@article {pmid41271358,
year = {2025},
author = {Li, Z and Chen, Y and Zheng, J and Su, J and Lu, Y and Xia, Y and Luo, H},
title = {From fungi to lactic acid bacteria: Dominant microorganisms govern stage-specific esters biosynthesis in pit microecology of strong-flavor baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {222},
number = {Pt 2},
pages = {117797},
doi = {10.1016/j.foodres.2025.117797},
pmid = {41271358},
issn = {1873-7145},
mesh = {*Esters/metabolism ; Fermentation ; *Lactobacillales/metabolism ; *Fungi/metabolism/genetics ; *Wine/microbiology/analysis ; *Flavoring Agents/metabolism ; Butyrates/metabolism ; Food Microbiology ; Taste ; },
abstract = {Esters are vital flavor compounds in strong-flavor baijiu (SFB). However, their biosynthetic mechanisms during pit fermentation are not fully understood. This study employed integrated metagenomic and metabolomic analyses to investigate stage-specific microecological dynamics governing ester biosynthesis and identified three distinct fermentation stages. Stage P1 (days 0-15) featured initial ester accumulation driven by fungal dominance (e.g., Saccharomyces, Aspergillus, and Rhizopus) and high α-diversity. Elevated esterase (EST) genes mainly involved to the ethyl acetate and ethyl butyrate synthesis. Stage P2 (15-35 d) exhibited minimal changes in esters content (except ethyl lactate increase linked to 42 EST genes). During this stage, acidogenic microorganisms, primarily Acetilactobacillus (> 64 % relative abundance), Lactobacillus, and Clostridium, proliferated and co-aggregated with methanogens, including Methanosarcina and Methanobacterium. In Stage P3 (35-117 d), Lactobacillus-Acetilactobacillus consortium (> 74 %) exhibited rapid ester accumulation alongside acids and alcohols increases, with high EST abundance for ethyl caproate and ethyl butyrate synthesis. Dominant microorganisms govern the ester synthesis, with catalytic dominance shifting from fungal (Aspergillus, Saccharomyces, etc.) to lactic acid bacteria (Lactobacillus, Acetilactobacillus, etc.) systems across stages. Five physicochemical properties exerted the stage-dependent control: pH and reducing sugars shaped the microbial structure in P1 (R[2] = 0.40, 0.46); temperature and ethanol drove community simplification in P2 (R[2] = 0.35, 0.64); Acidity and ethanol regulated functional dominance in P3 (R[2] = 0.85, 0.64). PLS-SEM confirmed direct inhibition/promotion effects on α/β-diversity. This microecology-guided framework provided references for manipulation of ester profiles via phase-specific environmental control, offering a scientific basis for improving the quality of SFB flavor.},
}

*Esters/metabolism
Fermentation
*Lactobacillales/metabolism
*Fungi/metabolism/genetics
*Wine/microbiology/analysis
*Flavoring Agents/metabolism
Butyrates/metabolism
Food Microbiology
Taste

@article {pmid41270974,
year = {2025},
author = {Wang, L and Zhao, Z and Zhao, Y and Dong, S and Feng, S and Cao, L and Song, K},
title = {Comparative Diagnostic Accuracy of Metagenomic Next-Generation Sequencing and Targeted Next-Generation Sequencing for Periprosthetic Joint Infection: A Systematic Review and Meta-Analysis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106661},
doi = {10.1016/j.jinf.2025.106661},
pmid = {41270974},
issn = {1532-2742},
abstract = {OBJECTIVES: The aim of this meta-analysis was to assess the diagnostic performance of metagenomic next-generation sequencing and targeted next-generation sequencing for periprosthetic joint infection (PJI).

BACKGROUND: Next-generation sequencing (NGS) is increasingly used for diagnosing periprosthetic joint infection (PJI), but its clinical utility remains poorly defined. Discrepancies between metagenomic NGS (mNGS) and targeted NGS (tNGS) results pose a significant clinical challenge for PJI diagnosis. To address this, we conducted a systematic review and meta-analysis comparing the diagnostic accuracy of mNGS and tNGS for PJI.

METHODS: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We comprehensively searched PubMed, EMBASE, Cochrane Library, Web of Science, and Scopus from inception through June 1, 2025. Two reviewers independently extracted data and assessed study quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), and the area under the hierarchical summary receiver operating characteristic curve (AUC) were calculated.

RESULTS: Following screening and eligibility assessment, 23 studies were included in the analysis. The pooled sensitivity and specificity for diagnosing PJI were 0.89 (95% CI: 0.84-0.93) and 0.92 (95% CI: 0.89-0.95) for mNGS, and 0.84 (95% CI: 0.74-0.91) and 0.97 (95% CI: 0.88-0.99) for tNGS. The DORs were 58.56 (95% CI: 38.41-89.26) for mNGS and 106.67 (95% CI: 40.93-278.00) for tNGS. The areas under the summary receiver-operating characteristic curves (AUCs) were 0.935 (95% CI: 0.90-0.95) for mNGS and 0.911 (95% CI: 0.85-0.95) for tNGS. Comparisons of DOR and AUC between mNGS and tNGS revealed no statistically significant differences (P > 0.05).

CONCLUSIONS: This meta-analysis indicates that mNGS demonstrates higher sensitivity and a numerically greater AUC than tNGS for diagnosing PJI, with acceptable specificity, although the difference in AUC was not statistically significant. Conversely, tNGS exhibits higher specificity and DOR, alongside acceptable sensitivity, making it valuable for confirming PJI. Overall, the diagnostic accuracy of both next-generation sequencing (NGS) methods is comparable, with each possessing distinct advantages and limitations.},
}

@article {pmid41270973,
year = {2025},
author = {Zhu, TY and Guo, JY and Zhang, D and Weng, L and Yang, QW and Peng, JM and Du, B},
title = {A Comparative Study of DNA- and RNA-Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Tract Infections.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106659},
doi = {10.1016/j.jinf.2025.106659},
pmid = {41270973},
issn = {1532-2742},
abstract = {OBJECTIVES: To compare the clinical utility of DNA- and RNA-metagenomic next-generation sequencing (mNGS) for pathogen detection in lower respiratory tract infections (LRTIs), and evaluate strategies to optimize RNA-mNGS performance.

METHODS: We retrospectively analyzed 82 patients with suspected LRTI undergoing simultaneous DNA-mNGS and RNA-mNGS testing. The concordance of two methods in detecting microorganisms was assessed. Performance in detecting causative pathogens was compared using multi-label classification metrics. Impacts of RNA-mNGS workflow adjustments were evaluated using mock samples.

RESULTS: In a total of 196 microbial detections, DNA-mNGS and RNA-mNGS showed poor overall agreement (Cohen's κ=0.166, p<0.01). In identifying causative pathogens, RNA-mNGS demonstrated significantly higher precision (1.00 vs. 0.50, p<0.05) and F1 scores (0.80 vs. 0.67, p<0.05) compared to DNA-mNGS. DNA-mNGS possessed higher sensitivity for bacteria, fungi, and atypical pathogens, while RNA-mNGS excelled in detecting RNA viruses. Improved RNA-mNGS sensitivity and significant DNA-RNA read correlations were observed in causative pathogens at high abundance. Neither homogenization nor increased sequencing depth improved RNA-mNGS testing.

CONCLUSIONS: DNA-mNGS and RNA-mNGS exhibited low overall consistency. However, RNA-mNGS showed superior precision in identifying causative pathogens in LRTI and additional capacity for RNA virus detections, while DNA-mNGS possessed essential sensitivity for low abundance pathogens.},
}

@article {pmid41270957,
year = {2025},
author = {Xu, Y and Zhao, J and Huang, N and Wang, Z and Liu, L and Wang, Y and Qu, Q and Li, Q and Yang, Q and Wang, G and Liu, G and Wang, Q and Wu, W},
title = {Metagenomic characterization of the resistome, bacteriome and mobilome in raw milk from intensive farming systems.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.017},
pmid = {41270957},
issn = {2090-1224},
abstract = {INTRODUCTION: Intensive farming, as the dominant paradigm in global dairy production, exacerbates antimicrobial resistance (AMR) risks via concentrated animal operations and routine antimicrobial prophylaxis. Nevertheless, the spatiotemporal dissemination patterns of antibiotic resistance genes (ARGs) in regional intensive dairy systems remain insufficiently elucidated.

OBJECTIVES: Elucidating the spatiotemporal dissemination patterns of ARGs in regional intensive dairy systems by characterizing ARGs across diverse sample matrices.

METHODS: This investigation employed an integrated approach, combining metagenomic sequencing with comprehensive experimental validation, including bacterial isolation, antimicrobial susceptibility testing, PCR based detection of ARGs, biofilm formation assays, and conjugation experiments to characterize the antibiotic resistome across 539 samples (encompassing raw milk, forage, water, and breast swabs) collected from 42 intensive farms in Shandong, China.

RESULTS: DY exhibited the most pronounced microbial diversity (16,347 species) and the highest ARG abundance (547 subtypes), which were predominantly β-lactamase genes (56.3 %). Multidrug-resistant determinants were pervasive across all sample types. Klebsiella pneumoniae (K. pneumoniae) was identified as a high-risk vector, showing 96.43 % resistance to β-lactam antibiotics and a 25 % rate of multidrug resistance (MDR). Crucially, conjugation experiments confirmed the horizontal transfer of the blaSHV gene to Escherichia coli (E. coli), demonstrating its potential for cross-species transmission. Furthermore, a significant correlation (P < 0.05) was found between biofilm formation and enhanced β-lactam resistance, implicating biofilms in the maintenance of resistance.

CONCLUSION: This pioneering regional ARG atlas delineates K. pneumoniae's epidemiological significance in Shandong's intensive dairy continuum. Our findings advocate for precision intervention strategies and establish the utility of metagenomics for operational surveillance.},
}

@article {pmid41270896,
year = {2025},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {},
number = {},
pages = {149913},
doi = {10.1016/j.gene.2025.149913},
pmid = {41270896},
issn = {1879-0038},
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.

METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n = 23) prior to any treatment initiation, and unrelated healthy controls (n = 24) to elucidate their microbial diversity and relative abundance.

RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2] = 0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY:aerobactin biosynthesis.

CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}

@article {pmid41270740,
year = {2025},
author = {Yi, X and Cai, H and Liu, H and Xu, S and Meng, R and Rao, J and Wu, M and Yang, L and Shi, Y and Zhang, J and Zhu, T and Yang, Y and Wen, P and Qin, Y and Song, W and Li, JT and Shu, W and Dai, J and Sun, J and Lin, L and Guan, WJ and Brightling, CE and Zheng, XY and Wang, Z},
title = {Environmental exposure augments the abundance and transferability of antibiotic resistance genes in the respiratory tract.},
journal = {Cell reports},
volume = {},
number = {},
pages = {116517},
doi = {10.1016/j.celrep.2025.116517},
pmid = {41270740},
issn = {2211-1247},
abstract = {Exposure to environmental pollutants has been linked to increased antibiotic resistance, a critical global health challenge. The respiratory microbiome constitutes a key reservoir of antibiotic resistance genes (ARGs). Here, we constructed a respiratory ARG catalog from sputum metagenomes of 1,128 individuals. We demonstrate that exposures, particularly to cigarette smoke and biofuels, are associated with increased abundance and enhanced mobility of respiratory ARGs. These resistome alterations correlate inversely with lung function, with elevated mobile ARG abundance detectable even in individuals with mild airflow limitation within normal spirometry. Specific ARGs, including opmD and tet(K), interact with smoking in relation to lung function impairment. Murine experiments recapitulate these findings, showing exposure-induced increases in homologous ARGs that confer heightened phenotypic resistance in cultured respiratory bacteria. Our results elucidate a pathway through which environmental pollutants augment the respiratory resistome, suggesting the need for actions to mitigate the antimicrobial resistance burden by addressing environmental pollution.},
}

@article {pmid41270667,
year = {2025},
author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T},
title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.},
journal = {Chemosphere},
volume = {393},
number = {},
pages = {144767},
doi = {10.1016/j.chemosphere.2025.144767},
pmid = {41270667},
issn = {1879-1298},
abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.},
}

@article {pmid41270588,
year = {2025},
author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK},
title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180981},
doi = {10.1016/j.scitotenv.2025.180981},
pmid = {41270588},
issn = {1879-1026},
abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.},
}

@article {pmid41270407,
year = {2025},
author = {Zhang, T and Zhang, P and Zhang, J and Hu, Z and Zhang, J and Wah, TY and He, Y},
title = {Interfacial electron transfer between artificial carbon nanowires clusters and Cyt c: Enabling electron transport for methanogenesis.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124994},
doi = {10.1016/j.watres.2025.124994},
pmid = {41270407},
issn = {1879-2448},
abstract = {Intercellular electron transfer via microbial nanowires and Cytochrome c (Cyt c) is a key mechanism for syntrophic metabolism in anaerobic digestion, yet this functionality is encoded in only a limited number of microbial genomes. To address this limitation, we developed artificial carbon nanowire clusters (ACNCs) derived from plastic/sludge precursors, featuring densely arranged nanowires (Φ 20-60 nm), which form a conductive network supporting microbial colonization and electron transport. Calculations of pseudocapacitance and double-layer capacitance derived from cyclic voltammetry (CV), along with electrochemical impedance spectroscopy (EIS) characterization, revealed enhanced interfacial electron transfer between Cyt c and ACNC compared to biochar (BC) and, carbon nanotubes (CNT). Mott-Schottky analysis revealed superior energy level alignment between ACNC and Cyt c in comparison to BC/CNT, resulting in an enhanced current response in the ACNCCyt c complex, which is critical for efficient electron transfer. Circular dichroism and EPR spectroscopy revealed that ACNC induced an increase in β-sheet content in Cyt c, optimizing its electron transfer orientation. In microbial communities, ACNC supplementation enriched electroactive populations. Metagenomic analysis showed a 1.67-fold increase in Methanothrix abundance and a 1.16-fold upregulation of multiheme cytochromes (MtrC/Ech/Rnf), leading to a 123 % elevation in methanation rates compared to BC.},
}

@article {pmid41269405,
year = {2025},
author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q},
title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {102},
pmid = {41269405},
issn = {1559-0267},
support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; },
abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.},
}

Humans
*Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology
*Skin/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
Precision Medicine
Animals
Dysbiosis
Disease Susceptibility
Probiotics
Cellular Microenvironment/immunology

@article {pmid41269281,
year = {2025},
author = {Yazhini, A and Morice, É and Jochheim, A and Lieser, B and Söding, J},
title = {Evaluation of metagenome binning: advances and challenges.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf617},
pmid = {41269281},
issn = {1477-4054},
support = {101111457//Marie Skłodowska-Curie Actions/ ; //Horizon Europe programme of the European Union and from the Max Planck Society/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Computational Biology/methods ; Humans ; Algorithms ; },
abstract = {Several recent deep learning methods for metagenome binning claim improvements in the recovery of high-quality metagenome-assembled genomes. These methods differ in their approaches to learn the contig embeddings and to cluster them. Rapid advances in binning require rigorous benchmarking to evaluate the effectiveness of new methods. We have benchmarked newly developed state-of-the-art deep learning binners on CAMI2 and real metagenomic datasets. The results show that SemiBin2 and COMEBin give the best binning performance, although not always the best embedding accuracy. Interestingly, post-binning reassembly consistently improves the quality of low-coverage bins. We find that binning coassembled contigs with multi-sample coverage is effective for low-coverage dataset, while binning sample-wise assembled contigs with multi-sample coverage (multi-sample) is effective for high-coverage samples. In multi-sample binning, splitting the embedding space by sample before clustering showed enhanced performance compared with the standard approach of splitting final clusters by sample. Deep-learning binners using contrastive models emerged as the top-performing tools overall, with MetaBAT2 and GenomeFace demonstrating superior speed. To facilitate future development, we provide workflows for standardized benchmarking of metagenome binners.},
}

*Metagenome
*Metagenomics/methods
*Deep Learning
Computational Biology/methods
Humans
Algorithms

@article {pmid41268511,
year = {2025},
author = {Almeida, NEC and Kalil, AC and Gomez, CA},
title = {Prostatic Abscess due to Ureaplasma parvum in a Heart Transplant Recipient: Diagnostic Challenges and Clinical Utility of Metagenomics Next-Generation Sequencing (NGS).},
journal = {Case reports in infectious diseases},
volume = {2025},
number = {},
pages = {7511507},
pmid = {41268511},
issn = {2090-6625},
abstract = {Ureaplasma spp. are small and fastidious bacteria that may cause urogenital infections in healthy adults and, in rare cases, invasive disease. These bacteria have been increasingly recognized in immunocompromised patients and have been associated with hyperammonemia syndrome, particularly in lung transplant recipients. In this context, we present a unique clinical case of Ureaplasma parvum prostate abscess, a condition rarely observed in heart transplant recipients, diagnosed using next-generation sequencing (NGS).},
}

@article {pmid41268311,
year = {2025},
author = {Han, JA and Lee, J and An, HJ and Yi, ES and Kim, Y and Koo, BK and Lee, H and Kim, EY and Lee, HS},
title = {Exploring the Panax ginseng Meyer soil metagenome to uncover antagonistic bacteria against ginseng root rot disease.},
journal = {Journal of ginseng research},
volume = {49},
number = {6},
pages = {767-775},
pmid = {41268311},
issn = {1226-8453},
abstract = {BACKGROUND: Ginseng, renowned for its health benefits, is often cultivated with pesticides, which contradicts its health-enhancing properties. To address this, we identified Bacillus velezensis ARRI17 through a 5-year monitoring of ginseng yield on a national scale and comparative metagenome analysis. ARRI17 is a biocontrol agent that enhances ginseng growth and disease resistance under authentic field conditions.

METHODS: We identified ARRI17 through metagenomic analysis of soil samples collected from ginseng fields classified as high-yield (3.54 ± 0.46 kg per 1.62 m[2]) or low-yield (0.9 ± 0.21 kg per 1.62 m[2]), based on comparisons to the national 5-year average yield of 2.13 ± 0.35 kg per 1.62 m[2]. The biocontrol efficacy of ARRI17 was validated under laboratory conditions and field trials. Additionally, we analyzed the genomic and physiological characteristics of ARRI17 to clarify its antifungal mechanisms and adaptability to diverse environments.

RESULTS: ARRI17 exhibited strong inhibitory activity against multiple ginseng fungal pathogens, including Ilyonectria mors-panacis, in both controlled and field conditions. The application of ARRI17 improved ginseng growth parameters and reduced disease incidence in infested soil. Genomic analysis revealed that ARRI17 produces antimicrobial compounds, such as Iturin A, confirmed by HPLC. Furthermore, ARRI17 naturally thrived in rice straw compost, a traditional biofertilizer used in ginseng cultivation, suggesting its long-term presence and compatibility with standard ginseng farming practices.

CONCLUSION: Bacillus velezensis ARRI17 is an effective biocontrol agent that promotes ginseng growth and enhances disease resistance. Its natural compatibility with traditional farming practices, especially its presence with rice straw compost, positions ARRI17 as a promising and sustainable alternative.},
}

@article {pmid41268301,
year = {2025},
author = {Zhang, D and Zhou, M and Qiu, Y and Xu, H and Liu, H and Liu, Y and Xie, L},
title = {Cross-generational mechanisms of maternal gut microbiota in modulating offspring autism spectrum disorder risk: from the gut-brain axis to translational challenges in precision interventions.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1642240},
pmid = {41268301},
issn = {1663-4365},
abstract = {Autism Spectrum Disorder (ASD) manifests as a group of neurodevelopmental disorders with high clinical and genetic heterogeneity, characterized by core features including social communication deficits, repetitive behaviors, and restricted interests. Current research primarily focuses on genetic variations, immune dysregulation, synaptic dysfunction, and gene-environment interactions. Nowadays, accumulating evidence indicates that maternal gut microbiota dysbiosis, induced by high-fat diets, antibiotic overuse, and urbanization, significantly correlates with abnormal fetal neurodevelopment and increased ASD risk. This review systematically delineates three transplacental mechanisms whereby maternal dysbiosis regulates fetal neurodevelopment: Metabolite-mediated pathways, Immune pathway activation, and Epigenetic reprogramming. Meanwhile, the key translational challenges are highlighted. At last, metagenomics-metabolomics-fetal neuroimaging, Development of microbiota metabolite-treated brain organoids, and Artificial Intelligence-driven (AI-driven) probiotic screening were proposed as research directions in future.},
}

@article {pmid41268226,
year = {2025},
author = {Liu, Y and Zhang, Y and Li, Y and Yang, J},
title = {Liver abscess caused by Bacteroides thetaiotaomicron complicated by purulent pericarditis: a case report.},
journal = {American journal of translational research},
volume = {17},
number = {10},
pages = {8164-8170},
pmid = {41268226},
issn = {1943-8141},
abstract = {BACKGROUND: Liver abscess complicated by purulent pericarditis is a rare clinical condition. To date, no cases of liver abscess caused by Bacteroides thetaiotaomicron with concomitant purulent pericarditis have been reported. We present a rare case of this dual pathology to improve clinicians' understanding of liver abscess-related complications and uncommon pathogens.

CASE PRESENTATION: A 33-year-old female was admitted with hypothermia, chest tightness, and vomiting. Upon admission, laboratory tests showed elevated inflammatory markers. Ultrasound imaging revealed both pericardial effusion and a hepatic abscess, leading to a diagnosis of liver abscess complicated by purulent pericarditis. Metagenomic next-generation sequencing (mNGS) of pericardial fluid identified Bacteroides thetaiotaomicron. The patient received anti-infective therapy with meropenem and ornidazole, combined with pericardial effusion drainage. During the later stage of treatment, the patient developed thoracic empyema, necessitating thoracic drainage. Following treatment, the inflammatory markers significantly improved, the liver abscess reduced in size, and the pericardial effusion nearly resolved. At the 8-week follow-up after discharge, clinical and imaging findings were normal.

CONCLUSION: This case highlights the importance of recognizing atypical manifestations in immunocompromised patients and emphasizes the critical role of early comprehensive examination, prompt and effective anti-infective therapy, and puncture drainage for improving patient outcome. Pathogen identification methods such as mNGS can guide more precise treatment strategies, thereby shortening hospitalization and reducing complications.},
}

@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.

OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).

METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).

RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.

CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism
Male
Female
*Metabolome
Adult
Middle Aged
*Diet, High-Protein Low-Carbohydrate
*Diet, High-Protein

@article {pmid41267936,
year = {2025},
author = {Ogbuji, NG and Agogbua, JU},
title = {Genomics in plant pathogen identification and control.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1661432},
pmid = {41267936},
issn = {1664-462X},
abstract = {Recent advances in genomics have revolutionized plant pathogen detection and control by enabling faster and more accurate identification compared to traditional culture-based methods. Genomic tools like metagenomics and next generation sequencing (NGS) facilitate the detection of microorganisms (bacteria, fungi, viruses, and nematodes) directly from environmental samples. Genomics also provides information on plant-pathogen interactions, especially the detection of Resistance (R) genes and their role in plant defense against pathogens, aiding in the development of genetic markers for breeding disease-resistance crop species. Gene editing systems such as clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (CRISPR-Cas9), transcription activator-like effector nucleases (TALENs), and Zinc Finger nucleases (ZFNs) allow for precise genetic modification, either by incorporating a beneficial R genes or disabling susceptibility (S) genes of the host plant. RNA interference (RNAi) is another genomic tool used to suppress important pathogenic genes and inhibit disease development. Although the use of genomics in plant pathology is hampered by limitations such as high costs, complexity of data analysis and interpretation, and limited access to sequencing platforms, especially in developing countries, recent innovations and multi-disciplinary collaborations are tackling these issues. In general, genomics offers powerful tools that can be employed in the development of sustainable and effective plant disease management strategies, which will help to enhance crop protection and contribute to global food security.},
}

@article {pmid41267688,
year = {2025},
author = {Song, K and Ren, L and Guo, X and Ren, G and Sun, Y and Tian, X and Hu, C and Pan, M and Yu, Q and Luo, Z and Hao, Y and Lei, P and Yu, H and Yang, S and Chen, Q and Li, Y and Wang, S and He, Y and Hui, Z and Zheng, W and Jiang, J and Wang, L},
title = {Microbiota-responsive oral nano-amifostine enables colorectal-specific radioprotection and tumor immunity via gut microenvironment reprogramming.},
journal = {Advanced composites and hybrid materials},
volume = {8},
number = {6},
pages = {432},
pmid = {41267688},
issn = {2522-0136},
abstract = {UNLABELLED: Radiotherapy for abdominal malignancies is limited by intestinal toxicity and secondary colorectal cancers. Here, we develop an oral, microbiota-responsive nano-amifostine (CS/PEC-AMF NPs) system that achieves site-specific radioprotection in the colorectum without compromising antitumor efficacy. By conjugating amifostine to pectin and encapsulating it with chitosan, the nanoparticles enable pH- and microbiota-triggered release in the large bowel, safeguarding drug bioactivity during gastrointestinal transit. In murine models, CS/PEC-AMF NPs attenuate both acute and chronic radiation-induced bowel injury, restore epithelial integrity, preserve stem cell populations, and promote tight junction repair. Integrated metagenomic and metabolomic analyses reveal that the system normalizes gut microbiota diversity and composition, increases short-chain fatty acid production, and facilitates macrophage polarization towards the anti-inflammatory M2 phenotype. Notably, the formulation synergistically enhances tumor suppression and extends survival in orthotopic colorectal tumor models undergoing radiotherapy and reduces the incidence of secondary colorectal tumors post-irradiation. Mechanistically, transcriptomic analysis demonstrates the suppression of proinflammatory pathways and the promotion of DNA repair programs. This study provides a paradigm for leveraging functional nanomaterials to orchestrate precise, tissue-specific radioprotection and immune modulation, addressing a key challenge in abdominal cancer therapy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42114-025-01492-x.},
}

@article {pmid41267624,
year = {2025},
author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J},
title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70234},
doi = {10.1111/1758-2229.70234},
pmid = {41267624},
issn = {1758-2229},
support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; },
mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; },
abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.},
}

*Eutrophication
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota
RNA, Ribosomal, 16S/genetics
Ecosystem
Metagenomics
Phylogeny

@article {pmid41267035,
year = {2025},
author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z},
title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {236},
pmid = {41267035},
issn = {2049-2618},
support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; },
abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.

RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.

CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Mammals/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Altitude
Tibet
Symbiosis

@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}

*Metagenomics/methods
*Genome, Bacterial
*Metagenome
*Microbiota/genetics
Humans

@article {pmid41266391,
year = {2025},
author = {Pairoh, S and Mhuantong, W and Boonyapakron, K and Yuvaniyama, J and Kanokratana, P and Bunterngsook, B and Lekakarn, H and Arunrattanamook, N and Laothanachareon, T and Champreda, V},
title = {Machine learning-guided discovery of thermophilic carbonic anhydrases from environmental metagenomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40969},
pmid = {41266391},
issn = {2045-2322},
support = {B13F670055//Program Management Unit for Human Resources & Institutional Development, Research and Innovation (PMU-B)/ ; },
mesh = {*Carbonic Anhydrases/genetics/chemistry/metabolism ; *Machine Learning ; *Metagenome ; Metagenomics/methods ; Hot Springs/microbiology ; },
abstract = {Thermophilic carbonic anhydrases (CAs) are promising biocatalysts for carbon capture utilization and storage (CCUS) due to their stability and efficiency at elevated temperatures. This study presents a machine learning (ML)-guided approach to discover thermostable γ-class CA (γ-CA) from metagenomic datasets derived from Fang Hot Spring, Northern Thailand. To develop classification models, two sets of protein descriptors-dipeptide composition (DPC) and physicochemical/biochemical properties (AAindex)-were used to train classification models. Fourteen ML algorithms were systematically evaluated for each feature set. AdaBoost achieved the best performance for the DPC-based model, while LightGBM performed best with AAindex-based features. External validation with known CA sequences confirmed the ability of the models to discriminate thermophilic from non-thermophilic proteins. Applying the optimized models, we screened 1,534 predicted CAs and identified three high-confidence candidates (TtCA, CrCA, and ToCA). These were heterologously expressed in E. coli, purified, and biochemically validated. All candidates exhibited carbonic anhydrase activity, trimeric oligomeric structures, and high melting temperatures (Tm ranging from 97.0 °C to 109.1 °C). Although their hydration activity was modest compared to α-class CAs, their thermal robustness highlights their potential for industrial CO2 capture. This study demonstrates an approach in which ML integrated with metagenomics enables efficient discovery and validation of robust enzymes from extreme environments, providing a scalable strategy for CCUS applications.},
}

*Carbonic Anhydrases/genetics/chemistry/metabolism
*Machine Learning
*Metagenome
Metagenomics/methods
Hot Springs/microbiology

@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}

Animals
*Enterococcus faecalis/physiology/genetics
Bees/virology/microbiology
*Symbiosis
Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Larva/virology/microbiology
Apoptosis

@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {1OT3HL14715//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; K01HL157658//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL157069//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01HL136266//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01MD011389//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}

Adult
Female
Humans
Male
Middle Aged
*Asthma/genetics/microbiology/epidemiology/ethnology
Body Mass Index
Cross-Sectional Studies
Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Hispanic or Latino/genetics
Obesity/microbiology/genetics/complications
Risk Factors
United States/epidemiology

@article {pmid41265635,
year = {2025},
author = {Wang, S and Huang, Y and Wang, N and Zhou, H and Ren, X and Li, K and Xia, Y and Xu, J and Huang, L and Cai, H},
title = {Epstein-Barr virus in suspected intracranial infection: a multicenter, retrospective study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108235},
doi = {10.1016/j.ijid.2025.108235},
pmid = {41265635},
issn = {1878-3511},
abstract = {OBJECTIVES: The clinical relevance of Epstein-Barr virus (EBV) detection in cerebrospinal fluid (CSF) using metagenomic next-generation sequencing (mNGS) in patients with suspected intracranial infections has not been fully clarified. This study aimed to assess the clinical features, imaging characteristics, and outcomes in EBV-positive patients.

METHODS: We retrospectively enrolled patients with suspected intracranial infection who underwent commercial mNGS of CSF samples between December 2019 and October 2023 across 13 hospitals in four cities. Clinical data were collected, and multivariable logistic regression was performed to assess the association between EBV positivity and unfavorable outcomes.

RESULTS: Among 507 patients, 51 (10.1%) were EBV-positive in CSF. EBV-positive cases showed higher CSF mononuclear cell proportions (83.8% vs. 32.8%, p<0.001), lower chloride levels (123.0 vs. 126.1 mmol/L, p=0.019), and more frequent herpesvirus co-detection (21.6% vs. 8.6%, p=0.007). Imaging abnormalities did not differ significantly. After adjustment, multivariable logistic regression showed that EBV was not an independent risk factor for clinical outcomes (OR 1.005, 95% CI 0.516 - 1.972, p = 0.988).

CONCLUSIONS: EBV was detected in 10.1% of patients in CSF samples from patients with suspected intracranial infections. EBV positivity correlated with a lymphocytic CSF profile and co-detection of other herpesviruses but was not independently associated with unfavorable outcomes.},
}

@article {pmid41265331,
year = {2025},
author = {Zeng, Y and Gao, H and Huang, H and Xiong, W and Bin, L and Liao, B and Chen, W and Chen, X and Wen, S and Li, P and Huang, S and Tang, B},
title = {Performance, metabolism, and resistance of an SMX-stressed continuous-flow AGS-MBR system: Microscopic mechanism of macroscopic instability phenomena.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124968},
doi = {10.1016/j.watres.2025.124968},
pmid = {41265331},
issn = {1879-2448},
abstract = {To clarify how long-term sulfamethoxazole (SMX) pressure converts macro-scale performance loss into micro-level mechanistic change, a continuous-flow aerobic granular sludge membrane bioreactor (AGS-MBR) was operated for 140 days at SMX concentrations ranging from 0 to 5 mg L[-1]. At 0.2-1 mg L[-1], the system remained resilient: TN and TP removal stabilized at 90 % and 72.8 %, respectively, and the volume-mean granule diameter remained 282 µm. Metagenomics revealed significant up-regulation of the glycogen-metabolising gene glk and the polyphosphate gene ppk, which fuelled an energy-compensation pathway that supplied ATP and precursors for TB-EPS synthesis and reinforced granule scaffolding. When influent SMX rose to 5 mg L[-1] this compensation collapsed: EPS dropped 45 %, Dv shrank 38 %, granules disintegrated, TN removal fell to 70 % and TP to 44.8 %. The community shifted to a filamentous bacteria dominated state with Thiothrix >25 % relative abundance. Concurrently, the non-pathogen Rubrivivax became a shared host for antibiotic resistance genes (sul1, sul2) and multiple transposases; mobile genetic elements mediated the co-transfer of resistance and virulence genes and eroded functional redundancy. LC-MS further showed that the major transformation products P4 and P6 exhibited 2.3 folds higher chronic toxicity than the parent compound and imposed additional chemical stress on the already impaired granule microbiota. SMX dose dictated a cascade in which metabolic compensation was followed by selection of filamentous hosts prone to gene mobility and finally by chemical toxicity, progressively dismantling granule structure, nutrient removal services and ecological safety. These results elucidate the dose-dependent macro-to-micro cascade under SMX stress and provide insights for mitigating ecological risks in antibiotic laden wastewater.},
}

@article {pmid41264852,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00349},
pmid = {41264852},
issn = {1520-4995},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}

@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}

@article {pmid41263111,
year = {2025},
author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC},
title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1234},
pmid = {41263111},
issn = {1362-4962},
support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; },
abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.},
}

@article {pmid41263098,
year = {2025},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1185},
pmid = {41263098},
issn = {1362-4962},
support = {R01GM140370/NH/NIH HHS/United States ; R03OD039979/NH/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}

@article {pmid41262935,
year = {2025},
author = {Zhang, B and Meng, D and Wang, X and Hu, J and Fan, J and Li, X and Yang, Z and He, W and Zhou, D and Cheng, Y and Li, J and Zou, J and Liu, Z},
title = {Additive of cow dung weakened the influences of microbial interactions on nitrogen dynamic during composting of rice husks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641502},
pmid = {41262935},
issn = {1664-302X},
abstract = {Rice husk (RH) and cow dung (CD) are two of the most abundant agricultural solid waste. Converting these residues into peat-free substrates through co-composting supports sustainable agricultural development. A 40-day rice husk composting experiment was conducted to assess the effects of cow dung addition on microbial networks and carbon-nitrogen dynamics using 16S rRNA and metagenomic analyses. Furthermore, Furthermore, we prepared seedling substrates from composts of RH alone and RH combined with CD (RHCD), and evaluated their plant growth-promoting effects. The addition of cow dung (CD) to rice husk (RH) composting increased the average temperature from 52.8 °C to 60.1 °C and acted as a pH buffer, maintaining values around 7.4. CD significantly (p < 0.05) enhanced microbial network complexity, as indicated by larger network size and higher average degree, but disrupted the linear correlations between network properties and carbon or nitrate nitrogen contents (p > 0.05). This decoupling suggests that CD weakened the linkage between microbial interactions and carbon or nitrogen biotransformation processes. CD also significantly suppressed (p < 0.05) denitrification-related genes (norB, nir and nar) after the thermophilic phase, implying reduced nitrogen loss during compost maturation. We further found that larger network size or higher average degree reduced the abundance of key genes involved in assimilatory nitrite reduction (e.g., nirBD), while increasing those related to denitrification (e.g., nirK and nirS). Moreover, seedling substrates derived from RH (95.06%) and RHCD (93.21%) composts achieved higher germination rates of Solanaceae crops than the commercial peat-based substrate (81.48%). Germination rate and seedling biomass were positively correlated with dissolved organic carbon (r = 0.820, p = 0.045) and ammonium nitrogen (r = 0.858, p = 0.029), respectively. These findings advance the understanding of microbial interaction regulating carbon and nitrogen cycling during RH composting, and support the sustainable production of peat-free seedling substrates from agricultural waste.},
}

@article {pmid41262931,
year = {2025},
author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A},
title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1704392},
pmid = {41262931},
issn = {1664-302X},
abstract = {INTRODUCTION: Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neurocognitive issues in people without HIV. Recently characterized, the brain and cerebrospinal fluid (CSF) viromes represent a new avenue to understand brain and mental health in PWH.

METHODS: This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA and RNA viruses. Taxonomic composition (reads and contigs), diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV status, markers of neuroinflammation/neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of hEV, non-human viruses (NHV) and blood-brain barrier permeability were performed. Multivariable models assessed the relationship between cognition and clusters.

RESULTS: Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. PWH displayed lower α diversity, although p > 0.05. At β diversity analysis, HIV status explained 3.4% of the variation in viral composition (p = 0.016). Contigs assembly yielded 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (rho 0.36, p = 0.002) and β-Amyloid 1-42 fragment (βA-42, rho 0.27, p = 0.026), whereas higher RA of nhEV with poorer cognitive performance (rho 0.26, p = 0.022). Conversely, higher RA of hEV correlated with better cognition (rho -0.38, p = 0.003) and lower βA-42 (rho -0.30, p = 0.012). Sensitivity analyses restricted to only CSF samples with detectable reads confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and NHV-enriched CSF (all p < 0.05).

CONCLUSION: This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.},
}

@article {pmid41262456,
year = {2025},
author = {Ma, Y and Li, Z and Liu, P and Wei, Y and Jiang, K and Yue, Y and Zhang, A and Wang, W and Li, L and Zhang, P and Gu, X and Liu, Q and Lu, L},
title = {Metagenomics research on the gut microbiota of the Marmota himalayana of the Sanjiangyuan National Nature Reserve in Qinghai Province, China.},
journal = {Biosafety and health},
volume = {7},
number = {5},
pages = {281-294},
pmid = {41262456},
issn = {2590-0536},
abstract = {With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau, the scope of human activities has continuously expanded, increasing opportunities for contact with wildlife, also exacerbating the outbreak rate of zoonotic emerging infectious diseases. Currently, research on the gut microbiota of wildlife, especially Marmota himalayana (M. himalayana), which are reservoir hosts for plague, is scarce. In this study, we investigated the composition, function, and regional variations of the gut microbiota in M. himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province. The results indicated that at the phylum level, the dominant bacterial phyla in the gut microbiota of the M. himalayana were Firmicutes, Bacteroidota, and Proteobacteria, collectively accounting for 74.16 % of the community. At the genus level, the top three most abundant genera were Alistipes (11.86 % ± 1.56 %), Bacteroides (6.68 % ± 0.95 %), and Clostridium (4.92 % ± 1.04 %). Kyoto encyclopedia of genes and genomes (KEGG) database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism, genetic information processing (GIP), and environmental information processing (EIP). These active functions played a crucial role in food digestion, nutrient absorption, metabolic balance maintenance, and pathogen defense, aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau. The study provided critical insights into host-microbe interactions, highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.},
}

@article {pmid41262425,
year = {2025},
author = {Morelle-Hungría, E},
title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {244},
doi = {10.12688/openreseurope.21126.2},
pmid = {41262425},
issn = {2732-5121},
abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.},
}

@article {pmid41261745,
year = {2025},
author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z},
title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1243},
pmid = {41261745},
issn = {1362-4962},
support = {2022FY100905//Science & Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; },
abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.},
}

@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics/methods
Proteomics/methods
*Snails/microbiology
Phylogeny
Metagenome
Multiomics

@article {pmid41261035,
year = {2025},
author = {Rahman, T and Samia, NSN and Moon, SB and Islam, MS and Mahmud, ZH and Kabir, MS and Karim, MM and Rahman, M and Jubair, M},
title = {2024 Bangladesh Floodwaters Harbour Regional Hotspots of Pathogens and Antimicrobial Resistance.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70240},
doi = {10.1111/1758-2229.70240},
pmid = {41261035},
issn = {1758-2229},
support = {//International Centre for Diarrhoeal Disease Research, Bangladesh/ ; //Government of Bangladesh/ ; //Global Affairs Canada/ ; },
mesh = {Bangladesh ; *Floods ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; *Water Microbiology ; },
abstract = {Seasonal flooding in Bangladesh poses severe public health risks through waterborne disease, yet a comprehensive, genomic-level understanding of the associated microbial hazards is lacking. This study presents a comprehensive shotgun metagenomic analysis of floodwaters from four districts of Bangladesh (Cumilla, Feni, Lakshmipur, and Noakhali) during the devastating 2024 floods, profiling the distribution of pathogenic bacteria, antimicrobial resistance genes, and virulence factors. A total of 12 samples were collected during peak flooding periods and processed using Illumina sequencing. Taxonomic profiling and resistome analysis were performed using MetaPhlAn4, ABRicate, and MEGAHIT, referencing the NCBI and CZ ID databases. Across all regions, 301 operational taxonomic units were identified. Feni exhibited the highest diversity of pathogenic species, including multidrug-resistant Klebsiella pneumoniae, toxigenic Pseudomonas aeruginosa, and mobilizable resistance plasmids (e.g., IncP1, Col440I). Noakhali samples revealed co-detection of zoonotic and emerging pathogens such as Aliarcobacter spp. and Streptococcus suis, along with key resistance genes like blaOXA and ermB. Microbial community clustering revealed strong spatial heterogeneity. This study provides genomic evidence that floodwaters harbour emerging pathogens and AMR. It strongly advocates for incorporating metagenomic tools into Bangladesh's national flood response and AMR monitoring frameworks.},
}

Bangladesh
*Floods
*Bacteria/genetics/drug effects/isolation & purification/classification
Anti-Bacterial Agents/pharmacology
Metagenomics
*Drug Resistance, Bacterial/genetics
Virulence Factors/genetics
Drug Resistance, Multiple, Bacterial/genetics
*Water Microbiology

@article {pmid41260473,
year = {2025},
author = {Dyukova, K and Paloyan, A and Khoyetsyan, L and Mkhitaryan, A and Antranikian, G and Hambardzumyan, A},
title = {Characterization of thermostable β-glucosidase immobilized on linen fabric.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27014},
pmid = {41260473},
issn = {1525-3198},
abstract = {In this study, a thermostable β-glucosidase derived from a hot spring metagenome was successfully immobilized on linen fabric to create an eco-friendly and reusable biocatalyst for lactose hydrolysis. The enzyme is derived from a metagenome of the high-temperature Pisciarelli hot springs, an extreme environment known to yield robust biocatalysts with industrial relevance. Two immobilization strategies were employed: direct covalent binding (Lf-β-glucosidase) and binding via a spacer arm (LfEG-β-glucosidase). The latter exhibited superior enzymatic performance, retaining 76.6% of its initial activity and demonstrating enhanced thermal and operational stability. Both free and immobilized forms of enzyme showed similar pH and temperature optima, with the immobilized form exhibiting significantly improved long-term thermostability and storage stability-retaining full activity after 1 yr at 4°C. The LfEG-β-glucosidase biocatalyst was effectively applied in the enzymatic treatment of cheese whey, retaining 90% activity after 15 reuse cycles, yielding more than 6.4 g of glucose. These findings highlight the promising use of biodegradable, low-cost linen fabric as a carrier for thermostable enzymes in food biotechnology. The high efficiency and reusability of the developed biocatalyst offer a compelling solution for lactose hydrolysis and valorization of dairy industry by-products, particularly whey, within a circular and environmentally conscious production model.},
}

@article {pmid41260470,
year = {2025},
author = {Dilireba, E and Lu, Q and Chang, L and Luo, F},
title = {Antibiotic resistance profile and molecular mechanism of enterococci in traditional fermented yogurts.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27212},
pmid = {41260470},
issn = {1525-3198},
abstract = {Enterococci are present in traditional fermented foods, but their potential role as reservoirs of antibiotic resistance and virulence genes has raised concerns about food safety. To evaluate the prevalence of antibiotic-resistant enterococci in traditional fermented yogurt, microbial sequencing and culture methods were used to analyze the microbiota and Enterococcus composition in a total of 75 yogurts from Xinjiang Uygur Autonomous Region (Xinjiang, China). Enterococcus faecium and Enterococcus durans were the predominant enterococcal species and belonged to 20 and 5 biotypes, respectively, according to randomly amplified polymorphic DNA PCR analysis. Antibiotic resistance testing revealed that 98.92% of Enterococcus strains were resistant to at least one kind of antibiotic, of which E. faecium showed high resistance to gentamicin (96.92%), erythromycin (55.38%), and ciprofloxacin (49.23%), whereas E. durans was most resistant to tetracycline (58.82%) and chloramphenicol (55.82%), followed by gentamicin (47.06%). Multidrug-resistant strains were more abundant in E. faecium (37.3%). Furthermore, vancomycin resistance was observed in E. faecium strains, highlighting the risk of resistance spread. Molecular analysis revealed vancomycin and tetracycline resistance phenotypes were consistent with genotypes, but not for penicillin, gentamicin and erythromycin. Moreover, mobile genetic elements were detected, such as 5'ococs/3'ococs and IntI3, which facilitate gene transfer. Metagenomic sequencing further revealed the high abundance of antibiotic resistance genes, such as mlaF, macB, and ImrD. Additionally, the microbial co-occurrence network analysis revealed significant positive correlations between E. faecium and Acetobacter in the Zhaosu region. This study highlights that traditional fermented yogurt may serve as a reservoir for multidrug-resistant enterococci, posing a potential risk to public health.},
}

@article {pmid41161417,
year = {2025},
author = {Mussert, CMA and Miesbach, W and Chowdary, P and Lillicrap, D and Mahlangu, J and Peyvandi, F and Pipe, SW and Srivastava, A and Voorberg, J and Pierce, GF and Kaczmarek, R and Batty, P and Cutica, I and Nathwani, A and Leebeek, FWG},
title = {A comprehensive care pathway of gene therapy for hemophilia based on current guideline documents and summary of product characteristics: communication from the ISTH SSC working group on gene therapy.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2025.09.041},
pmid = {41161417},
issn = {1538-7836},
abstract = {BACKGROUND: Gene therapy for hemophilia has recently been implemented as standard clinical care, requiring organizational and multistakeholder preparedness and clear guidelines. In addition to pharmaceutical summaries of product characteristics (SMPCs), various (inter)national guidance documents have been published. However, no guidance document or SMPC covers the entire gene therapy care pathway.

OBJECTIVES: This study provides a complete and comprehensive overview of current guidance documents and SMPCs to develop a comprehensive care pathway for hemophilia gene therapy delivery.

METHODS: Published gene therapy guidance documents and collected SMPCs were complemented by a selective search in online databases, including PubMed and scientific societies' websites. Reference lists were checked for additional relevant articles.

RESULTS: Four SMPCs and 11 (inter)national guidance documents and recommendations were collected. The documents were focused on either the intervention or the care pathway, and none were comprehensive covering all aspects of hemophilia gene therapy delivery. Considerable differences were found between the 2 approved gene therapy products and between the SMPCs issued by the 2 regulatory authorities, the Food and Drug Administration and the European Medicines Agency. (Inter)national guidance documents provided additional information and recommendations not covered in SMPCs.

CONCLUSION: Based on SMPCs and (inter)national guidance documents and recommendations a care pathway has been developed and visualized in a Metro Map. This provides a clear and comprehensive overview of all activities, contact moments, and responsibilities within the longitudinal gene therapy treatment process. This comprehensive care pathway may help navigate gene therapy implementation, providing guidance to clinicians, patients, and caregivers.},
}

@article {pmid41260397,
year = {2025},
author = {Abbasi, E},
title = {Metagenomic Surveillance of Emerging Viruses in Mosquito Populations from High-Risk Regions of Iran.},
journal = {Journal of virological methods},
volume = {},
number = {},
pages = {115301},
doi = {10.1016/j.jviromet.2025.115301},
pmid = {41260397},
issn = {1879-0984},
abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.

METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.

RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.

CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.},
}

@article {pmid41260011,
year = {2025},
author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J},
title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119004},
doi = {10.1016/j.marpolbul.2025.119004},
pmid = {41260011},
issn = {1879-3363},
abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.},
}

@article {pmid41259923,
year = {2025},
author = {Wang, YC and He, LY and Wu, DL and Gao, FZ and Liu, YS and Ying, GG},
title = {Long-term manure applications promote persistent antibiotic resistance in soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140476},
doi = {10.1016/j.jhazmat.2025.140476},
pmid = {41259923},
issn = {1873-3336},
abstract = {Manure application has the potential to influence soil microbial composition and the antibiotic resistome; however, its long-term effects remain largely unknown. This study investigated the prolonged impacts of manure applications (pig and chicken manure/compost) on soil antibiotic resistance over a two-year period. Compared with the control (51.9-85.1 ng/g), manure-amended soils contained markedly higher antibiotic concentrations (356-26100 ng/g), remaining 4-300 times higher after 730 days, especially in pig compost treatments. The abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in amended soils (4.48 × 10[8]-2.74 × 10 [12] copies/g) consistently exceeded those in controls (1.24 × 10[7]-6.10 × 10[7] copies/g). Notably, 62.5 % of ARGs were located on plasmid-associated contigs, and high-risk genes such as floR and aph(3')-III persisted throughout incubation. Elevated MGE levels after 730 days indicated sustained horizontal gene transfer (HGT) potential under antibiotic selection pressure. Overall, these results reveal the long-lasting enrichment of ARGs and highlight the need for improved manure management and long-term.},
}

@article {pmid41259914,
year = {2025},
author = {Yang, W and Wang, X},
title = {Transmission mechanisms and risk tracing of antibiotic resistance genes in rivers driven by wastewater inputs.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140523},
doi = {10.1016/j.jhazmat.2025.140523},
pmid = {41259914},
issn = {1873-3336},
abstract = {Aquatic environments are critical for ARG dissemination, yet contributions from different wastewater sources, dominant HGT mechanisms, and residual risks in natural waters remain unclear. Based on 863 metagenomic samples across China, we systematically analyzed wastewater inputs, HGT mechanisms, and risks of riverine ARGs. Wastewater treatment plants were the primary source, contributing about 50 % of riverine ARGs. Conjugation dominated ARG transfer, primarily via F-type type IV secretion systems. High-transmission plasmids were widespread. Although phage-mediated transduction represented only 3 % of HGT, it facilitated cross-environmental spread of clinically significant blaGES-18. Metagenome-assembled genomes revealed 78 % of resistant bacteria belonged to Pseudomonadota; 42 % co-harbored virulence factors. Phylogenetic analysis showed high inter-generic mobility of sul1/sul2, explaining their environmental persistence. Overall risk in rivers decreased by 44 % - 93 % compared to wastewaters. However, Acinetobacter carrying blaOXA and Cellvibrio sp002483145 carrying blaKHM-1 were phylogenetically close to Acinetobacter baumannii and Pseudomonas aeruginosa, indicating potential pathways toward key pathogens. Our study identifies wastewater as the main source of riverine ARGs, reveals conjugation as the primary transmission mechanism with transduction playing a secondary role, and demonstrates that high-risk ARGs can still spread to pathogenic bacteria in rivers. These findings are crucial for developing effective strategies to mitigate ARG risks.},
}

@article {pmid41260377,
year = {2025},
author = {Chen, Z and Zhu, S and Gao, S and Wu, H and Tian, S and Wen, X},
title = {Fe3O4-Enhanced continuous production of medium-chain fatty acids from Sludge: Metagenomic Perspective on microbial synergy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133673},
doi = {10.1016/j.biortech.2025.133673},
pmid = {41260377},
issn = {1873-2976},
abstract = {Fe3O4 exhibits promising potential in enhancing chain elongation (CE) for medium-chain fatty acids (MCFAs) production from sludge, yet its application in continuous flow processes remains underexplored. In this study, MCFAs were continuously produced from sludge via a Fe3O4-enhanced CE process. Optimal performance was achieved with 20 g/L Fe3O4, 5.8 g COD/L/d ethanol loading rate (ELR), and 3-day hydraulic retention time (HRT), yielding 11.4 ± 0.8 g COD/L MCFAs and a production rate of 3.7 ± 0.1 g COD/L/d. n-Caproate and n-caprylate accounted for 40.9 % and 54.4 % of total MCFAs, respectively. Fe3O4 addition halved CE start-up time and increased MCFA production fourfold. Metagenomic analysis identified Clostridium kluyveri, Petrimonas sp., Alcaligenes faecalis, Proteiniphilum acetatigenes, and Anaerosalibacter sp. as biomarkers enhancing the fatty acid biosynthesis (FAB) cycle. These taxa could increase malonyl-ACP availability, improve reductive reaction efficiency, and promote acetyl-CoA generation, facilitating a streamlined microbial community with Pseudomonas caeni. This investigation offers strategic insights and data support for the high-value utilization of excess sludge.},
}

@article {pmid41260374,
year = {2025},
author = {Zhang, Q and Lin, L and Hu, T and Liu, Q and Wang, Y and Mo, H and Jin, W and Zhang, W and Chen, J and Zeng, H and Wang, X and Chen, S and Zhang, Y},
title = {Nitrogen removal driven by zonal supply of thiosulfate and pyrite in an up-flow blanket filter (UBF) reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133677},
doi = {10.1016/j.biortech.2025.133677},
pmid = {41260374},
issn = {1873-2976},
abstract = {Despite its effectiveness in nitrogen removal, the anammox process faces challenges in practical applications due to NO3[-]-N accumulation, which can lead to effluent breaches of discharge standards. This study developed a single-stage up-flow blanket filter (UBF) reactor featuring three axially stratified functional zones with multi-point supplementation of thiosulfate and pyrite. During stable operation, the high-intensity anammox layer (L1) contributed to 82.3 % of total nitrogen (TN) removal and generated alkalinity to support subsequent sulfur autotrophic denitrification (SAD). The SAD-coupled anammox layer (L2) effectively removed accumulated NO3[-]-N, reducing TN from 42.8 mg/L to 25.2 mg/L. The advanced nitrogen removal layer (L3) further polished the effluent to a TN concentration of 4.3 ± 2.8 mg/L and a pH of 7.1 ± 0.1, achieving advanced nitrogen removal and pH self-regulation. Anammox bacteria exhibited an inhibition-recovery response to thiosulfate addition, while pyrite served a triple role as a filter medium, metabolic accelerator, and electron donor. Metagenomic analysis revealed that thiosulfate supplementation selectively enrichedThiobacillusandPFJX01in each functional zone, with denitrification gene abundance increasing along the reactor's height. Notably, functional and associated microorganisms showed layer-specific gene expression and co-metabolism patterns. Even within the same genus, differential gene regulation in response to local microenvironments drove functional divergence at the genetic level. In summary, this work innovatively establishes spatially segregated functional layers within a single UBF reactor, offering a novel low-carbon strategy for advanced nitrogen removal and facilitating the resource utilization of tailings.},
}

@article {pmid41260114,
year = {2025},
author = {Ahmad, W and Ray, R and Khan, AL},
title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.},
journal = {The Science of the total environment},
volume = {1007},
number = {},
pages = {180812},
doi = {10.1016/j.scitotenv.2025.180812},
pmid = {41260114},
issn = {1879-1026},
abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.},
}

@article {pmid41259660,
year = {2025},
author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A},
title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf620},
pmid = {41259660},
issn = {1367-4811},
abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.

RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.

raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.},
}

@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}

Humans
*Dental Caries/microbiology
Adolescent
Male
*Microbiota/genetics
Female
Child
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
DMF Index
Reference Values

@article {pmid41258718,
year = {2025},
author = {Markkanen, M and Pezzutto, D and Virta, M and Karkman, A},
title = {Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0085725},
doi = {10.1128/spectrum.00857-25},
pmid = {41258718},
issn = {2165-0497},
abstract = {UNLABELLED: The introduction of the first broad-spectrum antibiotics, sulfonamide drugs, fundamentally revolutionized medicine in the 1930s. Shortly after, and ever since, sulfonamide resistance genes (sul genes) have been widely detected. Still, the most recent variant of these genes, sul4, was first described only in 2017, and its host range and transmission mechanisms are still largely unknown. Here, we applied PacBio long-read metagenomic sequencing and bacterial methylation signals to investigate the genetic contexts and bacterial carriage of the sul4 gene in wastewater. Furthermore, we extended our description of sul4 carriers to previously published data sets. Our results indicate that sul4 is prominently found in sludge and hosted by various bacteria, such as the species from the phyla Myxococcota and Chloroflexota and genera Trichlorobacter and Desulfobacillus, which are commonly found in activated sludge. Additionally, according to our results, sul4 has already spread into multiple strains of opportunistic human pathogens, such as Aeromonas and Moraxella, in addition to the previously described Salmonella. The sequence region flanking sul4 included a truncated folK gene and an ISCR28 element and exhibited a high degree of conservation across the investigated sequences. Furthermore, the module was associated with various integron integrase genes. Also, other mobility-related elements that could further increase the likelihood of sul4 mobilization were detected. Altogether, our results describing the sul4 hosts of bacteria from distant lineages indicate the efficient mobility of sul4 by genetic elements that traverse both clinical and environmental bacteria. Finally, we suggest that wastewater may provide favorable conditions for such horizontal gene transfer events.

IMPORTANCE: Antibiotic resistance is an ancient phenomenon and a common trait of many environmental bacteria. However, human activities in the post-antibiotic era, coupled with the bacteria's ability to exchange genetic material across different lineages, have drastically increased the spread of resistance traits among bacteria from various niches. The primary concern is the resistance genes encoded by infections causing pathogens, already causing over 1 million deaths annually and indirectly contributing to nearly 4 million more. Therefore, understanding the bacteria that harbor ARGs and the genetic mechanisms driving their mobilization is crucial for understanding the dynamics and emerging trends of resistance. Here, we focus on revealing these crucial aspects of the newly discovered sulfonamide resistance gene, sul4. Given the limitations of the metagenomic approach in linking the functional genes to their host genomes, the significance of our research lies in our workflow, which allows this linkage through the identification of shared methylation profiles.},
}

@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}

@article {pmid41258552,
year = {2025},
author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK},
title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1354},
pmid = {41258552},
issn = {1573-2959},
support = {core funding//Zoological Survey of India/ ; },
mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; },
abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.},
}

*Environmental Monitoring/methods
Public Health
*Eukaryota/classification/genetics
RNA, Ribosomal, 18S/genetics
Metagenomics
*Metagenome
Biodiversity

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41258468,
year = {2025},
author = {Bui, HT and Bui, ATP and Ngo, HT and Ngo, XT and Nguyen, HT and Nguyen, AH and Tran, VC and Pham, TD and Nguyen, ATV},
title = {Vaginal-spray Bacillus spore probiotics as a potential treatment and reducing recurrence of bacterial vaginosis: randomized, double-blind, and controlled pilot study.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-025-01236-4},
pmid = {41258468},
issn = {2730-664X},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal disorder characterized by reduced beneficial species and overgrowth of pathogens. Probiotics, especially direct vaginal sprays, offer a promising alternative to antibiotics by restoring healthy vaginal microbiota, relieving symptoms, and preventing recurrence.

METHODS: We conducted a clinical trial (ClinicalTrials.gov: NCT06165354; 8/12/2023) to evaluate the effectiveness of the vaginal-spray probiotic LiveSpo X-Secret, containing Bacillus subtilis, B. clausii, and B. coagulans spores (≥1 billion CFU/mL). A total of 120 women were randomized equally into Control and X-Secret groups at Bac Ninh CDC. Outcomes were assessed at day 7 (end of standard treatment) for symptom resolution and day 28 (21 days post-treatment) for recurrence. Both Per-Protocol and Intention-to-Treat analyses were performed to assess efficacy and account for attrition.

RESULTS: Here we show that no adverse events occur in either group. Compared to the Control, the X-Secret group exhibits a faster reduction in BV symptoms (odor, discharge, pH >4.5, and itching) by days 7 and 28, with odds ratios at day 28 of 3.61, 4.87, 2.95, and 3.34, respectively. Vaginal swab analysis reveals a 3.7-225.3-fold greater reduction in Gardnerella vaginalis. By day 28, metagenomic profiling indicates increases in beneficial species Lactobacillus crispatus (3.71-fold) and Streptococcus salivarius (from non-detectable to 2.1%), along with reductions in harmful species G. vaginalis (14.29-fold) and Sneathia sanguinegens (806-fold).

CONCLUSIONS: The vaginal-spray Bacillus spore probiotic (LiveSpo X-Secret) provides a safe, convenient, and effective approach for BV treatment and reducing recurrence, supporting its potential as an adjunctive therapy for maintaining vaginal health.

CLINICAL TRIAL NUMBER: ClinicalTrials.gov NCT06165354, first posted 8/12/2023.},
}

@article {pmid41258374,
year = {2025},
author = {Aydin, E and Karaynir, A and Ozkan, RG and Bozdogan, B},
title = {Metagenomic analysis of bacteriome and phageome of wastewater from a ceramic factory in Türkiye.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41258374},
issn = {1618-1905},
abstract = {Bacteriophages are major determinants of bacterial community dynamics. Industrial wastewaters constitute distinctive microbe-phage ecosystems shaped by heavy-metal and chemical stressors, yet they remain sparsely characterized by metagenomics. Most existing studies focus on municipal or hospital wastewaters, while phage and bacteriome communities in industrial effluents such as ceramic wastewater are largely unexplored. This study aimed to comprehensively characterize bacterial and phage communities in influent and effluent samples from a ceramic factory using metagenomic approaches. Phage DNA was sequenced on an Illumina NextSeq and processed with a standard bioinformatics pipeline for taxonomic and functional annotation. Of 657 million raw reads, 66% mapped to phage sequences. Caudovirales predominated, with Autographiviridae comprising 59% of classified viral reads. Functional annotation indicated that 64% of assigned genes encoded structural or replication functions. For the bacteriome, 16 S rRNA (V3-V4) amplicons were sequenced on an Illumina NovaSeq 6000 and classified with Kraken2. Proteobacteria dominated both sample types, but community structure shifted along the treatment line: the influent was enriched in environmental-water genera-Flavobacterium (25%), Aeromonas (16%), and Acinetobacter (11%) -whereas the effluent was dominated by Flavobacterium (37%), Hydrogenophaga (25%), and Rhodoferax (14%). Genus-level richness contracted from 228 (influent) to 67 (effluent), and the number of reads entering taxonomic classification declined sharply (1,482,914 vs. 55,847), consistent with selective removal and physicochemical filtering during treatment. Collectively, these results demonstrate that ceramic wastewater harbors a distinct microbe-phage ecosystem molded by chemical and particulate stress. By illuminating an understudied industrial niche, this work provides actionable insights for wastewater treatment, environmental bioremediation, and microbial risk assessment.},
}

@article {pmid41258115,
year = {2025},
author = {Yepes-García, J and Novoa-Montenegro, N and Otero-Jiménez, V and Uribe-Vélez, D and Barreto-Hernández, E and Falquet, L},
title = {Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1823},
pmid = {41258115},
issn = {2052-4463},
mesh = {*Oryza ; Colombia ; Metagenomics ; *Metagenome ; *Soil Microbiology ; Bacillus/genetics ; Agriculture ; Fermentation ; },
abstract = {Extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. In the quest for enhanced RS degradation systems, we recovered 146 Metagenome-Assembled Genomes (MAGs) from experiments aiming at decomposing RS. Such assays included the application of a Bacillus strain, a Trichoderma-based commercial product, organic and inorganic compounds in different combinations during a solid-state fermentation in Colombian rice fields. The set of MAGs comprises 30 MAGs from bulk soil and 116 MAGs from RS surface, for which taxonomic classification indicates that 67% of them may constitute novel taxa. Furthermore, functional analysis through different approaches suggests the presence of both mid-quality and high-quality MAGs with potential to biotransform RS within this dataset. Finally, these MAGs represent a valuable resource for exploring uncharacterized microbial diversity in Colombian agricultural ecosystems.},
}

*Oryza
Colombia
Metagenomics
*Metagenome
*Soil Microbiology
Bacillus/genetics
Agriculture
Fermentation

@article {pmid41258100,
year = {2025},
author = {Wang, C and Zheng, R and Sun, C},
title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10134},
pmid = {41258100},
issn = {2041-1723},
mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; },
abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.},
}

*Seawater/virology/microbiology
*Viruses/genetics/classification/metabolism
Virome/genetics
Metagenomics
Geologic Sediments/virology/microbiology
*Host Microbial Interactions
Genome, Viral
Oceans and Seas
Ecosystem
RNA Viruses/genetics/classification
Microbiota
Biodiversity
Carbon Cycle
Transcriptome

@article {pmid41258067,
year = {2025},
author = {Zhang, Q and Sun, Y and Liu, W and Zhao, Q and Yuan, K and Chen, D},
title = {Clinical characteristics of Torquetenovirus infected immunocompromised patients explored by metagenomic next-generation sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40857},
pmid = {41258067},
issn = {2045-2322},
support = {Grant No. MTP2022D027//Medical Talent Program for High-hroughput Sequencing Technology in Infectious Diseases, China/ ; },
mesh = {Humans ; *Immunocompromised Host ; *Torque teno virus/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; *DNA Virus Infections/virology/immunology/diagnosis ; *Metagenomics/methods ; Adult ; Aged ; },
abstract = {Since the recent application of metagenomic next-generation sequencing (mNGS) techniques to clinics, Torquetenoviruses (TTV) have received much attention due to their high positive rates. However, there is an insufficient understanding in clinical settings of the pathogen, especially in immunocompromised patients. This study explores the clinical characteristics of TTV infection in immunocompromised patients using mNGS. We enrolled a total of 120 TTV-infected patients in the study, including 81 immunocompromised and 39 immunocompetent individuals. The prevalence, diagnosis, treatment, and co-pathogens were compared between the two groups. The microbial diversity and presence of co-pathogens in patients infected with Torquetenovirus (TTV) were elucidated through comprehensive analysis. T-tests compared the normally distributed continuous data. The immunocompromised patients exhibited significantly elevated TTV loads, and a notable proportion of these patients also presented with hematopoietic disorders. Importantly, our investigation revealed that current treatments showed no efficacy against TTV infection.Furthermore, the presence of copathogens such as Staphylococcus, Bacillus, Mycobacterium, and Acinetobacter was observed in TTV-infected individuals. Immunocompromised patients exhibited a significantly higher abundance of Staphylococcus and Shewanella compared to immunocompetent patients (p < 0.05). Cautious use of antiviral therapy is recommended for patients with TTV mono-infection. However, greater attention should be given to co-pathogens, such as Staphylococcus spp. and Shewanella spp. This cohort study provides valuable insights into the clinical significance of TTV infection, particularly in immunocompromised patients. We found that TTV is frequently detected in this population, often with higher viral loads and an increased burden of co-pathogens. These findings suggest that TTV may serve primarily as a marker of immune dysfunction rather than as a sole pathogen. Incorporating TTV monitoring into mNGS-based diagnostics could help identify high-risk patients, support early intervention, and guide tailored management strategies in immunocompromised settings.},
}

Humans
*Immunocompromised Host
*Torque teno virus/genetics
*High-Throughput Nucleotide Sequencing/methods
Female
Male
Middle Aged
*DNA Virus Infections/virology/immunology/diagnosis
*Metagenomics/methods
Adult
Aged

@article {pmid41257635,
year = {2025},
author = {Liu, J and Wu, J and Zheng, Z and Xue, J and Zhang, W},
title = {Clinical spectrum of Talaromyces marneffei infections in HIV-negative patients: an 18-case series including a rare presentation with gastrointestinal onset, adrenal mass, and hemophagocytic lymphohistiocytosis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1616},
pmid = {41257635},
issn = {1471-2334},
support = {2024J0112//Nature Science Foundation of Fujian Province of China/ ; },
mesh = {Humans ; Male ; Female ; *Talaromyces/isolation & purification/genetics ; Middle Aged ; *Lymphohistiocytosis, Hemophagocytic/microbiology ; *Mycoses/diagnosis/microbiology/pathology/complications ; Retrospective Studies ; Aged ; Adult ; Coinfection ; *Gastrointestinal Diseases/microbiology ; HIV Seronegativity ; },
abstract = {BACKGROUND: The diverse manifestations of Talaromyces marneffei (TM) infection in HIV-negative patients complicate and often delay diagnosis. This study reviews 18 cases to better characterize the clinical spectrum of this disease, with the goal of improving recognition of its varied presentations.

METHODS: Retrospective analysis of 18 patients assessing underlying diseases, manifestations, co-infections, diagnostics, treatment, and outcomes. Diagnosis required TM positivity via culture, histopathology, or metagenomic next-generation sequencing(mNGS).

RESULTS: This cohort (14 males and 4 females; mean age 57.94 ± 11.12 years) exhibited diverse comorbidities, including renal transplantation (27.8%), tuberculosis (22.2%), cancer (16.7%), bronchiectasis (16.7%), and anti-interferon-γ autoantibody (AIGA) syndrome (11.1%). Common manifestations included respiratory symptoms (72.2%), fever (55.6%), and anemia (50.0%). Immunodeficiency was frequent, with an abnormal CD4/CD8 ratio in in 10/15 patients (66.7%). Notably, 94.4% of cases were initially misdiagnosed-often as tuberculosis (35.3%) or bacterial pneumonia (23.5%)-leading to a mean diagnostic delay of 8.97 ± 7.02 weeks. mNGS provided diagnosis in 77.8% of cases. Overall mortality was 22.2%, with two relapses linked to AIGA syndrome. We report the first documented TM triad in a patient with systemic lupus erythematosus (SLE) and Epstein-Barr virus (EBV) coinfection: concurrent gastrointestinal onset (manifesting as ileocolonic ulcers), adrenal mass, and hemophagocytic lymphohistiocytosis (HLH).

CONCLUSIONS: TM infection in HIV-negative hosts demonstrates broad clinical heterogeneity, often masked by comorbidities and leading to delayed diagnosis. mNGS is critical for early identification. The unprecedented triad of gastrointestinal onset, adrenal mass, and HLH underscores TM's capacity for atypical dissemination. AIGA may predict relapse.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
Female
*Talaromyces/isolation & purification/genetics
Middle Aged
*Lymphohistiocytosis, Hemophagocytic/microbiology
*Mycoses/diagnosis/microbiology/pathology/complications
Retrospective Studies
Aged
Adult
Coinfection
*Gastrointestinal Diseases/microbiology
HIV Seronegativity

@article {pmid41257101,
year = {2025},
author = {He, X and Wang, M and Sun, T and Tang, J and Zeng, Y},
title = {Metagenomic Next-Generation Sequencing Diagnosis of Streptococcus agalactiae Meningitis in a Diabetic Patient.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94759},
pmid = {41257101},
issn = {2168-8184},
abstract = {Streptococcus agalactiae meningitis is primarily observed among neonates and is uncommon in adults. We present a rare case of Streptococcus agalactiae meningitis in an adult. The patient was a 74-year-old male with a history of gastric perforation surgery, chemotherapy for neck lymphoma, and hypertension. He presented to the emergency department with an 11-day history of neck pain, one day of limited mouth opening and dysphagia, and eight hours of altered consciousness. On examination, he exhibited impaired consciousness (Glasgow Coma Scale score: 8) and cervical rigidity. He was intubated and received oxygen therapy. Laboratory findings revealed elevated infection markers and turbid cerebrospinal fluid (CSF). Metagenomic next-generation sequencing (mNGS) of the CSF detected Streptococcus agalactiae. Enhanced MRI of the head and neck showed a small subdural effusion, spinal cord edema at C5-C6, thickening and enhancement of the anterior and posterior longitudinal ligaments and meninges at the skull base, suggestive of Streptococcus agalactiae infection. After 10 days of anti-infective treatment with ceftriaxone, the patient's condition improved, and he was transferred to a local hospital for continued management.},
}

@article {pmid41256608,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.02.680046},
pmid = {41256608},
issn = {2692-8205},
abstract = {UNLABELLED: Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, 'reverse translation' experiments are performed where intact fecal microbiomes collected from trial participants prior to and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because 'no treatment' control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes microbial gene expression consistent with a less virulent gut ecosystem and changes in expression of (i) components of gut epithelial cell junctions in the enterocytic and goblet cell lineages, (ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and (iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.

SIGNIFICANCE STATEMENT: Undernutrition is a global health problem. Recent clinical trials of a gut microbiome-directed complementary food (MDCF-2) designed to repair the perturbed gut microbiomes of undernourished Bangladesh children produced superior growth outcomes versus a standard nutritional supplement. Given ethical considerations and tissue sampling constraints associated with these types of studies, we colonized gnotobiotic mice postnatally with microbiome samples obtained from trial participants before and after treatment to model "unrepaired" and "repaired" gut ecosystems. Using a multi-omics approach, we uncover heretofore unappreciated changes in expressed chemosensory tuft cell, mucus-producing goblet cell and absorptive enterocytic functions and interactions accompanying microbiome repair. Extending microbiome clinical trials back to preclinical models ('reverse translation') provides mechanistic insights that can inform design/interpretation of future interventions.},
}

@article {pmid41256588,
year = {2025},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandon, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.679827},
pmid = {41256588},
issn = {2692-8205},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8 [+] and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA [+] cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.},
}

@article {pmid41256293,
year = {2025},
author = {Agrawal, H and Agarwal, N and Gupta, N},
title = {Impact of gut microbiome on outcomes following endoscopic interventions in gastrointestinal disease.},
journal = {World journal of gastrointestinal endoscopy},
volume = {17},
number = {11},
pages = {110207},
pmid = {41256293},
issn = {1948-5190},
abstract = {BACKGROUND: Endoscopic interventions play a vital role in diagnosing and managing gastrointestinal diseases, but complications such as bleeding, infection, and delayed healing can adversely affect patient outcomes. The influence of the gut microbiome on these outcomes is increasingly being recognized.

AIM: To evaluate the role of the gut microbiome in influencing clinical outcomes after endoscopic interventions, focusing on microbial diversity, specific taxa, metabolic functions, and emerging predictive models.

METHODS: A systematic literature search was conducted in PubMed, EMBASE, and Cochrane databases up to May 2025, selecting human studies that analyzed gut microbiome composition or function in relation to endoscopic interventions and clinical outcomes. Microbiome analysis techniques included 16S rRNA gene sequencing, metagenomics, and metabolomics.

RESULTS: Forty-two studies met the inclusion criteria. Our review identifies key beneficial microbes, such as Faecalibacterium prausnitzii and Bacteroides spp., which support mucosal healing. In contrast, dysbiosis (e.g., an increased abundance of Proteo bacteria) is associated with poorer healing and higher complication rates. Notably, microbiome-informed predictive models have shown strong potential for forecasting post-procedural complications, offering a pathway to personalized treatment strategies. Probiotics have also emerged as a promising intervention, helping to restore microbial balance and reduce complications such as infection and delayed healing.

CONCLUSION: The gut microbiome plays a significant role in recovery after endoscopy. Integrating microbiome analysis into clinical decision-making could improve outcomes through personalized predictions and targeted therapies. Future research should focus on standardizing microbiome assessment protocols and validating predictive models to optimize patient care.},
}

@article {pmid41255950,
year = {2025},
author = {Li, S and Peng, X and Tang, Z and Li, W and Song, X},
title = {Talaromyces marneffei Infection in Non-Endemic Areas: Two Case Reports, Diagnostic Insights, and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5895-5903},
pmid = {41255950},
issn = {1178-6973},
abstract = {PURPOSE: Talaromycosis is an invasive fungal infection caused by the pathogenic fungus Talaromyces marneffei (T. marneffei), prevalent in Southeast Asia and Southern China. This disease is rare in non-endemic areas and primarily affects the respiratory system with atypical manifestations. Therefore, the condition is often misdiagnosed as other respiratory infections. This article presents two cases of talaromycosis in non-endemic areas, aiming to provide diagnostic and therapeutic references for this rare fungal infection.

CASE PRESENTATION: Two cases of talaromycosis in non-endemic areas were retrospectively analyzed. The first case involved a human immunodeficiency virus (HIV)-infected patient with tracheobronchial talaromycosis. Bronchoscopy revealed multiple nodular neoplasms in the trachea and bilateral main bronchi. Histopathological examination of the biopsy tissue showed histiocyte aggregation and intracellular pathogens. T. marneffei was identified by microbial culture of bronchoalveolar lavage fluid (BALF). The second case was an HIV-negative patient with pulmonary talaromycosis. Bronchoscopy revealed mucosal congestion and edema, and T. marneffei was detected by metagenomics next-generation sequencing (mNGS) of BALF.

CONCLUSION: Talaromycosis warrants more clinical attention in both HIV-negative individuals and non-endemic areas. In addition, clinicians should improve diagnostic recognition of this disease for timely management. Bronchoscopy combined with mNGS can facilitate early diagnosis of talaromycosis, particularly in culture-negative cases where conventional methods fail. This strategy directly addresses a major diagnostic challenge and improves patient prognosis.},
}

@article {pmid41255826,
year = {2025},
author = {Jin, J and Chao, X and Zhu, Z and Zhang, B and Fu, Y and Xu, J and Ma, S and Chen, T and Wang, Y and Ding, J},
title = {Metagenomic Analysis of Tick-Borne Viruses Associated With Hyalomma asiaticum From Different Hosts in the Surrounding Areas of Urumqi, China.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {9985595},
pmid = {41255826},
issn = {1865-1682},
mesh = {Animals ; China/epidemiology ; Metagenomics ; *Ixodidae/virology ; Phylogeny ; Horses ; Sheep ; Tick-Borne Diseases/veterinary/epidemiology/virology ; *RNA Viruses/isolation & purification/genetics/classification ; },
abstract = {Tick-borne viruses (TBVs) represent a serious risk to global public and animal health. Despite the remarkable species diversity of ticks documented in Urumqi and its adjacent regions of China, scientific investigations into TBVs in this ecologically significant area have been strikingly scarce. In this study, we conducted metagenomic sequencing on 752 Hyalomma asiaticum (H. asiaticum), including questing ticks from Wujiaqu and blood-feeding ticks collected from sheep and horses in the Changji area. A total of 11 different RNA viruses were detected, belonging to six viral families and some unclassified families, with double-stranded RNA viruses being the most prevalent (49.1%), including Totiviridae and Sedoreoviridae. Single-stranded RNA viruses accounted for 11.9% of the virome, encompassing Chuviridae, Flaviviridae, Rhabdoviridae, and Phenuiviridae. Notably, 39.0% of the viral sequences remained unclassified, highlighting a substantial reservoir of uncharacterized viral diversity. Genomic and phylogenetic characterizations were performed on six highly abundant viruses, including Bole tick virus 1, Mivirus boleense, Bole tick virus 4, Lonestar tick totivirus, Hubei toti-like virus 24, and a novel strain of Hulunbuir Totiv tick virus 1. However, their zoonotic potential requires further investigation. By integrating cytochrome c oxidase subunit Ⅰ (COI) gene-based tick species identification with viral metagenomics, this study provided a comprehensive assessment of tick species and TBVs diversity in Urumqi and its surrounding areas, China. These results provide new insights into both the genetic diversity of tick-borne RNA viruses and their phylogenetic connections, while also expanding knowledge about the geographical distribution patterns of these pathogens.},
}

Animals
China/epidemiology
Metagenomics
*Ixodidae/virology
Phylogeny
Horses
Sheep
Tick-Borne Diseases/veterinary/epidemiology/virology
*RNA Viruses/isolation & purification/genetics/classification

@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetic Neuropathies/microbiology/therapy/metabolism
*Dysbiosis/microbiology
Animals
Probiotics/therapeutic use

@article {pmid41255157,
year = {2025},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}

@article {pmid41254499,
year = {2025},
author = {Bring Horvath, ER and Winter, JM},
title = {SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {280},
pmid = {41254499},
issn = {1471-2105},
support = {1R01AI155694/NH/NIH HHS/United States ; },
mesh = {*Software ; *Sequence Alignment/methods ; Databases, Genetic ; *Genomics/methods ; Amino Acid Motifs ; Metagenomics/methods ; },
abstract = {BACKGROUND: The rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST + remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers.

RESULTS: We developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST + database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage.

CONCLUSIONS: SeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.},
}

*Software
*Sequence Alignment/methods
Databases, Genetic
*Genomics/methods
Amino Acid Motifs
Metagenomics/methods

@article {pmid41254331,
year = {2025},
author = {Bersch-Ferreira, ÂC and Fonseca, DC and Tramujas, L and Schiavon, CA and Nakagawa Santos, RH and V Machado, RH and Biasi Cavalcanti, A and Marcadenti, A},
title = {Gut Microbiota Composition and Arterial Hypertension Improvement Post-Roux-en-Y Gastric Bypass: GATEWAY Trial Sub-Analysis After 5 Years.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {41254331},
issn = {1708-0428},
abstract = {INTRODUCTION: The aim of this study was to explore the relationship between gut microbiota composition and hypertension remission in individuals with obesity and hypertension who underwent Roux-en-Y gastric bypass (RYGB) surgery five years prior.

METHODS: This is a sub-analysis of the GATEWAY trial using cross-sectional data from participants five years post-surgery. Three groups were included: patients who underwent RYGB and achieved hypertension remission (Group 1, n = 12), patients who underwent RYGB but did not achieve remission (Group 2, n = 12), and a control group of individuals with obesity and hypertension who did not undergo surgery (Group 3, n = 15). Gut microbiota composition was evaluated using metagenomic sequencing of fecal samples, with taxonomic classification at the phylum, class, and order levels.

RESULTS: No statistically significant differences were found in overall microbiota composition between the groups. However, microbial richness was higher in both surgical groups compared to the control group, suggesting a potential link between bariatric surgery and increased gut microbial diversity.

CONCLUSION: While gut microbiota composition did not significantly differ between individuals with and without hypertension remission, the observed increase in microbial richness among those undergoing bariatric surgery underscores the complex interplay between obesity treatment, gut microbiota, and blood pressure regulation. Further research is needed to elucidate these long-term relationships.},
}

@article {pmid41253025,
year = {2025},
author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP},
title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157550},
doi = {10.1016/j.phymed.2025.157550},
pmid = {41253025},
issn = {1618-095X},
abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.

PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.

METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-κB), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.

RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-α, IL-17, and IFN-γ), inhibit the expression of TLR4/NF-κB, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.

CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-κB and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.},
}

@article {pmid41252983,
year = {2025},
author = {Cao, S and Zhu, J and Gan, X and Fu, Q and Hu, H and Huang, Q},
title = {Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140491},
doi = {10.1016/j.jhazmat.2025.140491},
pmid = {41252983},
issn = {1873-3336},
abstract = {The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ[13]C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.},
}

@article {pmid41252855,
year = {2025},
author = {Oh, S and Wijaya, J},
title = {Predictive surveillance and diagnosis of COVID-19: An integrative machine learning and wastewater multi-omics approach.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124981},
doi = {10.1016/j.watres.2025.124981},
pmid = {41252855},
issn = {1879-2448},
abstract = {COVID-19 has had major global impacts, highlighting the importance of robust predictive surveillance and diagnostic systems to ensure effective public health responses. Traditional surveillance methods based on passive case counting and diagnostic testing of individual patients often suffer from delays and resource constraints, preventing timely responses. This study proposed an integrative framework integrating machine learning (ML)-derived predictive surveillance with wastewater-based diagnosis, aiming to predict temporal trends in Korea and identify disease-causing agents. The ML model utilized crowdsourced COVID-19-related keywords, climatic, and environmental data, optimized via model selection and feature selection. The integrated data-driven model predicted COVID-19 cases over three years more accurately than those using single source data (i.e., baseline model). The explainable AI technique (i.e., helping to inform how the model made those predictive decisions) identified six keywords (reducing phlegm, throat pain, long COVID-19, sore throat, COVID-19 self-kit, and COVID-19 kit) as robust predictors of disease trends. In a proof-of-concept experiment, wastewater-based genotyping of disease-causing agents and affected human communities in sewershed areas was conducted. Metatranscriptomics of municipal wastewater was conducted to identify COVID-19 viral variants, evolutionarily related to those clinically isolated strains, distinguishable from conventional diagnostic testing of individual patients. Wastewater-derived metagenomics was also performed to assess genomic variation in the affected human populations. The integrative framework proposed in this study offers a rapid, cost-effective approach for the surveillance and diagnosis of COVID-19 and other infectious diseases, thus strengthening or complementing existing health systems.},
}

@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; },
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}

Humans
*Microbiota
*Software
*Gastrointestinal Microbiome
Algorithms
*Computational Biology/methods
*Metagenomics/methods
Phylogeny

@article {pmid41189540,
year = {2026},
author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S},
title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70066},
doi = {10.1111/1755-0998.70066},
pmid = {41189540},
issn = {1755-0998},
support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project ‛Ocean DNA'/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; },
abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
*Biodiversity
Internet
*DNA, Environmental/genetics
*Computational Biology/methods
*Aquatic Organisms/classification/genetics
*Metagenomics/methods
*Software

@article {pmid41168956,
year = {2026},
author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD},
title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70069},
doi = {10.1111/1755-0998.70069},
pmid = {41168956},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; },
abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Fishes/genetics/classification
*Electron Transport Complex IV/genetics
Benchmarking
*Metagenomics/methods
*DNA, Environmental/genetics
Cluster Analysis
Biodiversity
Computational Biology/methods

@article {pmid41257040,
year = {2023},
author = {Gündoğdu, A and Charyyeva, A and Nalbantoğlu, ÖU},
title = {Metagenomic Profiling of Human Protozoan Parasites in Wastewater and Hospital Effluents.},
journal = {Journal of clinical practice and research},
volume = {45},
number = {5},
pages = {435-446},
pmid = {41257040},
issn = {2980-2156},
abstract = {OBJECTIVE: Advancements in metagenomic techniques have provided new tools for profiling human parasites in environmental matrices such as wastewater. This study aimed to profile protozoan parasites in wastewater from a major city, rural area, and hospital in Kayseri, Türkiye, using metagenomic techniques.

MATERIALS AND METHODS: Shotgun metagenome sequencing was conducted on ten water samples collected from five sampling sites over a two-week period. The sequences were aligned to 80 human parasite genomes to evaluate the presence and relative abundance of each parasite species. A comparative bioinformatic analysis was performed on the metagenomes from each sampling point.

RESULTS: The diversity of parasites in the city wastewater exceeded that of the rural and hospital sampling points. Blastocystis spp. subtypes and Giardia intestinalis were dominant in rural wastewater, while Plasmodium falciparum, Plasmodium ovale, Toxoplasma gondii, and Acanthamoeba species showed significant abundance in hospital effluent (p<0.01). Moreover, protozoan parasites not previously reported in a clinical setting were identified in the water samples.

CONCLUSION: This is the first study in Türkiye investigating the presence of human parasites in wastewater using metagenomics. The study highlights the risk posed by human parasites in treated wastewater to population using natural resources. Implementing a specialized wastewater treatment targeting parasites could mitigate the potential spread of these pathogens in the environment. The study revealed certain sequences associated with species not previously identified in clinical instances. This finding may result from genomic resemblances with other eukaryotic organisms that were not systematically excluded, or alternatively, the displacement of protozoa linked to the increasing influx of refugees.},
}

@article {pmid41252801,
year = {2025},
author = {Gacem, A and Soltane, R and Wanale, SG and Mohammed, SA and Almulla, N and Eltayeb, LB and Alreshidi, MA and Alasiri, A and Albakri, GS and Raghuvanshi, U and Abdulmonem, WA and Qasim, MT and Gupta, R and Islam, S and Yadav, KK},
title = {Advances in molecular methodologies and nanotechnology-enabled drug delivery in biomedicine: An overview of current progress.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 1},
pages = {108765},
doi = {10.1016/j.compbiolchem.2025.108765},
pmid = {41252801},
issn = {1476-928X},
abstract = {Recent advances in molecular techniques and nanosystems have significantly transformed biomedical research, particularly in pathogen detection and drug delivery. Traditional culture-based methods are being increasingly replaced by rapid and precise molecular approaches, offering greater accuracy in identifying pathogens and uncovering the genetic mechanisms underlying antimicrobial resistance (AMR). This review highlights key molecular tools, including matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing, DNA microarrays, metagenomics, and polymerase chain reaction (PCR) and others with a critical evaluation of their strengths, limitations, and applications in global surveillance. Alongside, the integration of nanostructured systems has opened new avenues for designing advanced drug-delivery platforms with improved bioavailability, targeted action, and reduced toxicity. Together, these innovations emphasize the potential of molecular and nanoscale technologies to address pressing challenges in diagnostics, therapeutics, and the management of infectious diseases.},
}

@article {pmid41252568,
year = {2025},
author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G},
title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2592078},
pmid = {41252568},
issn = {1747-4132},
abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.

AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.

EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.},
}

@article {pmid41252442,
year = {2025},
author = {Zentgraf, J and Schmitz, JE and Rahmann, S},
title = {Cleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf632},
pmid = {41252442},
issn = {1367-4811},
abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.

RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.

Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/) and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).

SUPPLEMENTARY INFORMATION: Available online.},
}

@article {pmid41252249,
year = {2025},
author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS},
title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116573},
doi = {10.1016/j.celrep.2025.116573},
pmid = {41252249},
issn = {2211-1247},
abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.},
}

@article {pmid41251845,
year = {2025},
author = {Saggu, SK and Kumar, M and Kumar, S},
title = {Metagenomics and its impact on environmental and therapeutic microbiology.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {24},
pmid = {41251845},
issn = {1432-072X},
mesh = {*Metagenomics/methods ; *Environmental Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Humans ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metagenomics has significantly advanced our understanding of microbial life by enabling the direct analysis of environmental DNA, thereby deciphering the vast microbial dark matter comprising unknown and uncultivable microbial diversity that remains inaccessible through conventional culture-dependent methods. The culture-independent approach provides a comprehensive view of microbial composition, function, and evolution, facilitating discoveries across environmental and clinical domains. Recent developments in high-throughput sequencing, hybrid long-read assemblies, and AI/ML-based genome binning have enhanced our understanding to reconstruct complete genomes, predict metabolic pathways, and engineer microbial consortia. This review summarizes the impact of metagenomics on environmental and therapeutic microbiology, emphasizing its contributions in the field of bioremediation, greenhouse gas mitigation, sustainable agriculture, industrial enzyme discovery, and novel drug development. It further explores metagenomics-driven innovations in pathogen detection, antimicrobial resistance surveillance, and multi-omics integration. Furthermore, it discusses methodological developments, computational challenges, and translational limitations, offering future perspectives for harnessing metagenomic insights in sustainable biotechnology and precision medicine.},
}

*Metagenomics/methods
*Environmental Microbiology
*Bacteria/genetics/classification/isolation & purification
Humans
High-Throughput Nucleotide Sequencing

@article {pmid41251544,
year = {2025},
author = {Pang, X and Zhang, B and Zhang, Q and Jiang, J},
title = {Freeze-Thaw Cycling Accelerates Microbial Reduction and Immobilization of Vanadium(V) in Groundwater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11332},
pmid = {41251544},
issn = {1520-5851},
abstract = {As global warming intensifies, freeze-thaw cycling has become more pronounced, significantly impacting microbial metabolic processes. In this study, microbial vanadium(V) [V(V)] reduction under freeze-thaw conditions was investigated. Temperature fluctuations between -4 and +4 °C accelerated V(V) reduction, together with the faster decrease in organic matter and total nitrogen in the sediment, compared to constant-temperature incubations at either -4 or +4 °C. V(V) was bioreduced to vanadium(IV) precipitates, increasing the acid-soluble, reducible, and oxidizable fractions of vanadium in the sediment. Freeze-thaw cycling enhanced microbial carbon and nitrogen utilization, as well as the richness and diversity of the microbial community. Metagenomics, real-time quantitative polymerase chain reaction quantification, and electron-transfer measurements revealed the underlying mechanisms. During thawing, microorganisms such as Flavobacterium sp., Stutzerimonas sp., and Giebergeria sp. reduced V(V) via denitrification genes (narG, nirS, and nosZ). Under freezing conditions, enriched Pseudomonas sp. and Acinetobacter sp. achieved V(V) reduction through the electron-transfer gene (mtrC), with increased cytochrome c concentration. Key cold-adaptation genes, including cspA, HSP, SOD, katG, and SCD, were prevalent in these microorganisms, supporting antifreeze activities. This study offers insights into microbial V(V) reduction under freeze-thaw cycling scenarios and is helpful in developing pertinent remediation strategies.},
}

@article {pmid41251358,
year = {2025},
author = {Wilson, A and Jauregui, R and Bueno, R and Begg, D and Hannah, M and Sheeba, E and Bestbier, M and Green, D and O'Keefe, J and McCulley, M},
title = {Genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0108325},
doi = {10.1128/mra.01083-25},
pmid = {41251358},
issn = {2576-098X},
abstract = {We report the draft genome sequence of Babesia gibsoni detected in a domestic dog in New Zealand. A high-quality near-complete genome, comprised of an apicoplast, mitochondrion, and four chromosomes, was produced through long-read metagenomic sequencing.},
}

@article {pmid41251138,
year = {2025},
author = {Shukla, M and Wattam, AR and Aleman, A and Bhattacharya, R and Bowers, N and Brettin, T and Capria, A and Chia, N and Cucinell, C and Davis, JJ and Dempsey, DM and Dickerman, A and Dietrich, EM and Gokdemir, O and Hendrickson, RC and Kenyon, RW and Klahn, B and Kuscuoglu, M and Lefkowitz, EJ and Ma, H and Machi, D and Macken, C and Mann, CM and Mao, C and Nguyen, M and Olsen, GJ and Olson, RD and Overbeek, R and Owens, SM and Parrello, B and Poretsky, R and Pusch, GD and Ramanathan, A and Sheriff, JT and Singh, I and Stewart, L and VanOeffelen, M and Vonstein, V and Warren, AS and Wilke, A and Zmasek, CM and Zuniga, A and Stevens, RL},
title = {BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1254},
pmid = {41251138},
issn = {1362-4962},
support = {//National Institute of Allergy and Infectious Diseases/ ; /NH/NIH HHS/United States ; U24AI183849/HH/HHS/United States ; },
abstract = {The Bacterial and Viral Bioinformatics Resource Center (BV-BRC; https://www.bv-brc.org) is a comprehensive resource supporting research on bacterial and viral pathogens. It currently hosts over 14 million publicly available genomes and 33 high-throughput bioinformatic analysis services with numerous visual analytic tools allowing researchers to analyze their private data, generate comparisons with public data, and share data and results with colleagues. In recent years, the BV-BRC has added several new analysis services to support rapid comparative genomics and epidemiological analysis, viral genome assembly and annotation, viral subspecies classification, wastewater analysis, and molecular docking. In addition, several existing services have been updated to incorporate state-of-the-art tools, including assembly, annotation, taxonomic classification, metagenomic read mapping, and RNA-seq analysis. A new tool, called BV-BRC Copilot, provides an AI-powered natural-language interface that combines large language models with retrieval-augmented generation to guide users through data exploration, analysis workflows, and knowledge integration. With expanded outbreak tracking pages, training and educator engagement, and continued development of novel AI-driven analytics, BV-BRC continues to provide a unified resource to meet the evolving needs of the global research community.},
}

@article {pmid41250695,
year = {2025},
author = {Pathi, B and Sahoo, JP and Mahapatra, A and Panigrahy, R and Padhi, S and Lenka, PR and Mohanty, I and Ramadass, B and Panigrahi, K and Dixit, S and Das, MK},
title = {Genome Sequencing to Prevent Hospital-Acquired Infections Caused by Carbapenem-Resistant Acinetobacter baumannii Due to Importation and Intra-facility Transmission in a Regional Hospital Network: Study Protocol for Implementation Research.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94812},
pmid = {41250695},
issn = {2168-8184},
abstract = {BACKGROUND AND OBJECTIVES: Carbapenem-resistant Acinetobacter baumannii (CRAb) is among India's leading bacteria responsible for hospital-acquired infections (HAIs). The CRAb causing intra-facility and inter-facility (or importation) HAI transmissions may differ phylogenetically. For control and prevention of CRAb-associated HAIs within and across facilities, information about the phylogenetic lineage characterization and contextual risk factors is critical. To our knowledge, there is no preliminary state-level data available from Odisha state in India regarding the dynamics of CRAb transmission (intra- and inter-facility), phylogenetic lineages, risk factors, and geospatial epidemiology. This study shall document the dynamics of CRAb-associated HAIs, the phylogenetic lineages responsible for intra-facility and inter-facility transmissions, and the risk factors. We shall leverage the CRAb phylogenetic data and risk factors identified through an integrated laboratory-clinical-epidemiological-genomic surveillance for tackling the intra-facility and inter-facility transmissions and outbreaks using implementation research approaches with adoption of contextualized hospital infection control and prevention measures and antibiotic stewardship efforts in a hospital network in Odisha state, India.

METHODS: This study adopts an integrated prospective facility-based surveillance with a quasi-experimental design using the plan-do-study-act (PDSA) implementation research cycles with mixed-methods data collection approaches. The study will be conducted over three years at six tertiary care medical institutions in Odisha. Prospective surveillance over 24 months at these hospitals will monitor the CRAb isolates to identify HAI outbreaks and intra- and inter-facility transmissions. The metagenomic and genome-wide sequencing (GWS) shall document CRAb phylogenetic lineages for outbreaks and intra- and inter-facility transmissions. Geospatial mapping shall document the spatial characterization of CRAb transmission for the index cases. Formative research shall identify potential risk factors at various levels for HAIs, outbreaks, intra- and inter-facility CRAb transmissions, hospital infection prevention, surveillance, and antibiotic stewardship efforts, using the Consolidated Framework for Implementation Research (CFIR). Based on this information, contextualized strategies and interventions to strengthen hospital infection prevention, surveillance, and antibiotic stewardship efforts shall be implemented at these facilities using incremental PDSA cycles. Data from these PDSA cycles shall be compared to document the impact on CRAb outbreaks and process indicators. The practices' and interventions' feasibility, acceptability, and sustainability shall be documented.

RESULTS: We do not have any observations, as we have not started the study yet.

CONCLUSION: The study shall generate evidence on genoepidemiology, transmission dynamics of HAIs due to CRAb in Odisha, India, and the associated risk factors. The lessons from context-specific implementation strategies (covering infection surveillance, prevention strategies, and antibiotic stewardship domains) to tackle CRAb-associated HAIs outbreaks and the feasibility, acceptability, and sustainability shall inform the policy and practices. The geographic signatures of horizontal CRAb-associated HAIs will generate a new knowledge base to design future intervention measures.},
}

@article {pmid41250675,
year = {2025},
author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X},
title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf257},
pmid = {41250675},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.

RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.

Code is available at https://github.com/Ying-Lab/ICCTax.},
}

@article {pmid41250628,
year = {2025},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41250628},
issn = {2191-0286},
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}

@article {pmid41250240,
year = {2025},
author = {Gwak, HJ and Rho, M},
title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {393},
pmid = {41250240},
issn = {1474-760X},
support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; },
abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Electron Transport Complex IV/genetics
*Software
Biodiversity
Large Language Models

@article {pmid41250148,
year = {2025},
author = {Lam, AY and Lau, CH and Tam, WY and Chan, CT and Lok, TM and Suen, LK and Lee, LK and Yeung, EY and Lam, TK and Cheung, WK and Chui, MW and Soong, HS and Chow, FW and Lam, SC and So, SN and Yuen, SK and Siu, GK},
title = {Targeted probe capture metagenomics-enabled surveillance of multidrug-resistant organisms and antimicrobial resistance genes in post-handwashing areas of public washrooms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {143},
pmid = {41250148},
issn = {2524-6372},
support = {2023-00-51 CRG230402//Tung Wah College/ ; 1-ZVZL//The Hong Kong Polytechnic University/ ; },
abstract = {BACKGROUND: Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities.

RESULTS: From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n = 10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n = 5), and methicillin-resistant Staphylococcus aureus (MRSA, n = 2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area.

CONCLUSIONS: Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.},
}

@article {pmid41250124,
year = {2025},
author = {Huang, SW and Lin, CR and Chang, YH and Ni, YH and Chen, HL and Liu, HH},
title = {Cross-country multi-modal evidence links Aspergillus to biliary atresia.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {94},
pmid = {41250124},
issn = {1757-4749},
abstract = {BACKGROUND: Biliary atresia (BA) is the leading cause of pediatric liver transplantation. It is characterized by progressive extrahepatic bile duct obstruction in young infants. Inspired by the success of antifungal treatment in a newborn with BA-related obstructive cholangitis, we explored a potential link between BA and fungi, particularly Aspergillus. Fecal DNA was analyzed using 18S ribosomal sequencing and validated with a published fecal metagenomic dataset. Epidemiological data from the UK, Taiwan, and Japan were also examined.

RESULTS: Gut Aspergillus was exclusively detected in BA cases, suggesting it may be a potential trigger. Independent fecal metagenomic data from China and epidemiological correlations further supported this hypothesis. In the UK, BA presentations strongly correlated (r = 0.98, 95% CI [0.36, 1.0], p = 0.02) with Aspergillosis, but not with Candidiasis, during the COVID-19 lockdown. In Taiwan, a decade of data showed BA incidence was significantly associated (r = 0.78, 95% CI [0.29, 0.94], p = 0.01) with yearly Aspergillus-positive isolates among cancer-adjusted hospital admissions. In Japan, BA cases over 25 years correlated significantly (r = 0.85, 95% CI [0.37, 0.97], p = 0.01) with visceral Aspergillus burdens in autopsied cases, but not with other fungal infections.

CONCLUSIONS: The resolution of obstructive cholangitis in the antifungal-treated index case, together with multi-modal, cross-country evidence, highlights a potential link between gut Aspergillus and BA. Although limited by small sample size, retrospective design, and lack of mechanistic validation, the study may still be interpreted as hypothesis-generating and underscores the need for prospective studies to validate and extend these observations.},
}

@article {pmid41249836,
year = {2025},
author = {Huang, Y and Sun, Y and Ronda, C and Mavros, CF and Li, J and Jacobse, J and Huang, LH and Resnick, SJ and Giddins, M and Freedberg, DE and Chavez, A and Goettel, JA and Wang, HH},
title = {Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41249836},
issn = {1546-1696},
support = {MCB-2025515//National Science Foundation (NSF)/ ; 1R01DK118044//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R01CA272898//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5U19AI067773//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R03DK123489//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1R21HG011855//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; N00014-17-1-2353//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; HR00111920009//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; S-168-4X5-001//United States Department of Defense | United States Air Force | AFMC | Air Force Research Laboratory (AFRL)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; Career Awards for Medical Scientists//Burroughs Wellcome Fund (BWF)/ ; 1061046//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; 1513935//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; IRIS Award//Columbia University/ ; },
abstract = {Metagenomic sequencing and metabolomics of fecal matter have revealed the impact of the gut microbiome on health and disease. In addition to microbiota, feces also contain shed or exfoliated host epithelial, secretory and immune cells, but RNA profiling of these cells is challenging owing to degradation and cross-contamination. Here we introduce exfoliome sequencing (Foli-seq) to profile fecal exfoliated eukaryotic messenger RNAs (feRNAs) originating from the upper and lower gastrointestinal regions and show that this 'fecal exfoliome' harbors stable RNAs that reflect intestinal and immune function. By selectively amplifying targeted transcripts, Foli-seq demonstrates robust, accurate, sensitive and quantitative measurement of feRNAs. In murine colitis models, feRNA reveals temporal processes of epithelial damage, immune response and intestinal recovery specific to different types of gut inflammation. Simultaneous exfoliome and microbiome profiling uncovers a dense host-microbe interaction network. Moreover, we demonstrate stratification of patients with inflammatory bowel disease into subgroups that correlate with disease severity. Fecal Foli-seq is a noninvasive strategy to longitudinally study the gut and profile its health.},
}

@article {pmid41249624,
year = {2025},
author = {Kocher, A and Krause, J and Spyrou, MA},
title = {Insights into infectious diseases through ancient pathogen genomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41249624},
issn = {1740-1534},
abstract = {Major advances in metagenomic and biomolecular techniques have opened avenues for the recovery and sequencing of rare and highly fragmented DNA molecules from ancient biological samples, including those of pathogens that may persist in the remains of infected hosts long after their death. Initially consisting of relatively rare findings for a few disease-causing agents of historical importance, the field of ancient pathogen genomics is rapidly progressing towards genome-level analyses of larger sample sets encompassing a wider range of bacterial, viral and eukaryotic taxa. These advances have provided important insights into past pathogen distribution and genomic make-up, and the unprecedented opportunity to track their evolution 'in action' over large timescales. In this Review, we explore the major contributions of ancient DNA research to the understanding of pathogen evolution and its association with past epidemics, as well as human sociocultural and migration history, including numerous important studies that have been published in recent years. Moreover, we discuss existing limitations and future prospects of ancient pathogen genomics and the relevance of the field to current public health challenges.},
}

@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}

Animals
Freezing
*Amphibians/physiology
Skin/microbiology
Cold Temperature
Acclimatization
Microbiota

@article {pmid41249299,
year = {2025},
author = {Wu, Y and Meng, X and Han, X and Bu, Z and Li, Y and Zhan, H and Zhang, S},
title = {Integrated metagenomic and metabolomic analysis reveals microbial metabolite interactions involved in the quality formation of Codonopsis Radix.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40278},
pmid = {41249299},
issn = {2045-2322},
mesh = {*Codonopsis/metabolism/microbiology/growth & development/chemistry ; *Metabolomics/methods ; *Metagenomics/methods ; Soil Microbiology ; *Drugs, Chinese Herbal/metabolism ; Plants, Medicinal/metabolism/microbiology ; },
abstract = {Due to the impact of various environmental factors, in conjunction with the ecological adaptability and biochemical diversity of Chinese medicinal materials, Codonopsis Radix from Shanxi Province has developed into two distinct commercial specifications, namely Tai Codonopsis Radix (TCP) and Lu Codonopsis Radix (LCP). The present study examined the relationships between TCP and LCP from Shanxi Province regarding their environment, secondary metabolites, and Traditional Chinese Medicinal plant authenticity using metagenomic, metabolomic, and comprehensive quality assessment methods. The findings revealed that the two types of CPs met the quality standards. With respect to the growing environment, TCP and LCP grow in the same longitudinal extent, with a maximum longitudinal span of only 53'. Both regions presented similar natural environments conducive to the growth of CP. Additionally, the Lobetyolin content in TCP was greater than that in LCP. The soil microbial abundance in the TCP group was considerably significantly greater than that in the LCP group, and a new genus, Ascobolus, was found in TCP. Additionally, comparison of the metallic element data of the two groups soils revealed that the contents of Ti, Mg, Cr (P < 0.01) in the TCP group were significantly greater than those in the LCP group. Through correlation analysis, the ternary network of microbial-metal-metabolite interactions was constructed. The rhizosphere fungus Ascobolus was found to enhance the bioavailability of Zn via mineralization processes, thereby underscoring the significance of rhizosphere microecology in promoting plant growth. This study offers novel insights and approaches for the cultivation and processing of Codonopsis Radix.},
}

*Codonopsis/metabolism/microbiology/growth & development/chemistry
*Metabolomics/methods
*Metagenomics/methods
Soil Microbiology
*Drugs, Chinese Herbal/metabolism
Plants, Medicinal/metabolism/microbiology

@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth & development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}

Animals
*Soil Microbiology
*Cucumis sativus/parasitology/growth & development
*Microbiota/drug effects
*Nitrification/drug effects
Plant Roots/parasitology
*Tylenchoidea
Soil/chemistry
*Plant Diseases/parasitology/prevention & control
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Brachyura/chemistry

@article {pmid41229281,
year = {2026},
author = {Richardson, RT and Avalos, G and Garland, CJ and Trott, R and Hager, O and Hepner, MJ and Raines, C and Goodell, K},
title = {Sensitive Environmental DNA Methods for Low-Risk Surveillance of At-Risk Bumble Bees.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70073},
doi = {10.1111/1755-0998.70073},
pmid = {41229281},
issn = {1755-0998},
support = {RC22-B5-7373//Environmental Security Technology Certification Program/ ; //Maryland Department of Natural Resources/ ; //University of Maryland/ ; },
mesh = {Animals ; Bees/genetics/classification/physiology ; *DNA, Environmental/genetics/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; },
abstract = {Terrestrial environmental DNA (eDNA) techniques have been proposed as a means of sensitive, non-lethal pollinator monitoring. To date, however, no studies have provided evidence that eDNA methods can achieve detection sensitivity on par with traditional pollinator surveys. Using a large-scale dataset of eDNA and corresponding net surveys, we show that eDNA methods enable sensitive, species-level characterisation of whole bumble bee communities, including rare and critically endangered species such as the rusty patched bumble bee (RPBB; Bombus affinis). All species present in netting surveys were detected within eDNA surveys, apart from two rare species in the socially parasitic subgenus Psithyrus (cuckoo bumble bees). Further, for rare non-parasitic species, eDNA methods exhibited similar sensitivity relative to traditional netting. Compared with flower eDNA samples, sequenced leaf surface eDNA samples resulted in significantly lower rates of Bombus detection, and these detections were likely attributable to high rates of background eDNA on environmental surfaces, perhaps due to airborne eDNA or eDNA movement during rainfall events. Lastly, we found that eDNA-based frequency of detection across replicate surveys was strongly associated with net-based measures of abundance across site visits. We conclude that the COI-based metabarcoding method we present is cost-effective and highly scalable for quantitative characterisation of at-risk bumble bee communities, providing a new approach for improving our understanding of species habitat associations.},
}

Animals
Bees/genetics/classification/physiology
*DNA, Environmental/genetics/isolation & purification
*DNA Barcoding, Taxonomic/methods
*Metagenomics/methods

@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41248761,
year = {2025},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhanced anaerobic digestion performance of food waste by Fe-Mn MOF-derived carbon composite: Methane production, microbial response, and intrinsic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133667},
doi = {10.1016/j.biortech.2025.133667},
pmid = {41248761},
issn = {1873-2976},
abstract = {This study investigated the effects of Fe-Mn MOF-derived carbon composite (Fe-Mn MDC) on anaerobic digestion (AD) performance of food waste (FW) and elucidated the underlying mechanisms. The methane yield increased to 457.44 ± 14.21 mL/g VS under 0.05 g/g TS Fe-Mn MDC addition, representing a 36.47 % increase compared to the control group. Metagenomics analysis indicated that Fe-Mn MDC altered the microbial community structure, enriched the abundance and mutualism of exoelectrogenic bacteria (Geobacter) and electroactive methanogenic microorganisms (Methanothrix) involved in direct interspecies electron transfer. The metabolic activity of hydrogenotrophic methanogens was enhanced under Fe-Mn MDC addition, and the content of dehydrogenase and coenzyme F420 was also stimulated, thereby accelerating substrate consumption and methane production. The physicochemical characterization results of Fe-Mn MDC demonstrated that it could act as an electron shuttle and facilitate proton transfer. Besides, AD system exhibited not only an increase in e-pili and c-type genes abundance, but also an enhanced representation of gene modules linked to the biosynthesis of V/A-type ATPases (M00159) and F-type (M00157), which further indicated that Fe-Mn MDC enhanced the proton-coupled electron transfer in AD system. These results provided potential applications in FW management and new insights into the mechanism of renewable energy recovery from AD.},
}

@article {pmid41248576,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127958},
doi = {10.1016/j.jenvman.2025.127958},
pmid = {41248576},
issn = {1095-8630},
abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.},
}

@article {pmid41249156,
year = {2025},
author = {Liu, L and Wang, Z and Zhang, W and Lin, W},
title = {Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1795},
pmid = {41249156},
issn = {2052-4463},
support = {T2225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Genome, Viral ; Desert Climate ; *Soil Microbiology ; *Mars ; *Genome, Microbial ; Metagenome ; Metagenomics ; Tibet ; },
abstract = {The Qaidam Basin on the northern Tibetan Plateau represents a terrestrial Mars-analog desert characterized by hyperaridity, low temperatures, intense ultraviolet radiation, and high-salinity soils. To unveil the largely unexplored genomic diversity of microbes and viruses in this extreme environment, we collected 58 soil samples from various landforms and depths for metagenomic sequencing and analysis. We reconstructed 1,773 microbial metagenome-assembled genomes (mMAGs) and 2,060 viral MAGs (vMAGs), the vast majority (>94%) of which represent novel taxa. Among these, 327 mMAGs (completeness ≥ 90% and contamination ≤ 5%) and 325 vMAGs (completeness ≥ 90%) were classified as high-quality genomes. Taxonomic classification revealed that the bacterial, archaeal, and viral phyla with the largest numbers of genomes were Actinomycetota (n = 565), Halobacteriota (n = 111), and Uroviricota (n = 836), respectively. This metagenomic and genomic dataset provides valuable reference data for advancing our understanding of the diversity and function of microbial and viral communities across global desert ecosystems. Furthermore, these data offer astrobiological insights for research on life in Mars-analog extreme environments.},
}

*Genome, Viral
Desert Climate
*Soil Microbiology
*Mars
*Genome, Microbial
Metagenome
Metagenomics
Tibet