@article {pmid41461486,
year = {2026},
author = {Kang, S and Lee, JY and Cho, KS},
title = {Bacterial and fungal metagenomes associated with atmospheric particulates in Republic of Korea: Comparison of PM2.5 and TSP larger than PM2.5.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {400-410},
doi = {10.1016/j.jes.2025.08.021},
pmid = {41461486},
issn = {1001-0742},
mesh = {*Particulate Matter/analysis ; Republic of Korea ; Bacteria/genetics ; *Air Pollutants/analysis ; *Environmental Monitoring ; Particle Size ; *Fungi/genetics ; *Metagenome ; *Air Microbiology ; Microbiota ; Air Pollution/statistics & numerical data ; },
abstract = {Particulate matter (PM) significantly contributes to air pollution, potentially causing health issues, with PM-associated microorganisms implicated in some cases. While studies have explored microbial concentration and structure in PM based on particle size, comprehensive analysis of microbial functional traits and environmental influences is limited. This study evaluated microbial concentrations and diversity in PM with a diameter of 2.5 µm or lower (PM2.5) and total suspended particles (TSP) greater than PM2.5 (PM>2.5) samples relative to air temperature and other factors. DNA extracted from PM2.5 and PM>2.5 filters was sequenced to characterize bacterial and fungal community structures and functional genes. Results showed that microbial concentrations and diversity were greater in PM>2.5, with similar dominant species across PM sizes. Higher air temperatures correlated with increased microbial concentrations and diversity in PM>2.5, attributed to enhanced microbial growth. An Asian dust event from the Mongolian desert disrupted the PM microbiome. Despite consistent species dominance, gene function analysis revealed abundant drug resistance pathways in bacterial communities of both particle types, while pathotroph prevalence was higher in PM2.5 fungal communities. These findings indicate that PM2.5 microbial community analysis suffices for understanding PM ecosystems, offering valuable insights for air quality management and microbial pollution control, especially concerning potential pathogens.},
}

*Particulate Matter/analysis
Republic of Korea
Bacteria/genetics
*Air Pollutants/analysis
*Environmental Monitoring
Particle Size
*Fungi/genetics
*Metagenome
*Air Microbiology
Microbiota
Air Pollution/statistics & numerical data

@article {pmid41461466,
year = {2026},
author = {Cui, M and Chen, S and Zhang, Z and Yu, Y and Xu, Y and Liu, L and Gao, H and Chen, X and Liu, Z and Zhang, X and Yuan, W and Chen, S and Li, D and Chen, L and Xing, X and Xiao, Y and Chen, W and Liu, Y and Wang, Q},
title = {Nanoplastics and triclosan co-exposure aggravates DSS-induced colitis in mice by interfering with Akkermansia muciniphila and tryptophan metabolism.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {189-200},
doi = {10.1016/j.jes.2025.06.029},
pmid = {41461466},
issn = {1001-0742},
mesh = {Animals ; Mice ; *Colitis/chemically induced ; *Tryptophan/metabolism ; *Triclosan/toxicity ; Dextran Sulfate/toxicity ; *Microplastics/toxicity ; Akkermansia ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; },
abstract = {The global incidence of inflammatory bowel disease (IBD) has been escalating. Recent studies have identified co-exposure to polystyrene nanoplastics (PSNP) and triclosan (TCS), two prevalent environmental pollutants, as emerging risk factors for IBD. However, the molecular mechanisms contributing to its deteriorative effect remain elusive. To explore the mechanisms, we conducted an integrative analysis of metagenomic and metabolomic data in a mouse model of colitis induced by dextran sulfate sodium (DSS) following co-exposure to PSNP and TCS. Results demonstrated that co-exposure to PSNP and TCS significantly exacerbated DSS-induced colitis, as evidenced by elevated disease activity indices and pro-inflammatory cytokine levels. Mechanistically, this aggravation correlated with a marked reduction in Akkermansia muciniphila abundance, which was further associated with the disruption of tryptophan metabolism. Specifically, the disruption of this metabolic pathway led to decreased production of two key tryptophan-derived metabolites: indole acetic acid (IAA) and indole acetamide (IAM). In-vitro experiments confirmed that co-exposure to PSNP and TCS inhibited the growth of A. muciniphila rather than affecting the integrity of intestinal epithelial cells. Additionally, IAA and IAM reduced inflammatory cytokine secretion in THP-1 cells. These findings suggest that the reduction in A. muciniphila abundance might decrease the production of IAA and IAM by disrupting tryptophan metabolism. This disruption ultimately contributes to the inflammatory response induced by co-exposure to PSNP and TCS. Our study offers a novel insight into microbiota-host interactions and potential therapeutic targets for intestinal disease.},
}

Animals
Mice
*Colitis/chemically induced
*Tryptophan/metabolism
*Triclosan/toxicity
Dextran Sulfate/toxicity
*Microplastics/toxicity
Akkermansia
Mice, Inbred C57BL
Gastrointestinal Microbiome/drug effects
*Environmental Pollutants/toxicity

@article {pmid41460777,
year = {2025},
author = {Geraerts, M and Gombeer, S and Nebesse, C and Akaibe, D and Akaibe, D and Baelo, P and Chaber, AL and Gaubert, P and Gembu, GC and Joffrin, L and Laudisoit, A and Laurent, N and Leirs, H and Mande, C and Mariën, J and Ngoy, S and Těšíková, J and Vanderheyden, A and van Vredendaal, R and Verheyen, E and Gryseels, S},
title = {A wide diversity of viruses detected in African mammals involved in the wild meat supply chain.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013643},
doi = {10.1371/journal.ppat.1013643},
pmid = {41460777},
issn = {1553-7374},
mesh = {Animals ; *Meat/virology ; *Mammals/virology ; *Animals, Wild/virology ; Democratic Republic of the Congo ; *Viruses/genetics/isolation & purification/classification ; Zoonoses/virology ; Humans ; Phylogeny ; Belgium ; Genetic Variation ; },
abstract = {The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome of many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. Here, we present the findings of a metagenomic viral screening of 101 mammalian specimens belonging to 28 wild African species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected in various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of sixteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during close interactions with wildlife in the wild meat supply chain.},
}

Animals
*Meat/virology
*Mammals/virology
*Animals, Wild/virology
Democratic Republic of the Congo
*Viruses/genetics/isolation & purification/classification
Zoonoses/virology
Humans
Phylogeny
Belgium
Genetic Variation

@article {pmid41459746,
year = {2025},
author = {Duncan, A and Koon, W and Sidorczuk, K and Quince, C and Frioux, C and Hildebrand, F},
title = {Detecting signatures underlying the composition of biological data.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1388},
pmid = {41459746},
issn = {1362-4962},
support = {BB/Z516168/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //UK Research and Innovation/ ; //Earlham Institute Strategic Programme/ ; BBX011070/1//Grant Cellular Genomics/ ; BBS/E/ER/230001C//workpackage/ ; BBS/E/ER/230002A//workpackage/ ; BBS/E/F/000PR13631//workpackage/ ; ISP BBX011089/1//Decoding Biodiversity/ ; ISP BB/X011054/1//Quadram Institute Bioscience/ ; erc-stg-948219/ERC_/European Research Council/International ; ANR-22-PEAE-001//French National Research Agency/ ; //Earlham Institute and Quadram Institute Bioscience/ ; },
mesh = {Humans ; *Software ; Metagenome ; Rhizosphere ; Microbiota/genetics ; *Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology ; Lung Neoplasms/genetics/pathology ; },
abstract = {Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decomposition of large compositional data and to capture gradients in co-occurring features, called signatures, we developed a new software package 'cvaNMF'. Our benchmarks on synthetic data show the effectiveness of cross-validation and our novel signature-similarity method to identify a suitable decomposition using non-negative matrix factorization (NMF). This software provides a complete set of tools to identify and visualize biologically informative signatures which we demonstrate in a wide range of microbial and cellular datasets: 'Enterosignatures' detected in gut metagenomes differentiated human hosts with diverse diseases; five 'terrasignatures' from rhizosphere metagenomes differentiated root- or soil-associated microbiomes, while being refined enough to infer geographic distances between plants. Large-scale data from >13 000 metagenomes representing 25 biomes were decomposed into environmental and host-associated microbiomes based on five newly discovered signatures. Finally, analysis of the cell composition of non-small cell lung cancer samples allowed separation of cancerous and inflamed tissues based on four cell-type signatures.},
}

Humans
*Software
Metagenome
Rhizosphere
Microbiota/genetics
*Metagenomics/methods
Gastrointestinal Microbiome/genetics
Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology
Lung Neoplasms/genetics/pathology

@article {pmid41459106,
year = {2025},
author = {Wróbel, M and Gawryś, R and Tereba, A and Frąk, M and Sikora, K and Sokołowski, K and Boczoń, A},
title = {Dependence of Bacterial OTUs on Selected Features of Beaver Ponds.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72790},
pmid = {41459106},
issn = {2045-7758},
abstract = {Ponds created by beavers represent unique aquatic ecosystems that influence hydrological, chemical and biological conditions, including the microbiology of the water. The activity of these animals promotes biodiversity and water purification processes, but can also lead to the accumulation of pollutants. Water retention in beaver ponds promotes the development of bacteria and other microorganisms that play an important role in biogeochemical cycles. Long-term water stagnation can lead to anaerobic conditions and the formation of toxic compounds, which in turn can limit the diversity of benthic organisms. Beavers play a key role in shaping these habitats, and microbiological studies of their reservoirs provide a better understanding of their impact on aquatic ecosystems, self-purification processes and potential biological threats. Metagenomic analysis revealed the presence of 365 bacterial species in water and sediment samples, belonging to 174 genera and 83 families. 83 operational taxonomic units (OTUs) were identified, 62 of which were present in both water and sediments. Although the overall OTU composition was similar in both environments, greater variability was observed in the sediments. The statistical differences in OTU distribution between water and sediments were confirmed using the Wilcoxon test.},
}

@article {pmid41455002,
year = {2025},
author = {Karim, F and Lin, Q and Xie, H and Nargis, S and Xiao, H and Yang, S and Xiong, Y and Xie, M and Ni, Q and Yao, Y and Xu, H},
title = {Seasonal dynamics of gut microbiota in rhesus macaques (Macaca mulatta) from western Sichuan Plateau and their adaptability to high altitude climate change.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {99},
pmid = {41455002},
issn = {1432-0991},
support = {31870355//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; Seasons ; Altitude ; Feces/microbiology ; *Climate Change ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; China ; },
abstract = {Seasonal fluctuations in diet and climate shape animal gut microbiota, especially those living in extreme climatic conditions. Yet their role in facilitating primate adaptation to high-altitude remains unclear. This study investigates the seasonal dynamics in gut microbiome of wild rhesus macaques (Macaca mulatta) from high altitude (over 3,000 m) in Yajiang couke. We collected 117 fecal samples across four seasons and analyzed using 16S rRNA high-throughput sequencing combined with predictive functional metagenomics. We observed clear seasonal shifts in gut microbial diversity and composition. High α-diversity in autumn and winter reflected increased dietary diversity during these periods. Firmicutes predominated in summer, while Bacteroidota increased during winter. LEfSe analysis revealed seasonal specific taxa: UCG-005, Christensenellaceae R-7, and Prevotella_9 were dominated in winter but declined in summer and spring, whereas Blautia peaked during summer and decreased toward winter. Redundancy analysis showed that temperature, humidity, and precipitation were positively associated with Blautia and Sarcina, but negatively with Monoglobus and Helicobacter, underscoring the strong influence of climatic variables on gut community structure. Functional predictions revealed seasonal differences in gut microbiota related to energy metabolism (spring), glycan biosynthesis (summer), membrane transport (autumn), and environmental adaptation (winter) indicating microbial contributions to host adaptation under fluctuating climatic conditions. These findings demonstrate that gut microbiome of high-altitude macaques is highly responsive to changes in seasonal diet and climate. By integrating microbiome dynamics with climatic drivers, our study provides new insights into host-microbe-environment interactions and advances our understanding of primate adaptation under extreme climatic conditions.},
}

Animals
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
Seasons
Altitude
Feces/microbiology
*Climate Change
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
China

@article {pmid41452254,
year = {2026},
author = {Pan, LH and Hu, WF and Fu, ZY and Yu, XC and Li, ZQ and Guo, MF and Wu, JW and Zhu, H},
title = {Yacon (Smallanthus sonchifolius) Root Increases Bowel Movement Frequency in Healthy Adults via Modulating Gut Microbiota and Intestinal Metabolites: A Pilot Study.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {1},
pages = {e70358},
doi = {10.1002/mnfr.70358},
pmid = {41452254},
issn = {1613-4133},
support = {TZKY2024RC01//Scientific Research Starting Foundation for High-level Talents of Taizhou School of Clinical Medicine, Nanjing Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Adult ; *Plant Roots/chemistry ; Male ; Female ; Middle Aged ; Young Adult ; *Intestines/microbiology/drug effects ; *Plant Extracts/pharmacology ; *Defecation/drug effects ; },
abstract = {Yacon root (YR) is a functional food that can increase bowel movement frequency, but with an unclear mechanism. In this study, a UPLC-Orbitrap-MS/MS system was employed to characterize the chemical composition of YR. Subsequently, a 10-day pilot intervention trial involving 11 healthy adults was conducted to evaluate the effects of YR on bowel movement frequency. Concurrently, the involved mechanisms were explored through metagenomic and metabolomic approaches. A total of 82 chemical components were identified in YR. Clinical trials indicated that continuous intake of YR significantly increased bowel movement frequency without noticeable adverse effects. Metagenomic analysis revealed that YR substantially increased the abundance of beneficial bacteria such as Bifidobacterium and inhibited the generation of potential pathogens, including Escherichia-Shigella, thereby promoting a more balanced and healthier gut microbiota structure. Metabolomic analysis indicated that YR significantly upregulated metabolites, including cholic acid, taurine, and amino acids, which mainly focus on the biosynthesis of primary bile acid and the metabolism of taurine and hypotaurine. In summary, YR can safely and effectively increase bowel movement frequency in healthy individuals. The mechanism may involve synergistic regulation of gut microbiota and metabolites, which offered new insights to support YR as a natural functional food for laxative effects.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Adult
*Plant Roots/chemistry
Male
Female
Middle Aged
Young Adult
*Intestines/microbiology/drug effects
*Plant Extracts/pharmacology
*Defecation/drug effects

@article {pmid41450573,
year = {2025},
author = {Zhang, G and Zeng, L and Chen, B and Dai, H and Tang, K and Huang, R and Xiang, X and Yang, J and Yang, J and Song, X and Ma, Y and Lin, R and Huang, Y},
title = {Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1674341},
pmid = {41450573},
issn = {2235-2988},
mesh = {Humans ; *Bile/microbiology ; *Biliary Tract/microbiology ; Drainage/adverse effects ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Despite years of research, knowledge about the microbial populations of human physiological bile has remained limited. Bile sampling techniques, such as Endoscopic Retrograde Cholangiopancreatography (ERCP), percutaneous biliary drainage, and intra-operative sampling, are invasive procedures typically performed only in the presence or suspicion of biliary tract disease. Furthermore, the increased incidence of bacterial infections following biliary drainage poses a significant clinical concern; however, the relationship between biliary drainage and biliary flora remains poorly understood. In this study, we present a distinct taxonomic composition of bacterial communities identified in bile samples from disease-free individuals, as well as from obstructive and post-drainage biliary tracts.

METHODS: A metagenomic sequence analysis of bile samples from patients with MBO who underwent percutaneous biliary drainage (PTBD) at our center from 1st May 2021 to 1st March 2022, which were divided into 2 groups, as the MBO group (n = 29) and BD group (n = 27). Eight liver donors were included as a control group.

RESULTS: Abundant bacterial populations were detected in the bile of liver donors, revealing a highly similar microbial composition in both disease-free and malignant obstructive biliary trees. Notably, biliary drainage was found to alter the composition of bile microbiota, resulting in decreased microbial diversity and an association with an increase in antibiotic resistance genes.

DISCUSSION: These findings provide fundamental knowledge on the composition of the human bile microbiota and present new evidence to support that biliary drainage induces a shift in bile microbiota, rendering it more aggressive and resistant to antibiotics.},
}

Humans
*Bile/microbiology
*Biliary Tract/microbiology
Drainage/adverse effects
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Female
Male
Middle Aged
Aged
Metagenomics
Adult

@article {pmid41447958,
year = {2025},
author = {Lee, Y and Liu, Q and Sun, Y and Maszczyk, P and Wang, M and Yang, Z and Lee, JS},
title = {Hypoxia and the microbiome: Significance and application for ecotoxicological studies.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119171},
doi = {10.1016/j.marpolbul.2025.119171},
pmid = {41447958},
issn = {1879-3363},
abstract = {Hypoxia, or low oxygen availability, is a growing environmental concern that significantly impacts microbial communities. Recent studies highlight the effects of hypoxia on microbial composition and function, favoring anaerobic taxa involved in nitrogen, sulfur, and carbon cycling. These shifts influence ecotoxicological processes by modulating pollutant degradation, metal bioavailability, and greenhouse gas emissions. For instance, oxygen depletion enhances the activity of anaerobic dechlorinators but may reduce heavy metal detoxification. Advances in metagenomics and multi-omics have offered new perspectives on microbial adaptation under hypoxic stress, revealing key metabolic pathways linked to pollutant transformation. However, knowledge gaps remain in our understanding of the long-term ecological consequences of hypoxia-induced microbiome shifts. This review synthesizes recent findings on hypoxia-microbiome interactions, focusing on both environmental (e.g., sediment and water column) and host-associated (e.g., gut) microbiomes, and emphasizes their application in ecotoxicology. In addition, we discuss how hypoxia-induced microbial shifts in hypoxic environments and highlight potential applications of microbiome-based approaches for environmental risk assessment. Future research integrating experimental and modeling approaches is crucial to better predict the ecological impacts of hypoxia-driven microbial changes in contaminated environments.},
}

@article {pmid41446276,
year = {2025},
author = {Chen, S and Jiang, Y and Lv, D and Zheng, Y and Zhang, R and Dai, H and Wang, Z and Li, S and Qi, R and Xu, H and Yu, Y and Xu, C and Lu, X and Xu, Y and Jin, S and Wu, X},
title = {Identification of subtypes and construction of a predictive model for novel subtypes in severe community-acquired pneumonia based on clinical metagenomics: a multicenter, retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1676502},
pmid = {41446276},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Community-Acquired Infections/microbiology/mortality/classification/diagnosis ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; China/epidemiology ; *Pneumonia/microbiology/classification/mortality ; Adult ; Microbiota/genetics ; Prognosis ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Intensive Care Units ; High-Throughput Nucleotide Sequencing ; Nomograms ; Community-Acquired Pneumonia ; },
abstract = {OBJECTIVE: It is well recognized that high heterogeneity represents a key driver of the elevated mortality in severe community-acquired pneumonia (sCAP). Precise subtype classification is therefore critical for both treatment strategy formulation and prognostic evaluation in this patient population. This study aimed to develop a predictive model for novel clinical subtypes of sCAP, leveraging microbiome profiles identified via metagenomic next-generation sequencing (mNGS).

METHODS: This retrospective multicenter cohort study enrolled adult patients with sCAP who underwent clinical mNGS testing of bronchoalveolar lavage fluid in intensive care units (ICUs) across 17 medical centers in China. Based on mNGS-identified microbiome characteristics, unsupervised machine learning (UML) was employed for clustering analysis of sCAP patients. LASSO regression and random forest (RF) algorithms were applied to screen and identify predictors of novel sCAP subtypes. A predictive model for the new clinical subtypes was constructed according to the screening results, with a nomogram generated. The discriminative ability, calibration, and clinical utility of the model were evaluated using ROC curves, calibration curves, and decision curve analysis, respectively.

RESULTS: A total of 1,051 sCAP patients were included in the final analysis. The 28-day all-cause mortality rate was 45% (473/1,051). UML clustering identified two distinct sCAP subtypes: the 28-day mortality rate was 42.19% (343/813) in subtype 1 and 54.62% (130/238) in subtype 2. Incorporating clinical and microbial features, a predictive model for the novel sCAP subtypes was developed using the following predictors: immunosuppression (OR = 37,411.46, P < 0.001), connective tissue disease (CTD) (OR = 12,144.60, P = 0.004), hematological malignancy (HM) (OR = 107,768.13, P < 0.001), chronic kidney disease (CKD) (OR = 49.71, P < 0.001), cytomegalovirus (CMV) (OR = 0.00, P < 0.001), Epstein-Barr virus (EBV) (OR = 131.97, P < 0.001), Pneumocystis (OR = 47,949.56, P < 0.001), and Klebsiella (OR = 0.02, P = 0.003). The model demonstrated excellent discriminative ability with an area under the ROC curve (AUC) of 0.992. Calibration curves showed good agreement between predicted and observed outcomes. Decision curve analysis confirmed high clinical utility for predicting novel sCAP subtypes.

CONCLUSION: This study identified novel clinical subtypes of sCAP based on mNGS-derived microbiome characteristics. This approach exhibits superior performance in identifying high-risk sCAP patients, facilitating precise subtyping.},
}

Humans
Retrospective Studies
*Community-Acquired Infections/microbiology/mortality/classification/diagnosis
Male
Female
Middle Aged
*Metagenomics/methods
Aged
China/epidemiology
*Pneumonia/microbiology/classification/mortality
Adult
Microbiota/genetics
Prognosis
ROC Curve
Bronchoalveolar Lavage Fluid/microbiology
Intensive Care Units
High-Throughput Nucleotide Sequencing
Nomograms
Community-Acquired Pneumonia

@article {pmid41444596,
year = {2025},
author = {Tang, R and Shi, M and Ji, X and Zhang, Y and Fan, L and Huang, F and Li, X},
title = {Integrative oral and gut microbiome profiling highlights microbial correlates of complications in type 1 diabetes: a cross-sectional analysis.},
journal = {Cardiovascular diabetology},
volume = {24},
number = {1},
pages = {461},
pmid = {41444596},
issn = {1475-2840},
support = {2024XQLH049//Graduate Innovation Project of Central South University/ ; grant 2023ZD0508200 and 2023ZD0508205//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; grant 82470871//National Natural Science Foundation of China/ ; grant R2023001//Hunan Provincial Health High-Level Talent Scientific Research Project/ ; LYF2022039//Sinocare Diabetes Foundation/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications ; Male ; Female ; Adult ; Dysbiosis ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Mouth/microbiology ; Case-Control Studies ; Middle Aged ; *Diabetic Angiopathies/microbiology/diagnosis ; Young Adult ; Risk Factors ; Feces/microbiology ; Biomarkers/blood ; Host-Pathogen Interactions ; Risk Assessment ; Metagenomics ; Blood Glucose/metabolism ; },
abstract = {BACKGROUND/OBJECTIVE: Chronic vascular complications are the primary threat in long-standing type 1 diabetes (T1D) patients. We examined the associations between oral-gut microbiome dysbiosis and these complications, offering novel insights into therapeutic strategies and underlying mechanisms.

METHODS: This cross-sectional study enrolled 75 T1D participants (disease duration ≥ 10 years) and 43 healthy controls who underwent comprehensive clinical assessment, including blood glucose, lipid profile, and complication-related examinations. Fecal and oral rinse samples were collected for shotgun metagenomic sequencing. T1D participants were stratified by the presence of microvascular (retinopathy, nephropathy, or neuropathy) or macrovascular complications separately. Microbial differences across groups were assessed.

RESULTS: Significant differences in oral and gut microbiota compositions were observed between T1D participants with and without complications (both microvascular and macrovascular). A core set of 26 gut and 8 oral microbial species was specifically associated with vascular complications. Butyrate-producing gut bacteria (Blautia wexlerae, Anaerobutyricum hallii, Roseburia inulinivorans, A. soehngenii) and specific oral Neisseria species were enriched in T1D without complications individuals, suggesting protective effects against complications. Mediation analysis indicated associations consistent with partial mediation between certain microbial species and the relationships of glycemic control or insulin resistance (HbA1c, glucose risk index, estimated glucose disposal rate) with complication risk. Moreover, potential oral-gut microbiome interconnections were implicated in complication development. Finally, classification models integrating both oral and gut microbial features significantly outperformed models based on either site alone in distinguishing T1D patients with complications.

CONCLUSIONS: Distinct oral and gut microbiome features are associated with chronic vascular complications in T1D. These findings highlight the potential of microbiome-targeted strategies for understanding and preventing T1D-related complications.},
}

Humans
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications
Male
Female
Adult
Dysbiosis
*Bacteria/genetics/metabolism/classification/isolation & purification
*Mouth/microbiology
Case-Control Studies
Middle Aged
*Diabetic Angiopathies/microbiology/diagnosis
Young Adult
Risk Factors
Feces/microbiology
Biomarkers/blood
Host-Pathogen Interactions
Risk Assessment
Metagenomics
Blood Glucose/metabolism

@article {pmid41440692,
year = {2025},
author = {Lv, X and Wang, H and Wang, W},
title = {Agaricus sinodeliciosus and Coprinus comatus Improve Soil Fertility and Microbial Community Structure.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {41440692},
issn = {2309-608X},
support = {41761107//National Natural Science Foundation of China/ ; 2025-ZJ-969T//The Natural Science Foundation of Qinghai Province/ ; W2412148//International (Regional) Cooperation and Exchange (ICE) Projects of the National Natural Science Foundation of China (NSFC)/ ; D23029//111 Project/ ; },
abstract = {Agaricus sinodeliciosus (A. sinodeliciosus) and Coprinus comatus (C. comatus) are precious macrofungi found in Qinghai Province, China. As decomposers, they play a crucial role in the terrestrial ecosystem. The article takes A. sinodeliciosus and C. comatus growing in the saline-alkali land of the Qaidam Basin in Qinghai Province as the research objects, and deeply analyzes the influence of the two macrofungi on soil. The results show that, compared with the control soil, the total carbon (TC) content in the soil of A. sinodeliciosus and C. comatus increased by 27.48% and 113.24%, the total nitrogen (TN) content increased by 95.16% and 108.06%, the hydrolyzable nitrogen (HN) increased by 87.36% and 97.90%, and the available potassium (AK) increased by 182.72% and 596.09%, respectively. In addition, C. comatus significantly increased the available phosphorus (AP) by 163.14%. This proves that both macrofungi can enhance soil fertility, and C. comatus has a stronger fertilization effect. In terms of soil microorganisms, A. sinodeliciosus significantly influenced the distribution of soil bacteria and fungi, increasing the abundance of Streptomyces and reducing alpha diversity. C. comatus had a greater impact on bacteria, significantly increasing the relative abundance of Pseudomonas in the soil, but had no significant effect on fungi. Additionally, there was a close relationship between soil microbial abundance and physicochemical properties. pH, AP, TC, and AK were the main factors influencing bacteria, while total salt was the main factor affecting fungi. These findings reveal that A. sinodeliciosus and C. comatus influence the soil microenvironment by regulating soil physicochemical properties and microbial communities.},
}

@article {pmid41439481,
year = {2026},
author = {Zou, Y and Li, N and Li, X and Kuang, M and Xu, X and Guan, L and Li, X and Zheng, P and Li, L and Wan, J and Lu, N and Liu, J and He, C and Zhu, Y},
title = {Gut microbiota dysbiosis exacerbates acute pancreatitis via Escherichia coli-driven neutrophil heterogeneity and NETosis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606480},
doi = {10.1080/19490976.2025.2606480},
pmid = {41439481},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/microbiology/immunology/complications ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Neutrophils/immunology ; *Extracellular Traps/immunology/metabolism ; *Escherichia coli/physiology ; *Pancreatitis/microbiology/immunology/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Specific Pathogen-Free Organisms ; },
abstract = {Gut microbiota dysbiosis contributes to acute pancreatitis (AP) severity, but the specific microbes and mechanisms remain unclear. In this study, we employed both germ-free (GF) and specific-pathogen-free (SPF) murine models of AP to investigate the role of the intestinal microbiota. Our findings demonstrate that GF mice exhibited markedly attenuated pancreatic injury, inflammatory cell infiltration, and neutrophil extracellular traps (NETs) formation. Through fecal microbiota transplantation (FMT) from AP patients, differential antibiotic modulation, and single-bacterial colonization experiments, we identified Gram-negative bacteria, particularly Escherichia coli (E. coli), as critical microbial drivers of disease exacerbation. Single-cell RNA sequencing revealed that microbiota dysbiosis profoundly reprogrammed both local pancreatic and systemic immune landscapes. Specifically, dysbiosis promoted emergency granulopoiesis in the bone marrow, enhanced neutrophil mobilization and activation, and facilitated the expansion of pro-inflammatory neutrophil subpopulations (Neutrophils_2 and Neutrophils_3). These subsets exhibited upregulated signaling through NETosis-associated pathways, including TLR, NF-κB, and IL-17 axes. Conversely, in GF conditions, we observed a predominance of an anti-inflammatory neutrophil subset (Neutrophils_4), characterized by the expression of tissue repair-associated genes such as Reg1 and Reg2. Shotgun metagenomic profiling of fecal samples from patients with AP revealed an enrichment of E. coli during the acute phase, positively correlating with circulating cell-free DNA, a marker of NETosis. Together, these insights suggest that gut microbiota dysbiosis, notably increased E. coli abundance, may aggravate AP by reshaping immunity and promoting aberrant NETs formation, supporting microbiota or NETs targeted therapies.},
}

Animals
*Dysbiosis/microbiology/immunology/complications
*Gastrointestinal Microbiome
Mice
Humans
*Neutrophils/immunology
*Extracellular Traps/immunology/metabolism
*Escherichia coli/physiology
*Pancreatitis/microbiology/immunology/pathology
Male
Mice, Inbred C57BL
Disease Models, Animal
Fecal Microbiota Transplantation
Female
Specific Pathogen-Free Organisms

@article {pmid41437205,
year = {2026},
author = {Dinesh, D and Morgan, XC and Kim, H and Scott, TM and Garelnabi, M and Lee, JS and Mangano, KM and Nguyen, LH and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Gut Microbial Variations Associated With Proton Pump Inhibitor Use in the Boston Puerto Rican Health Study.},
journal = {Pharmacology research & perspectives},
volume = {14},
number = {1},
pages = {e70205},
pmid = {41437205},
issn = {2052-1707},
support = {RF1AG075922/AG/NIA NIH HHS/United States ; P01 AG023394/NH/NIH HHS/United States ; R01 NS09772/NH/NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; P50 HL105185/NH/NIH HHS/United States ; R01 AG055948/NH/NIH HHS/United States ; //University of Massachusetts/ ; R01 AG055948/AG/NIA NIH HHS/United States ; P50 HL105185/HL/NHLBI NIH HHS/United States ; P01 AG023394/AG/NIA NIH HHS/United States ; },
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Boston ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Hispanic or Latino ; Prospective Studies ; *Proton Pump Inhibitors/adverse effects/pharmacology ; Puerto Rico/ethnology ; },
abstract = {Proton pump inhibitors (PPI), used to treat gastrointestinal disorders, are associated with alterations in the gut microbiome. However, this is understudied in Puerto Ricans who have unique lifestyle characteristics. Puerto Ricans, including participants of the Boston-Puerto Rican Health Study (BPRHS), report high PPI use. Therefore, we examined gut microbial variations associated with PPI use in the BPRHS. BPRHS is a prospective cohort. 309 BPRHS participants self-reported PPI use and self-collected, metagenomically profiled, stool samples. PPI use was classified as any use in the past 30 days. Cross-sectional associations between gut microbial taxa, functional pathways, and PPI use were examined using omnibus analyses, multivariate linear modeling in MaAsLin2, and random forest classifier in feature-wise analyses. We further compared our results with the non-Hispanic Health Professionals Follow-Up Study (HPFS) to validate key findings and examine ethnicity-related differences. Among 309 participants (mean age 68.8 years; female 74.6%), 112 (36%) self-reported PPI use. After adjusting for relevant covariates, we observed an enrichment of Streptococcus parasanguinis (β = 3.16, FDR p = 0.01), S. anginosus (β = 2.89, FDR p < 0.01), S. salivarius (β = 2.56, FDR p = 0.01), S. gordonii (β = 1.98, FDR p = 0.15), and Rothia mucilaginosa (β = 1.54, FDR p = 0.06), among PPI users compared to non-users. Streptococci, Lactobacilli, and Enterococci predominantly contributed to the functional pathways associated with PPI use. The observed enrichment of oral-typical taxa, such as Streptococci, among PPI users in the BPRHS suggests the potential of PPIs to alter gut microbial composition. More studies are needed to understand the impact of PPI use on the gut microbiome in different ethnicities. Trial Registration: Parent study (BPRHS) NCT01231958.},
}

Aged
Female
Humans
Male
Middle Aged
Boston
Cross-Sectional Studies
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Hispanic or Latino
Prospective Studies
*Proton Pump Inhibitors/adverse effects/pharmacology
Puerto Rico/ethnology

@article {pmid41431864,
year = {2026},
author = {Dowrick, JM and Roy, NC and Carco, C and James, SC and Heenan, PE and Frampton, CMA and Fraser, K and Young, W and Cooney, J and Trower, T and Keenan, JI and McNabb, WC and Mullaney, JA and Bayer, SB and Talley, NJ and Gearry, RB and Angeli-Gordon, TR},
title = {Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604871},
doi = {10.1080/19490976.2025.2604871},
pmid = {41431864},
issn = {1949-0984},
mesh = {Humans ; Cluster Analysis ; *Gastrointestinal Diseases/physiopathology/microbiology/classification ; Male ; Female ; *Brain/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Multiomics ; },
abstract = {Rome IV disorders of gut-brain interaction (DGBI) subtypes are known to be unstable and demonstrate high rates of non-treatment response, likely indicating patient heterogeneity. Cluster analysis, a type of unsupervised machine learning, can identify homogeneous sub-populations. Independent cluster analyses of symptom and biological data have highlighted its value in predicting patient outcomes. Integrated clustering of symptom and biological data may provide a unique multimodal perspective that better captures the complexity of DGBI. Here, integrated symptom and multi-omic cluster analysis was performed on a cohort of healthy controls and patients with lower-gastrointestinal tract DGBI. Cluster stability was assessed by considering how frequently pairs of participants appeared in the same cluster between different bootstrapped datasets. Functional enrichment analysis was performed on the biological signatures of stable DGBI-predominant clusters, implicating disrupted ammonia handling and metabolism as possible pathophysiologies present in a subset of patients with DGBI. Integrated clustering revealed subtypes that were not apparent using a singular modality, suggesting a symptom-only classification is prone to capturing heterogeneous sub-populations.},
}

Humans
Cluster Analysis
*Gastrointestinal Diseases/physiopathology/microbiology/classification
Male
Female
*Brain/physiopathology
*Gastrointestinal Microbiome
Adult
Middle Aged
*Gastrointestinal Tract/physiopathology
Multiomics

@article {pmid41431647,
year = {2025},
author = {Lu, X and Dai, H and Gu, X and Xie, J and Zhong, X and Dong, X and Su, B and Su, J and Wang, L and Sun, T and Geng, L},
title = {The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20526},
pmid = {41431647},
issn = {2167-8359},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Case-Control Studies ; Biomarkers ; *Gastrointestinal Diseases/microbiology ; Clinical Relevance ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions-particularly intestinal transit and gas handling-rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.

METHODS: Fecal samples from 20 COPD & FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.

RESULTS: COPD/COPD & FABD patients showed significantly higher fecal microbiota α-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD & FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. β-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD & FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD & FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04-26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).

CONCLUSION: Gut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Aged
Feces/microbiology
Case-Control Studies
Biomarkers
*Gastrointestinal Diseases/microbiology
Clinical Relevance

@article {pmid41431641,
year = {2025},
author = {Nguyen, BN and Nguyen, LTN and Trinh, DTM and Nguyen, HT and Tran, TTT},
title = {Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20521},
pmid = {41431641},
issn = {2167-8359},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology ; Vietnam ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Pilot Projects ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; },
abstract = {In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam.},
}

Humans
*Arthritis, Rheumatoid/microbiology
Vietnam
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Pilot Projects
Adult
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Aged

@article {pmid41431440,
year = {2026},
author = {Wang, W and Huang, H and Zhao, K and Lv, J and Liu, X and Xie, S and Feng, J},
title = {The Differing Responses of Chlorophyta and Bacillariophyta to Available Resources Result in Diverse Community Patterns in Lakes Situated to the East of the Hu Line During the Autumn.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {1},
pages = {e70248},
doi = {10.1002/wer.70248},
pmid = {41431440},
issn = {1554-7531},
support = {32270220//National Natural Science Foundation of China/ ; U22A20445//National Natural Science Foundation of China/ ; 2020KJ029//Excellent Achievement Cultivation Project of Higher education in Shanxi/ ; 2024-007//Research Project Supported by Shanxi Scholarship Council of China/ ; 202203021211313//Sanjin Talent Innovation Teams in Natural Sciences and Engineering Technology/ ; },
mesh = {*Lakes ; *Diatoms/genetics/physiology ; *Chlorophyta/genetics/physiology ; Seasons ; Biodiversity ; Ecosystem ; },
abstract = {Phytoplankton communities are of vital importance to the functioning of freshwater ecosystems, but the role of the metabolic capacity of the community in regulating community dynamics under natural conditions has yet to be sufficiently considered. This study investigated 26 lakes situated along the eastern section of the Hu Line, combining field surveys with metagenome-assembled analyses to ascertain the factors responsible for the divergence in Chlorophyta and Bacillariophyta communities. The results demonstrated that the diversity of Chlorophyta was markedly higher than that of Bacillariophyta whereas the abundance was significantly lower. These discrepancies in community attributes were predominantly attributable to variations in the response of the two algal groups to nutrients. The abundance and diversity of diatom metabolic genes were significantly higher than those of green algae. The greater diversity and extent of metabolic genes in Bacillariophyta confer enhanced metabolic capacity and, consequently, greater adaptive capacity. Such differences in metabolic gene composition may be attributed to the disparate evolutionary pathways that these organisms have followed.},
}

*Lakes
*Diatoms/genetics/physiology
*Chlorophyta/genetics/physiology
Seasons
Biodiversity
Ecosystem

@article {pmid41429819,
year = {2025},
author = {Chen, Q and Xu, J and Yang, J and Qin, X and Fan, J and Ke, H and Yang, Z and Zheng, W and Li, X and Huang, L and Ning, W},
title = {Gut microbiota analysis in children with autism spectrum disorder and their family members.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44282},
pmid = {41429819},
issn = {2045-2322},
support = {Grant No.3502Z20214001//Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China/ ; 2022YFC2704300//National Key Research and Development Program of China/ ; 32400532//National Natural Science Foundation of China/ ; 2024GGB18//Fujian Provincial Health Technology Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology ; Child ; Male ; Female ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; Siblings ; Bifidobacterium/isolation & purification/genetics ; Clostridium/isolation & purification/genetics ; Bacteroides/isolation & purification/genetics ; Metagenomics/methods ; Family ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication and interaction, alongside restricted, and repetitive behaviors. Emerging evidence suggests that gut microbiota alterations may contribute to ASD pathogenesis via the gut-brain axis. However, many previous studies have not adequately controlled for confounding genetic and environmental variables. In this study, we examined the gut microbiota profiles of 19 children with ASD, 8 siblings with non-ASD, and 36 parents from 17 families, providing a unique design that minimized biases related to shared genetic and familial environments. Metagenomic sequencing revealed significant differences in gut microbiota diversity and composition between groups. Specifically, children with ASD had lower abundances of Bifidobacterium and higher abundances of both Bacteroides and Clostridium species compared to their siblings, with notable dysbiosis correlated to ASD-specific symptoms. These findings highlight the potential role of microbiota alterations in ASD pathogenesis and suggest familial microbiota traits influenced by both genetic and environmental factors. Further exploration of gut microbial therapies could offer promising avenues for ASD intervention.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/microbiology
Child
Male
Female
Child, Preschool
Dysbiosis/microbiology
Feces/microbiology
Siblings
Bifidobacterium/isolation & purification/genetics
Clostridium/isolation & purification/genetics
Bacteroides/isolation & purification/genetics
Metagenomics/methods
Family

@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth & development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}

Animals
Larva/microbiology
*Gastrointestinal Microbiome
*Salmonella/growth & development
Manure/microbiology
*Diptera/microbiology
Chickens
Bacillus
Metagenomics
*Antibiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid41428281,
year = {2025},
author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y},
title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {110},
pmid = {41428281},
issn = {1559-0267},
support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; },
abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology
Gastrointestinal Microbiome/immunology
Animals
Host-Pathogen Interactions/immunology
Dysbiosis
Disease Susceptibility
*Virus Diseases/immunology/complications
Superantigens/immunology
Immunoglobulin A/immunology/metabolism
Cytokines/metabolism

@article {pmid41426650,
year = {2025},
author = {Wang, C and Wei, H and Duan, R and Jin, S and Wen, J and Li, H and Cheng, A and Gao, C and Xue, H and Hou, Y},
title = {Habitat Diversity Sustains Ecosystem Functioning in Plateau Arid-Region Wetlands.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72747},
pmid = {41426650},
issn = {2045-7758},
abstract = {Plateau arid-region wetlands constitute critical ecosystems for regional ecological security, yet exhibit heightened vulnerability under multiple stressors. Current understanding of the mechanisms sustaining the functions of these systems, particularly the pivotal role of habitat diversity, remains limited. Targeting the Jinzihai Wetland (Qaidam Basin, Qinghai-Tibet Plateau), we integrated metagenomic and geochemical profiling to characterize three representative habitats: sandy meadows, peat bogs, and lake sediments. Our analyses revealed that pronounced cross-habitat physicochemical gradients drive community structure differentiation predominantly through species replacement, establishing habitat diversity as a fundamental driver of wetland biodiversity. Concurrently, community differentiation drives spatial divergence in functional gene composition, manifesting distinct functional dominance: sandy meadows govern assimilation and saline-alkaline stress response; peat bogs orchestrate nutrient enrichment and transformation; lake sediments mediate element release and burial. These functionally complementary habitats collectively catalyze biogeochemical cycling. We demonstrate that within plateau arid-region wetlands, habitat diversity stabilizes ecosystem functioning by sustaining both biodiversity and functional diversity of biogeochemical processes. Consequently, prioritizing habitat diversity conservation is imperative for safeguarding the long-term stability of these vulnerable ecosystems within management frameworks.},
}

@article {pmid41422081,
year = {2025},
author = {Arnaud-Haond, S and Trouche, B and Liautard-Haag, C and Alain, K and Aubé, J and Bonhomme, F and Brandt, MI and Caillarec-Joly, A and Cambon, MA and Cornette, F and Cueff-Gauchard, V and Durand, P and de Vargas, C and Felix, C and Fuchs, S and , and Günther, B and Henry, N and Hourdez, S and Jollivet, D and Le Port, AS and Lesongeur, F and Maignien, L and Comtet-Marre, S and Matabos, M and Omnes, E and Peyret, P and Pradillon, F and Sarrazin, J and Schauberger, C and Tran Lu Y, A and Ulloa, O and Vaz, S and Zeppili, D and Viard, F and Gavory, F and Gaz, S and Guy, J and Jacoby, E and Oliveira, PH and Samson, G and Aury, JM and Wincker, P and Pesant, S and Poulain, J and Belser, C},
title = {Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1982},
pmid = {41422081},
issn = {2052-4463},
support = {ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0003//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-POCE-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 678760//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 669947//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; },
mesh = {*Biodiversity ; Metagenomics ; Oceans and Seas ; DNA, Environmental ; DNA Barcoding, Taxonomic ; },
abstract = {The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.},
}

*Biodiversity
Metagenomics
Oceans and Seas
DNA, Environmental
DNA Barcoding, Taxonomic

@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}

*Snails/microbiology
*Metagenomics/methods
Animals
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41419973,
year = {2025},
author = {Rojas, MA and Serrano, G and Torres, J and Ortega, J and Gálvez, G and Vilches, E and Parra, V and Reyes-Jara, A and Maracaja-Coutinho, V and Pizarro, L and Latorre, M and Di Genova, A},
title = {Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {153},
pmid = {41419973},
issn = {2524-6372},
support = {ACT210004//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {BACKGROUND: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community.

RESULTS: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival.

CONCLUSIONS: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.},
}

@article {pmid41419527,
year = {2025},
author = {Takeda, Y and Kato-Kogoe, N and Sakaguchi, S and Ieda, S and Tasaka, Y and Mizobata, N and Omori, M and Hamada, W and Nakamura, S and Nakano, T and Ueno, T and Matsumura, T},
title = {Characteristics of salivary IgA responses to oral microbiota in patients with oral lichen planus.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44167},
pmid = {41419527},
issn = {2045-2322},
mesh = {Humans ; *Lichen Planus, Oral/microbiology/immunology ; *Saliva/immunology/microbiology ; Female ; Male ; Middle Aged ; *Microbiota/immunology ; RNA, Ribosomal, 16S/genetics ; Adult ; *Immunoglobulin A, Secretory/immunology ; Aged ; *Immunoglobulin A/immunology ; Bacteria/genetics/classification ; Metagenomics ; Case-Control Studies ; },
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa with a risk of malignant transformation. Oral bacteria are associated with OLP development and progression; however, the immune response, especially the salivary immunoglobulin A (IgA) response to these bacteria remains poorly understood. Therefore, this study aimed to characterize the salivary microbiota in patients with OLP and evaluate the corresponding salivary IgA response. Stimulated saliva samples were collected from 21 patients with OLP and 56 control participants, and 16S rRNA metagenomic analysis was performed to characterize the composition of the microbiota. In addition, IgA-enriched and non-enriched fractions from the saliva samples were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. To evaluate differences in IgA responses to each bacterium between the two groups, we calculated the IgA index. The diversity and bacterial composition of the salivary microbiota differed considerably between the OLP and control groups. Several bacterial genera, including Leptotrichia, Fusobacterium, and Streptococcus, showed markedly lower IgA index in the OLP group than the control group. In conclusion, patients with OLP exhibited a distinctive salivary IgA response to salivary microbiota, suggesting a potential association between OLP and this altered response.},
}

Humans
*Lichen Planus, Oral/microbiology/immunology
*Saliva/immunology/microbiology
Female
Male
Middle Aged
*Microbiota/immunology
RNA, Ribosomal, 16S/genetics
Adult
*Immunoglobulin A, Secretory/immunology
Aged
*Immunoglobulin A/immunology
Bacteria/genetics/classification
Metagenomics
Case-Control Studies

@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation & purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}

Female
Humans
*Trichomonas vaginalis/genetics/isolation & purification
*Metagenomics/methods
Adult
*Vagina/microbiology/parasitology/pathology
*Trichomonas Vaginitis/diagnosis/microbiology
*Microscopy/methods
Microbiota/genetics
*Coinfection/microbiology/diagnosis/parasitology
Young Adult
Middle Aged
Lactobacillus/isolation & purification/genetics

@article {pmid41415804,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671267},
pmid = {41415804},
issn = {1664-302X},
abstract = {Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L[-1]) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L[-1] in hypoxic vs. 66.56-255.63 μmol L[-1] in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L[-1]), and nitrate depletion (0.30-22.50 μmol L[-1]), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.},
}

@article {pmid41413663,
year = {2026},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {55},
number = {1},
pages = {29-34},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; Mice/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Sample Size ; Mice, Inbred C57BL ; Male ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}

Animals
Mice/microbiology
*Feces/microbiology
*Gastrointestinal Microbiome
Sample Size
Mice, Inbred C57BL
Male

@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}

*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Ficus/chemistry
*Signal Transduction/drug effects
*Lung/metabolism/drug effects
Mice
*Fatty Acids, Volatile/metabolism
*Plant Extracts/pharmacology
Male
Mice, Inbred C57BL
Disease Models, Animal
Polysaccharides/pharmacology

@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation & purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}

*Cheese/microbiology/analysis
*Seasons
*Microbiota
Animals
*Food Microbiology
Italy
Fungi/classification/genetics/isolation & purification
*Dairying/methods
Bacteria/classification/genetics
Milk/microbiology
Food Handling/methods
Cattle
Metagenomics

@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; R01 HL170904/HL/NHLBI NIH HHS/United States ; R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.

RECENT FINDINGS: Evidence on gut microbial α-diversity and β-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology/metabolism
Metabolomics/methods
Metagenomics
Dysbiosis
Proteomics
Multiomics

@article {pmid41410786,
year = {2025},
author = {Senel, E and Ramos-Barbero, MD and Santos, F and Villamor, J and Mutlu, MB and Antón, J},
title = {Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.},
journal = {Archives of virology},
volume = {171},
number = {1},
pages = {28},
pmid = {41410786},
issn = {1432-8798},
support = {208F135//the Anadolu University Research Foundation No. 1208F135. ES. was an MSc student of the Erasmus program./ ; },
mesh = {*Lakes/virology/chemistry ; Salinity ; Turkey ; Salts/chemistry ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Biodiversity ; Metagenomics ; Genome, Viral ; },
abstract = {The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).},
}

*Lakes/virology/chemistry
Salinity
Turkey
Salts/chemistry
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Biodiversity
Metagenomics
Genome, Viral

@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.

METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.

RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p < 0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p < 0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p < 0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.

CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}

Humans
*Pancreatic Neoplasms/microbiology/drug therapy/pathology
*Klebsiella pneumoniae/drug effects/genetics/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Male
Female
Middle Aged
Aged
*Drug Resistance, Multiple, Bacterial
Metagenomics
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Klebsiella Infections/microbiology

@article {pmid41409544,
year = {2025},
author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT},
title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719025},
pmid = {41409544},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; },
abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.

METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.

RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).

DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.},
}

*Gastrointestinal Microbiome
*Antelopes/microbiology/parasitology
Animals
*Blastocystis
*Blastocystis Infections/veterinary/parasitology/microbiology
Tibet
Metagenome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Feces/microbiology/parasitology

@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.

METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.

RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.

CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}

Humans
Female
*Bone Density
Middle Aged
Saliva/microbiology
*Osteoporosis, Postmenopausal/microbiology
*Postmenopause
*Microbiota
Dental Plaque/microbiology
*Mouth/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Absorptiometry, Photon

@article {pmid41403401,
year = {2025},
author = {Lin, H and Zhu, X and Zhu, J and Chen, N and Bao, W and Peng, Z},
title = {High-Throughput Sequencings Revealed That Gut Microbiota Dysbiosis is Implicated in Gouty Arthritis of Red-Crowned Crane (Grus japonensis).},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {2422900},
pmid = {41403401},
issn = {1865-1682},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Arthritis, Gouty/veterinary/microbiology ; *Dysbiosis/veterinary/microbiology/complications ; High-Throughput Nucleotide Sequencing/veterinary ; *Bird Diseases/microbiology ; Feces/microbiology ; China/epidemiology ; RNA, Ribosomal, 16S ; },
abstract = {The red-crowned crane (Grus japonensis) is one of the rarest cranes with a global population of less than 4000 individuals. The population of red-crowned crane could be influenced by health threats, including metabolic and infectious diseases. In the Wildlife Rescue Center of Suining County of Jiangsu Province, gouty arthritis (GA) was observed in all four red-crowned cranes since March 2024. A pooled fecal supernatant was first submitted to metagenomics sequencing for screening disease-associated pathogens. Enterobacteria phage phiEcoM-GJ1 was detected as the predominant virus while Escherichia coli and Aeromonas hydrophila were the dominated bacteria in the mixed fecal sample from red-crowned cranes. The 16S rRNA gene sequencing was further performed on both the mixed fecal sample and four individual samples, which showed that Escherichia-Shigella, Lactobacillus, and Enterococcus were the most abundant gut flora in both mixed and individual fecal samples. Furthermore, bacteria isolation and identification with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) confirmed that Escherichia coli was predominant (19/29 colonies, 65.52%) in the feces. Therefore, anti-uricacid and antibacteria treatments using plantain herb, doxycycline, Vitamin AD3 and multivitamin B were adopted, leading to a full behavioral recovery within 1 month. Overall, this case-based observational study provides first clue on the gut-joint axis in red-crowned cranes, supporting that gut microbiota dysbiosis is closely associated with GA in red-crowned cranes.},
}

*Gastrointestinal Microbiome
Animals
*Arthritis, Gouty/veterinary/microbiology
*Dysbiosis/veterinary/microbiology/complications
High-Throughput Nucleotide Sequencing/veterinary
*Bird Diseases/microbiology
Feces/microbiology
China/epidemiology
RNA, Ribosomal, 16S

@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {257},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/virology/metabolism ; *Lactation ; Cattle ; Female ; *Bacteriophages/classification/genetics/isolation & purification/physiology ; *Metabolome ; *Bacteria/classification/virology/genetics/metabolism/isolation & purification ; Milk/metabolism ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.

RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.

CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}

Animals
*Rumen/microbiology/virology/metabolism
*Lactation
Cattle
Female
*Bacteriophages/classification/genetics/isolation & purification/physiology
*Metabolome
*Bacteria/classification/virology/genetics/metabolism/isolation & purification
Milk/metabolism
Longitudinal Studies
*Gastrointestinal Microbiome
Metagenomics

@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Animal Feed/analysis
Plant Leaves/chemistry
Aquaculture
Diet/veterinary
*Perciformes/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Bacteria/classification/genetics
Diet, Plant-Based

@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.

AIM: This study aimed to investigate the effects of the JWC on gastric mucosal inflammation and the expression of drug-resistance genes in H. pylori-infected mice.

METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.

RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1β, and tumor necrosis factor-α (TNF-α) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.

CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}

Animals
*Helicobacter Infections/drug therapy/microbiology/pathology
*Helicobacter pylori/drug effects
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Disease Models, Animal
*Gastric Mucosa/pathology/drug effects/microbiology
*MAP Kinase Signaling System/drug effects
*Drug Resistance, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Male
Inflammation/drug therapy
*Gastritis/drug therapy/microbiology
Capsules

@article {pmid41392335,
year = {2025},
author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J},
title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.},
journal = {Journal of diabetes},
volume = {17},
number = {12},
pages = {e70175},
pmid = {41392335},
issn = {1753-0407},
support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).

METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.

RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-α, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.

CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism/immunology
*Diabetic Nephropathies/microbiology/metabolism/immunology
Male
Middle Aged
Female
*Inflammation/metabolism/microbiology
Cytokines/blood
Case-Control Studies
Aged
Adult
Feces/microbiology

@article {pmid41391220,
year = {2025},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {235},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; },
mesh = {*Azithromycin/pharmacology/therapeutic use ; Female ; Humans ; *Chlamydia trachomatis/drug effects/genetics ; *Chlamydia Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects ; *Drug Resistance, Bacterial ; Vagina/microbiology ; Metagenomics ; Adult ; Gardnerella vaginalis/drug effects/genetics/isolation & purification ; Cervix Uteri/microbiology ; Rectum/microbiology ; Biofilms/drug effects/growth & development ; Lactobacillus/drug effects/genetics ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

*Azithromycin/pharmacology/therapeutic use
Female
Humans
*Chlamydia trachomatis/drug effects/genetics
*Chlamydia Infections/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Microbiota/drug effects
*Drug Resistance, Bacterial
Vagina/microbiology
Metagenomics
Adult
Gardnerella vaginalis/drug effects/genetics/isolation & purification
Cervix Uteri/microbiology
Rectum/microbiology
Biofilms/drug effects/growth & development
Lactobacillus/drug effects/genetics

@article {pmid41390498,
year = {2025},
author = {Freel, KC and Tucker, SJ and Freel, EB and Stingl, U and Giovannoni, SJ and Eren, AM and Rappé, MS},
title = {New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67043-6},
pmid = {41390498},
issn = {2041-1723},
abstract = {The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.},
}

@article {pmid41389890,
year = {2026},
author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW},
title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.},
journal = {Journal of ethnopharmacology},
volume = {358},
number = {},
pages = {121035},
doi = {10.1016/j.jep.2025.121035},
pmid = {41389890},
issn = {1872-7573},
mesh = {Animals ; *Fatigue/drug therapy/metabolism/etiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Signal Transduction/drug effects ; Male ; Mice ; Physical Conditioning, Animal ; Gastrointestinal Microbiome/drug effects ; Hippocampus/drug effects/metabolism/pathology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.

PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.

METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.

RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2 (COX-2), MAPK14, BCL2, TLR4, TNF-α, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.

CONCLUSION: SQFNXNP regulated the TNF/NLR signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.},
}

Animals
*Fatigue/drug therapy/metabolism/etiology
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Signal Transduction/drug effects
Male
Mice
Physical Conditioning, Animal
Gastrointestinal Microbiome/drug effects
Hippocampus/drug effects/metabolism/pathology
Mice, Inbred C57BL
Brain/drug effects/metabolism
*Brain-Gut Axis/drug effects
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41389554,
year = {2026},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica sinensis/microbiology/growth & development/metabolism ; *Plant Growth Regulators/metabolism ; *Microbiota ; *Microalgae/metabolism/physiology ; Nitrogen/metabolism ; Soil Microbiology ; Coumaric Acids/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Biomass ; Soil/chemistry ; Metagenomics ; Metabolomics ; Carbon/metabolism ; Chlorella vulgaris/metabolism ; Multiomics ; },
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}

*Rhizosphere
*Angelica sinensis/microbiology/growth & development/metabolism
*Plant Growth Regulators/metabolism
*Microbiota
*Microalgae/metabolism/physiology
Nitrogen/metabolism
Soil Microbiology
Coumaric Acids/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Biomass
Soil/chemistry
Metagenomics
Metabolomics
Carbon/metabolism
Chlorella vulgaris/metabolism
Multiomics

@article {pmid41388659,
year = {2025},
author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G},
title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70214},
pmid = {41388659},
issn = {1462-2920},
support = {C03X1802//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Biofilms/drug effects/growth & development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation & purification ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; },
abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.},
}

*Biofilms/drug effects/growth & development
*Seawater/microbiology
*Plastics
Fungi/genetics/classification/drug effects/isolation & purification
*Bacteria/genetics/classification/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
*Microbiota/drug effects

@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02272-x},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantová Agentura České Republiky/ ; 22-03662S//Grantová Agentura České Republiky/ ; 22-33245S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; 21-21990S//Grantová Agentura České Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut für Gewässerökologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercetării şi Inovării/ ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.

RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.

CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}

@article {pmid41387397,
year = {2025},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11003},
pmid = {41387397},
issn = {2041-1723},
support = {2020-03545//Vetenskapsrådet (Swedish Research Council)/ ; 2024-04942//Vetenskapsrådet (Swedish Research Council)/ ; 2022-06250//Vetenskapsrådet (Swedish Research Council)/ ; ALTF 740-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Phylogeny ; *Caulobacter crescentus/genetics/classification ; *Phototrophic Processes/genetics ; Biological Evolution ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here, we establish an evolutionary and ecological context for the model organism Caulobacter crescentus-an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the phylogenetic relatedness and genetic potential of hundreds of Caulobacterales species, we reveal substantial diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light on the evolution of fundamental prokaryotic features.},
}

Phylogeny
*Caulobacter crescentus/genetics/classification
*Phototrophic Processes/genetics
Biological Evolution
Bacterial Proteins/genetics/metabolism

@article {pmid41385764,
year = {2025},
author = {Yang, H and Yu, Y and Cui, R and Zhang, Q and Chen, B and Zhang, Z and Xu, N and Sun, L and Lu, T and Qian, H},
title = {Environmental and Microbial Drivers of Global Rhizosphere Resistome Assembly.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {51},
pages = {32568-32576},
doi = {10.1021/acs.jafc.5c11060},
pmid = {41385764},
issn = {1520-5118},
mesh = {Soil Microbiology ; Rhizosphere ; *Bacteria/genetics/isolation & purification/drug effects/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Vegetables/microbiology ; Microbiota ; },
abstract = {Soil serves as a critical reservoir for antibiotic resistance genes (ARGs); however, the ecological mechanisms driving ARG assembly at the plant-soil interface remain poorly understood. In this study, we analyzed 383 metagenomic samples and identified 4803 predicted ARGs, which were classified into two distinct clusters. The ARG-abundant cluster exhibited higher rhizospheric ARG abundance and diversity but posed a relatively lower health risk compared to the ARG-scarce cluster. Warm and nutrient-rich soils promote diverse resistomes shaped by complex microbial interactions, whereas humid environments promote more homogeneously predicted ARG compositions. Environmental variables such as the temperature and nitrogen were found to indirectly influence resistome composition by modulating microbial diversity. Notably, relatively high proportions of high-risk predicted ARGs were detected in grains and raw-eat vegetables, highlighting a potential threat to public health. Our findings underscore the importance of incorporating both environmental and microbial perspectives into agricultural practices to mitigate ARG dissemination in soil.},
}

Soil Microbiology
Rhizosphere
*Bacteria/genetics/isolation & purification/drug effects/classification/metabolism
Soil/chemistry
Anti-Bacterial Agents/pharmacology
Vegetables/microbiology
Microbiota

@article {pmid41385173,
year = {2025},
author = {Othman, AA and Mohamed Zain, NI and Eshak, Z and Adman, MA and Abd Latif, Z and Aboshanab, KM and Ahmad, A},
title = {Diversity of necrophagous flies and microbiome profiling of Phumosia promittens as a rainforest health indicator.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01994-3},
pmid = {41385173},
issn = {2191-0855},
abstract = {Necrophagous flies play a critical role in decomposition and serve as bioindicators of environmental health and pollution. Malaysia's tropical rainforest ecosystems may host many necrophagous fly species, including unique blowflies and their associated bacteria. However, in many forest reserve areas, the diversity of these flies remains poorly studied. This study examines the diversity of necrophagous flies and their associated surface bacteria community, with a particular focus on Phumosia promittens (Walker in J Proc Linn Soc Lond Zool 4:90-96, 1859) in the Bangi Forest Reserve, Universiti Kebangsaan Malaysia. Sampling was conducted across three plots using baited traps, and collected flies were morphologically identified and processed under sterile conditions. Surface bacteria from P. promittens were isolated and analysed through metagenomic analysis targeting the 16S rRNA (V3-V4) amplicon sequencing gene to characterise their microbial communities comprehensively. Among 2,528 individuals collected, Chrysomya megacephala (Fabricius) was the most dominant species overall, while P. promittens was the most abundant among native forest species, suggesting their ecological adaptability and potential as a bioindicator of healthy rainforest. Shannon-Wiener and Simpson's diversity of flies in the study location were 0.67 ± 0.11 and 0.29 ± 0.06, respectively. Meanwhile, the Shannon-Wiener and Simpson's diversity of bacteria from P. promittens were 5.64 ± 0.70 and 0.96 ± 0.02, respectively. Bacterial microbiome analysis revealed the presence of core genera, including Wohlfahrtiimonas, Dysgonomonas, Vagococcus, and Ignatzschineria, which are implicated in both ecological symbiosis and public health concerns. These bacteria may contribute to nutrient cycling, such as heavy metals and antibiotics. Notably, several of these genera are emerging zoonotic pathogens with antimicrobial resistance, highlighting the dual role of necrophagous flies as ecosystem contributors and disease vectors. The findings underscore the importance of monitoring native fly species and their microbiota to assess the integrity of forest ecosystems and potential public health risks.},
}

@article {pmid41384994,
year = {2025},
author = {Zhang, J and Liu, J and Bayani, A},
title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.},
journal = {Journal of cancer research and clinical oncology},
volume = {152},
number = {1},
pages = {8},
pmid = {41384994},
issn = {1432-1335},
mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.},
}

Humans
*Hematologic Neoplasms/therapy/microbiology/immunology
*Phage Therapy/methods
Animals
*Bacteriophages
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41381437,
year = {2025},
author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J},
title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11067},
pmid = {41381437},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth & development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; },
abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.},
}

*Nitrogen/metabolism
*Triticum/metabolism/microbiology/growth & development
Soil Microbiology
*Crops, Agricultural/metabolism/microbiology
Plant Roots/metabolism/microbiology
*Agriculture/methods
Climate Change
Soil/chemistry
Nitrification
Nitrates/metabolism
*Conservation of Natural Resources
Metabolomics
Microbiota
Metagenomics
Bacteria/metabolism/genetics

@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}

*Copper/metabolism/chemistry
*Bacteria/metabolism/genetics/classification/isolation & purification
*Archaea/metabolism/genetics/classification/isolation & purification
*Sulfides/metabolism/chemistry
*Microbial Consortia
Metagenomics
*Minerals/metabolism/chemistry
*Microbiota
Plasmids/genetics

@article {pmid41380668,
year = {2025},
author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {Cell host & microbe},
volume = {33},
number = {12},
pages = {2148-2166.e8},
doi = {10.1016/j.chom.2025.11.011},
pmid = {41380668},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; },
abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.},
}

Humans
*Microbiota/genetics
*Lung/microbiology
Disease Progression
RNA, Ribosomal, 16S/genetics
*Pneumonia/microbiology/pathology
Metagenomics
Bacteria/classification/genetics/isolation & purification
Male
Female
Bacterial Load
Middle Aged
Aged

@article {pmid41380282,
year = {2025},
author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W},
title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104795},
doi = {10.1016/j.jconhyd.2025.104795},
pmid = {41380282},
issn = {1873-6009},
abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.},
}

@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation & purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.

METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n = 37; 66.1%), IBD-Unclassified (n = 9; 16.1%), ulcerative proctitis (n = 7; 12.5%), and Crohn's disease (n = 3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.

RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).

CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.},
}

Humans
*Virome/genetics
Female
Male
*Inflammatory Bowel Diseases/virology/pathology
Biopsy
High-Throughput Nucleotide Sequencing
Adult
Middle Aged
*Herpesviridae/genetics/isolation & purification
Retrospective Studies
Aged
Intestinal Mucosa/virology/pathology
*Intestines/virology/pathology
Colitis, Ulcerative/virology
Metagenomics
Young Adult

@article {pmid41379255,
year = {2025},
author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D},
title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {65},
pmid = {41379255},
issn = {1432-072X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; },
abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.},
}

Humans
*Dysbiosis/microbiology
*Leukoplakia, Oral/microbiology/pathology
Microbiota
*Host Microbial Interactions
Carcinogenesis
Mouth Neoplasms/microbiology/pathology

@article {pmid41379245,
year = {2025},
author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S},
title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {504},
pmid = {41379245},
issn = {1573-0972},
support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; },
mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation & purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.},
}

*Saccharum/parasitology
Animals
India
*Bacteria/classification/genetics/isolation & purification
*Hemiptera/microbiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Phylogeny
DNA, Bacterial/genetics

@article {pmid41379027,
year = {2025},
author = {Esvap, E and Ulgen, KO},
title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.},
journal = {Biotechnology journal},
volume = {20},
number = {12},
pages = {e70164},
doi = {10.1002/biot.70164},
pmid = {41379027},
issn = {1860-7314},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; },
abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Oxidation-Reduction
Child
Male
Feces/microbiology
*Autism Spectrum Disorder/microbiology/metabolism
Female
Child, Preschool
Metagenomics
Metabolomics
Bacteria/metabolism/classification/genetics
*Autistic Disorder/microbiology/metabolism

@article {pmid41378778,
year = {2025},
author = {Zhou, Y and Ren, X and Li, B and Tang, H and Guo, Y and Yang, L and Han, J and Zhou, B},
title = {Bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate Triggers IBD-like Pathology through the Gut Microbiota-Arachidonic Acid Axis: Protective Role of Akkermansia muciniphila.},
journal = {Environmental science & technology},
volume = {59},
number = {50},
pages = {27156-27172},
doi = {10.1021/acs.est.5c12302},
pmid = {41378778},
issn = {1520-5851},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Inflammatory Bowel Diseases/chemically induced ; Arachidonic Acid/metabolism ; Akkermansia ; Phthalic Acids ; },
abstract = {Environmental pollutants are increasingly recognized as modulators of gut microbiota and metabolic pathways, contributing to the rising global incidence of inflammatory bowel disease (IBD). The novel brominated flame retardant bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH) is increasingly detected in ecosystems and human tissues, yet its impact on intestinal health remains unclear. Here, we combined shotgun metagenomics, untargeted metabolomics, and targeted biochemical assays in a murine model to reveal how TBPH drives IBD-like pathology. TBPH exposure resulted in shortened colons, disrupted epithelial barriers, and elevated systemic pro-inflammatory cytokines, accompanied by gut microbiota dysbiosis marked by depletion of Akkermansia muciniphila (AKK). Decreased abundance of AKK correlated with arachidonic acid (AA) accumulation and hyperactivation of the phospholipase A2 (PLA2)-cyclooxygenase 2 (COX2)-prostaglandin E2 (PGE2) inflammatory cascade, leading to NF-κB activation and mucosal injury. Supplementation with viable AKK restored AA homeostasis, suppressed inflammatory signaling, and preserved the barrier integrity. These results demonstrate a microbiota-dependent mechanism linking TBPH exposure to AA-driven intestinal inflammation and identify AKK as a critical protective species, which highlights the gut microbiota-AA metabolic axis as a potential mechanism for pollutant-induced intestinal disorders.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Inflammatory Bowel Diseases/chemically induced
Arachidonic Acid/metabolism
Akkermansia
Phthalic Acids

@article {pmid41373884,
year = {2025},
author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L},
title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373884},
issn = {1422-0067},
support = {LF-ST-21-500002//LEO Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.},
}

Humans
*Dermatitis, Atopic/microbiology/drug therapy
*Microbiota/drug effects
*Skin/microbiology/drug effects
Adult
Female
Male
Middle Aged
Administration, Topical
Young Adult
Dysbiosis/microbiology
Skin Microbiome

@article {pmid41373768,
year = {2025},
author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373768},
issn = {1422-0067},
support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation & purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation & purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.},
}

*Metagenomics/methods/economics
Animals
RNA, Ribosomal, 16S/genetics
Cost-Benefit Analysis
Feces/microbiology
Benchmarking
*Metagenome
*DNA, Bacterial/isolation & purification/genetics
Reproducibility of Results
Geologic Sediments/microbiology
*DNA/isolation & purification
Gastrointestinal Microbiome/genetics

@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
Adult
Cross-Sectional Studies
Middle Aged
Aged
*Anti-Bacterial Agents/pharmacology
*Anti-Infective Agents/pharmacology
Feces/microbiology
Metagenomics
United Kingdom
*Bacteria/drug effects/classification/genetics
Young Adult

@article {pmid41369685,
year = {2025},
author = {Mohammadi, R and Morovati, H and Safari, F},
title = {The human mycobiome: a critical yet understudied component of health and disease.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
pmid = {41369685},
issn = {1465-2080},
mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; },
abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.},
}

Humans
*Mycobiome
*Fungi/genetics/classification/isolation & purification/physiology
COVID-19/microbiology/complications
Dysbiosis/microbiology
SARS-CoV-2
Metagenomics
Neoplasms/microbiology

@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}

*Seawater/virology
*Viruses/genetics/classification/isolation & purification
*Biodiversity
Ecosystem
Metagenomics
Phylogeny
Microbiota
Oceans and Seas
Metagenome

@article {pmid41368641,
year = {2025},
author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L},
title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1696701},
pmid = {41368641},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs & derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; },
abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.

METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.

RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/IκBα/NF-κB pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.

CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-κB signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.},
}

Humans
*Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology
Animals
NF-kappa B/metabolism
Mice
Signal Transduction/drug effects
Cyclic AMP/metabolism
Gastrointestinal Microbiome
Male
*Serotonin/analogs & derivatives/pharmacology/metabolism
Female
*Bacteroides/metabolism
Cyclic AMP-Dependent Protein Kinases/metabolism
Middle Aged
Cell Line, Tumor
Aged
Disease Models, Animal

@article {pmid41366428,
year = {2025},
author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW},
title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {285},
pmid = {41366428},
issn = {1742-2094},
support = {R21 NS131689/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; },
mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.

METHODS: C57BL6/J mice were randomized to CCI (6 m/s, 2 mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16 S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.

RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.

CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.},
}

Animals
*Brain Injuries, Traumatic/metabolism/complications
Mice
Mice, Inbred C57BL
*Fatty Acids, Volatile/metabolism/biosynthesis
*Gastrointestinal Microbiome/physiology
Male

@article {pmid41365917,
year = {2025},
author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D},
title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {227},
pmid = {41365917},
issn = {2055-5008},
support = {314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; 314733//Norges Forskningsråd/ ; },
mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; },
abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.},
}

Animals
Female
*Mammary Glands, Animal/microbiology
Cattle
*Mastitis, Bovine/microbiology
Longitudinal Studies
*Metagenomics/methods
*Microbiota
*Bacteria/genetics/classification/isolation & purification/pathogenicity
Lactation
RNA, Ribosomal, 16S/genetics
Genome, Bacterial

@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}

Antarctic Regions
*Soil Microbiology
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenome
*Anti-Bacterial Agents/biosynthesis
Ecosystem
Soil/chemistry
*Gases/metabolism

@article {pmid41361579,
year = {2025},
author = {Anunobi, OO and Abiola, RB and Ogah, CF},
title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {6},
pmid = {41361579},
issn = {1572-9699},
mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation & purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.},
}

*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation & purification
Humans
*Gastroenteritis/microbiology
*Genome, Bacterial
*Drug Resistance, Multiple, Bacterial/genetics
Virulence/genetics
Enterobacteriaceae Infections/microbiology
*Metagenome
Anti-Bacterial Agents/pharmacology
Virulence Factors/genetics
Computer Simulation
Computational Biology
Gastrointestinal Microbiome
Phylogeny

@article {pmid41360540,
year = {2026},
author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J},
title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117842},
doi = {10.1016/j.foodres.2025.117842},
pmid = {41360540},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; },
abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.},
}

*Fermentation
*Wine/analysis/microbiology
*Volatile Organic Compounds/analysis/metabolism
*Vitis/microbiology
Gas Chromatography-Mass Spectrometry
Taste
Odorants/analysis
China
Microbiota
Food Microbiology
*Flavoring Agents/analysis
*Bacteria/metabolism/classification
Solid Phase Microextraction
Hanseniaspora/metabolism

@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation & purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Ascaris lumbricoides/isolation & purification ; Strongyloides stercoralis/isolation & purification ; Necator americanus/isolation & purification ; Trichuris/isolation & purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Feces/parasitology/microbiology
Animals
Gabon/epidemiology
Female
Male
Child
*Helminthiasis/parasitology/epidemiology/microbiology
Metagenomics
*Helminths/isolation & purification/classification/genetics
Child, Preschool
Rural Population
Bacteria/classification/genetics/isolation & purification
Metagenome
Ascaris lumbricoides/isolation & purification
Strongyloides stercoralis/isolation & purification
Necator americanus/isolation & purification
Trichuris/isolation & purification
Biodiversity

@article {pmid41355553,
year = {2025},
author = {Kim, MJ and Park, JH and Eom, YB},
title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70197},
pmid = {41355553},
issn = {2045-8827},
support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; },
mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation & purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; },
abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.},
}

Humans
*Virome
*Skin/virology
Adult
*Viruses/classification/genetics/isolation & purification
Male
Female
Young Adult
Republic of Korea
Metagenome

@article {pmid41355481,
year = {2025},
author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD},
title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70121},
pmid = {41355481},
issn = {2045-8827},
support = {//This study was supported by Ministerio de Ciencia e Innovación, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; },
abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.},
}

*Polypropylenes/metabolism
*Polyethylene/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Agriculture
*Biodiversity
Biodegradation, Environmental
Phylogeny

@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43425},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ursidae/microbiology ; *Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use ; *Antibiotic Prophylaxis ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Cefotaxime/pharmacology/administration & dosage ; Feces/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/classification ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}

Animals
*Gastrointestinal Microbiome/drug effects/genetics
*Ursidae/microbiology
*Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use
*Antibiotic Prophylaxis
Metagenomics
RNA, Ribosomal, 16S/genetics
Cefotaxime/pharmacology/administration & dosage
Feces/microbiology
Metagenome
*Drug Resistance, Bacterial/genetics
Bacteria/genetics/drug effects/classification

@article {pmid41353034,
year = {2025},
author = {McCone, N and Hosokawa, M},
title = {Recovering genomes from uncultured fungi with single-cell genomics.},
journal = {Journal of bioscience and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jbiosc.2025.11.004},
pmid = {41353034},
issn = {1347-4421},
abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.},
}

@article {pmid41351142,
year = {2025},
author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A},
title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-025-12365-4},
pmid = {41351142},
issn = {1471-2164},
abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.

RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.

CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.},
}

@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {253},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
mesh = {*Microbiota/genetics ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; North America ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Adaptation, Physiological ; Metagenomics/methods ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.

RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.

CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}

*Microbiota/genetics
*Geologic Sediments/microbiology
*Rivers/microbiology
North America
*Bacteria/classification/genetics/metabolism/isolation & purification
Ecosystem
Metagenome
Sulfur/metabolism
Nitrogen/metabolism
Nitrogen Cycle
Adaptation, Physiological
Metagenomics/methods

@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}

*Soil Microbiology
Manure/microbiology
Fertilizers
*Soil/chemistry
Animals
Agriculture/methods
Poultry
Microbiota
Metagenomics
*Drug Resistance, Bacterial/genetics
Humans
Gene Transfer, Horizontal

@article {pmid41350329,
year = {2025},
author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T},
title = {Differences in prokaryotic and viral community between rumen and feces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43232},
pmid = {41350329},
issn = {2045-2322},
mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; },
abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.},
}

*Feces/microbiology/virology
Animals
*Rumen/microbiology/virology
Metagenomics/methods
*Viruses/genetics/classification
Metagenome
Bacteria/genetics
Virome
*Prokaryotic Cells/virology
Genome, Viral
Gastrointestinal Microbiome

@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Fecal Microbiota Transplantation/methods
*Virome
Male
Diet, High-Fat/adverse effects
Obesity/therapy/microbiology
*Feces/virology
Mice, Inbred C57BL
*Glucose/metabolism
Metabolic Syndrome/therapy/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf638},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}

*Virome
*Workflow
*Metagenomics/methods
*Software
High-Throughput Nucleotide Sequencing
*Computational Biology/methods
*Viruses/genetics/classification
Metagenome
Microbiota
Genome, Viral
Reproducibility of Results

@article {pmid41348453,
year = {2025},
author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z},
title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001493},
pmid = {41348453},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; },
abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.},
}

*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
Metagenomics/methods
Archaea/genetics/classification
Phylogeny
Biodiversity
Microbiota

@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}

Humans
Female
*Pelvic Inflammatory Disease/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Case-Control Studies
*Vagina/microbiology
Adult
*Cervix Uteri/microbiology
Vaginosis, Bacterial/microbiology
Gardnerella vaginalis/genetics
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Young Adult

@article {pmid41347789,
year = {2025},
author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS},
title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0098825},
pmid = {41347789},
issn = {1098-5336},
support = {S10 OD034282/OD/NIH HHS/United States ; 1-106223-01-01//Electric Power Research Institute/ ; },
mesh = {*Molybdenum/metabolism ; *Groundwater/microbiology/chemistry ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; },
abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.},
}

*Molybdenum/metabolism
*Groundwater/microbiology/chemistry
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Bacteria/metabolism/classification/genetics/isolation & purification
*Microbiota

@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022// Department of Biotechnology/ ; // Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}

Animals
*Perciformes/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Seafood/microbiology
Food Packaging/methods
Food Microbiology
RNA, Ribosomal, 16S/genetics
*Muscles/microbiology
Vacuum
Metagenomics
Food Storage

@article {pmid41346299,
year = {2025},
author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z},
title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11806},
pmid = {41346299},
issn = {1520-5851},
abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.},
}

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

*Metagenome
Pacific Ocean
*Transcriptome
*RNA, Transfer/genetics
*Seawater/microbiology
Ecosystem
Microbiota

@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}

*Estuaries
*Geologic Sediments/microbiology
Archaea/genetics
Metagenomics
Bacteria/genetics
Biodiversity
Ecosystem
Eukaryota/genetics
Viruses/genetics

@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; 27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}

Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Diet
Male
Female
Metabolome
Middle Aged
Metabolomics/methods
Aged
Metagenomics
Adult
Machine Learning

@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}

Fermentation
*Capsicum/microbiology/virology
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/virology
*Fermented Foods/microbiology/virology
Gene Transfer, Horizontal
*Viruses/genetics/classification/isolation & purification
Bacteriophages/genetics/classification/isolation & purification
*Microbiota
Food Microbiology

@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {1},
pages = {},
pmid = {41342600},
issn = {1574-6941},
support = {10.55776/COE7//Austrian Science Fund/ ; },
mesh = {Humans ; *Polysaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/metabolism/classification ; *Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; *Transcriptome ; Metagenomics ; Mucins/metabolism ; },
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}

Humans
*Polysaccharides/metabolism
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/metabolism/classification
*Intestinal Mucosa/metabolism/microbiology
*Metagenome
*Transcriptome
Metagenomics
Mucins/metabolism

@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Cross-Sectional Studies ; Czech Republic ; *Diet, Vegan ; *Gastrointestinal Microbiome ; Italy ; *Metabolome ; Metagenome ; Multiomics ; Vegans ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}

Adult
Female
Humans
Male
Middle Aged
*Bacteria/classification/metabolism/genetics/isolation & purification
Cross-Sectional Studies
Czech Republic
*Diet, Vegan
*Gastrointestinal Microbiome
Italy
*Metabolome
Metagenome
Multiomics
Vegans

@article {pmid41340249,
year = {2025},
author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER},
title = {Molecular insights into the gut-thyroid axis: microbiota-driven biomarkers and diagnostic applications.},
journal = {Expert review of molecular diagnostics},
volume = {25},
number = {12},
pages = {915-928},
doi = {10.1080/14737159.2025.2599225},
pmid = {41340249},
issn = {1744-8352},
mesh = {Humans ; *Biomarkers/metabolism ; *Gastrointestinal Microbiome ; *Thyroid Gland/metabolism ; *Thyroid Diseases/diagnosis/metabolism/microbiology/etiology ; Metabolomics/methods ; Metagenomics/methods ; },
abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.

AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.

EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.},
}

Humans
*Biomarkers/metabolism
*Gastrointestinal Microbiome
*Thyroid Gland/metabolism
*Thyroid Diseases/diagnosis/metabolism/microbiology/etiology
Metabolomics/methods
Metagenomics/methods

@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}

*Air Microbiology
*Metagenomics/methods
Humans
*Bacteria/genetics/classification/isolation & purification
*Aircraft
*Masks/microbiology
*Microbiota/genetics
*Air Filters/microbiology
Metagenome

@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1752},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Bacteria/metabolism/genetics/classification ; *Metagenome ; *Microbiota ; Genome, Bacterial ; Seawater/microbiology ; Phylogeny ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}

*Bacteria/metabolism/genetics/classification
*Metagenome
*Microbiota
Genome, Bacterial
Seawater/microbiology
Phylogeny

@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies