1080/19490976.2025.2493900},
pmid = {40237336},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; },
abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Breast Feeding
Female
*Bacteria/classification/genetics/isolation & purification
Male
Brazil
Feces/microbiology
Metagenomics
*Delivery, Obstetric/methods
Cohort Studies
Infant, Newborn

@article {pmid40234093,
year = {2025},
author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ},
title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {4},
pages = {},
doi = {10.1136/jitc-2025-011706},
pmid = {40234093},
issn = {2051-1426},
mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER: NCT03554083.},
}

Humans
*Melanoma/drug therapy/pathology/mortality
Female
Male
*Azetidines/therapeutic use/pharmacology
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Middle Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
*Neoadjuvant Therapy/methods
*Piperidines/pharmacology/therapeutic use
*Vemurafenib/pharmacology/therapeutic use
Aged
Neoplasm Staging
Adult
Gastrointestinal Microbiome
Treatment Outcome
*Skin Neoplasms/drug therapy

@article {pmid40233938,
year = {2025},
author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM},
title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.},
journal = {Journal of applied microbiology},
volume = {136},
number = {4},
pages = {},
doi = {10.1093/jambio/lxaf076},
pmid = {40233938},
issn = {1365-2672},
support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; },
mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation & purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.

METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.

CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.},
}

Biodegradation, Environmental
Metagenomics
*Microbiota/genetics
Metals, Heavy/metabolism
*Geologic Sediments/microbiology
*Bacteria/genetics/metabolism/drug effects/isolation & purification/classification
Water Pollutants, Chemical/metabolism
Polychlorinated Biphenyls/metabolism
*Drug Resistance, Bacterial/genetics
Metagenome