@article {pmid41381546,
year = {2025},
author = {Trubl, G and Roux, S and Borton, MA and Varsani, A and Li, YF and Sun, CL and Jang, HB and Woodcroft, BJ and Tyson, GW and Wrighton, KC and Saleska, SR and Eloe-Fadrosh, EA and Sullivan, MB and Rich, VI},
title = {Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67057-0},
pmid = {41381546},
issn = {2041-1723},
support = {DE-SC0010580, DE-SC0016440, DE-SC0248445, DE-SC0023307//DOE | SC | Biological and Environmental Research (BER)/ ; SCW1632//DOE | SC | Biological and Environmental Research (BER)/ ; 3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; SCGSR//DOE | Office of Science (SC)/ ; 21-LW-060//DOE | LDRD | Lawrence Livermore National Laboratory (LLNL)/ ; },
abstract = {Anthropogenic-driven climate change is accelerating permafrost thaw, threatening to release vast carbon stores through increased microbial activity. While microbial roles are increasingly studied, the contributions of viruses remain largely unexplored, in part due to soil-associated technical challenges that have hindered their detection and characterization. Here, we applied an optimized virion enrichment workflow along a permafrost thaw gradient, identifying 9,963 viral populations (vOTUs), including single- and double-stranded DNA viruses, with 99.9% novelty compared to other soils. Hosts were predicted for 38% of vOTUs, spanning nine archaeal, and 36 bacterial phyla, 22% of which were linked to metagenome-assembled genomes, including key carbon-cycling taxa. Genomic analyses revealed 811 putative auxiliary metabolic genes (AMGs) from 658 vOTUs, nearly half involved in carbon processing. These included 59 glycoside hydrolases (GH) across nine GH families, 45 for monosaccharide degradation, and seven involved in short-chain fatty acid and C1 metabolism, linking viruses to both early and late stages of carbon turnover. Additionally, six vOTUs carried racD, which may stabilize microbial necromass and promote long-term carbon storage. Viral and AMG functional diversity increased with thaw stage, indicating that viruses might participate in a broadening range of microbial metabolic processes as permafrost thaws. These findings expand our understanding of virus contributions in microbial carbon processing and suggest their important role in deciphering soil carbon fate under changing climate conditions.},
}

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

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

@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
doi = {10.1111/1758-2229.70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}

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

@article {pmid41380982,
year = {2025},
author = {Wei, B and Zhang, L and Zhang, H and Gui, B and Deng, Q and Chang, X and Yu, P and Dong, X and Zou, B and Zhang, X and Zhao, Y and Zhao, Z and Chen, J},
title = {An integrated ultrasonic and cellulase pretreatment strategy: simultaneously enhancing medium-chain fatty acid production and reducing antibiotic resistance genes in anaerobic digestion of animal manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133780},
doi = {10.1016/j.biortech.2025.133780},
pmid = {41380982},
issn = {1873-2976},
abstract = {Rapid expansion of animal husbandry poses significant environmental challenges, including waste management and pollution. While medium-chain fatty acid (MCFA) production from livestock manure via chain elongation (CE) process in anaerobic digestion (AD) offers a promising and economically valuable waste management strategy, the associated risks of antibiotic resistance genes (ARGs) propagation through AD products are often overlooked. Additionally, the impact of substrate pretreatments on MCFA production and ARGs abundances in livestock manure during CE process remains unclear. This study assessed synergistic effects of cellulase and ultrasonic pretreatments on MCFA yield, microbial community, and ARGs during CE process of co-digesting lignocellulosic goat manure and corn straw. The results demonstrated that cellulase pretreatment increased caproate yield by 46.72 % (from 6.93 to 10.17 g of chemical oxygen demand (COD)/L). Combined cellulase and ultrasonic pretreatments decreased ARGs relative abundance by 25.28 %. The underlying mechanism was further explored through metagenome, revealing the roles of microbial community shifts and gene regulation in the beneficial outcomes. Specifically, we found that cellulase pretreatment enriched Clostridia and modulated genes related to reverse β-oxidation and ethanol oxidation, contributing to enhanced MCFA production. The reduction in ARGs abundance, particularly with combined pretreatments, was linked to a decrease in Massilibacterium abundance. Additionally, co-occurrence analysis indicated Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota as primary ARG hosts. This study demonstrates the viability of lignocellulosic goat manure for MCFA production via CE. Pretreatments effectively boost MCFA yield and mitigate ARGs, providing a basis for comprehensive biorefinery systems integrating resource valorization and ARGs control in lignocellulosic animal waste management.},
}

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

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

@article {pmid41380611,
year = {2025},
author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X},
title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119550},
doi = {10.1016/j.ecoenv.2025.119550},
pmid = {41380611},
issn = {1090-2414},
abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.},
}

@article {pmid41380516,
year = {2025},
author = {Geng, Y and Lian, CA and Yang, L and Pavlostathis, SG and Qiao, X and Qiu, Z and Wang, Y and Dong, N and Li, A and Luo, X and Yu, K},
title = {Unlocking microbial synergy in mcroalgae-bcteria gnules: RSM -driven optimization and lifecycle microbial metagenomics for high-ammonia wastewater treatment.},
journal = {Water research},
volume = {290},
number = {},
pages = {125098},
doi = {10.1016/j.watres.2025.125098},
pmid = {41380516},
issn = {1879-2448},
abstract = {Landfill leachate is challenging to treat biologically due to high ammonia toxicity and low C/N ratio, while suspended co-cultures, despite easing carbon limitations, show poor settleability and instability under high-strength conditions. This work focuses on investigating microbial synergy in microalgae-bacteria granules through RSM-driven optimization and lifecycle microbial metagenomics for high-ammonia leachate treatment. Initially, granules removed Total inorganic nitrogen (TIN) at 167.5 mg/L/d, outperforming algae-only systems. 16S rRNA analysis showed 25 % more Halomonas sp. and enriched Proteobacteria, linked to improved pollutant removal. Subsequent RSM optimization elevated TIN removal to 193.3 mg/L/d, with synchronous improvement in chemical oxygen demand (COD) removal, flocculation, Extracellular Polymeric Substances (EPS) production, and granule stability. In addition, reactor operation over 8 cycles sustained TIN removal above 193.4 mg/L/d until Cycle IV and then dropped by 5.0 %, displaying a typica granule life cycle from growth to decline. Metagenomic analysis of 326 metagenome-assembled genomes (MAGs) revealed dynamic microbial synergy that shifted from nutrient assimilation to stress adaptation, explaining the system's resilience. During assimilation-dominated stages, synergy focused on coordinated nutrient utilization, supporting energy-intensive nitrogen assimilation. As metabolism shifted to dissimilation, synergy reoriented toward stress adaptation: assimilation genes decreased to 44.3 % of their peak levels, while stress genes hcp and cah increased by 11.2-fold. This dynamic synergy provides a blueprint for lifecycle management. These findings highlight the great potential of microalgae-bacteria granules as a resilient, low-footprint approach for nitrogen removal and circular wastewater treatment.},
}

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

@article {pmid41380256,
year = {2025},
author = {Yu, W and Zhang, J and Shi, Z and Wang, S and Lai, S and Huang, X and Zhang, J and Cai, Z and Zhao, J},
title = {Reductive soil disinfestation mitigates antibiotic resistance gene risk in the soil-lettuce continuum by restructuring dominant bacterial taxa and improving soil properties.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140745},
doi = {10.1016/j.jhazmat.2025.140745},
pmid = {41380256},
issn = {1873-3336},
abstract = {Reductive soil disinfestation (RSD) and chemical fumigation serve as effective methods for controlling soil-borne pathogens, yet their effects on soil antibiotic resistome remain poorly understood. This study combined high-throughput qPCR (HT-qPCR) and metagenomic sequencing to evaluate the impacts of dazomet fumigation (DZ) and RSD amended with alfalfa (AL) and molasses (MO) on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in an ARG-contaminated soil. Results demonstrated that both DZ and RSD treatments significantly altered the soil resistome and bacterial community. HT-qPCR revealed that DZ significantly increased the relative abundance of total ARGs, MGEs and high-risk ARGs (Rank I and Rank II) by 86.59 %, 43.12 %, 36.81 %, and 40.88 %, respectively, while RSD treatments effectively reduced MGEs by 53.96-63.30 % and significantly suppressed Rank II high-risk ARGs. Metagenomic sequencing further indicated that RSD, particularly AL, outperformed DZ in reducing most ARGs classes, with pronounced effects on predominant ARGs such as macB (16.32 %), tetA(58) (24.14 %), and TxR (29.31 %). Correlation analyses suggested that RSD mitigates ARGs contamination by modulating the dominant bacterial community, especially suppressing ARG hosts while enriching antagonists, and improving soil physicochemical properties. Variance partitioning analysis attributed greater explanatory power to bacterial community than to physicochemical properties in shaping high-risk (18.44 % vs. 3.72 %) and high-abundance (11.90 % vs. 2.79 %) ARG profiles. Moreover, RSD considerably reduced the ARGs transmission risk from soil to lettuce. These findings establish RSD as an effective strategy to curb ARGs dissemination in soil-plant system and support its adoption for safer agricultural production.},
}

@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
doi = {10.1371/journal.pone.0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation & purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.

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

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

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

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

@article {pmid41379644,
year = {2025},
author = {Capoferri, G and Battegay, R and Hamelin, B and Keller, PM and Mertz, KD and Weisser, M},
title = {Borrelia afzelii Hepatitis in Patient Treated with Venetoclax and Obinutuzumab, Switzerland.},
journal = {Emerging infectious diseases},
volume = {31},
number = {11},
pages = {2167-2171},
doi = {10.3201/eid3111.250584},
pmid = {41379644},
issn = {1080-6059},
mesh = {Humans ; *Sulfonamides/adverse effects/therapeutic use ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; Switzerland ; *Borrelia burgdorferi Group/genetics ; *Bridged Bicyclo Compounds, Heterocyclic/adverse effects/therapeutic use ; *Lyme Disease/diagnosis/microbiology/drug therapy ; Male ; *Hepatitis/diagnosis/etiology/microbiology ; Immunocompromised Host ; *Antineoplastic Agents/adverse effects/therapeutic use ; Aged ; Female ; },
abstract = {We report Borrelia afzelii hepatitis in an immunosuppressed patient in Switzerland receiving anti-CD20 therapy and venetoclax. Diagnosis was made by metagenomic sequencing and PCR. This case underscores the need to consider Lyme borreliosis in unexplained hepatitis cases and highlights the value of molecular diagnostics in immunosuppressed patients when serologic test results are negative.},
}

Humans
*Sulfonamides/adverse effects/therapeutic use
*Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use
Switzerland
*Borrelia burgdorferi Group/genetics
*Bridged Bicyclo Compounds, Heterocyclic/adverse effects/therapeutic use
*Lyme Disease/diagnosis/microbiology/drug therapy
Male
*Hepatitis/diagnosis/etiology/microbiology
Immunocompromised Host
*Antineoplastic Agents/adverse effects/therapeutic use
Aged
Female

@article {pmid41379519,
year = {2025},
author = {Aaby, M and Lalitha, P and Prajna, NV and Gunasekaran, R and Seitzman, GD and Doan, T and Redd, TK},
title = {Comparing Microbiologic Tests for Pathogen Detection in Infectious Keratitis Using Latent Class Analysis.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000004075},
pmid = {41379519},
issn = {1536-4798},
support = {K23EY032639/EY/NEI NIH HHS/United States ; P30EY010572/EY/NEI NIH HHS/United States ; Tom Wertheimer Career Development Award in Data Science//Research to Prevent Blindness/ ; unrestricted departmental funding//Research to Prevent Blindness/ ; },
abstract = {PURPOSE: To compare the diagnostic performance of traditional microbiologic tests and next-generation sequencing methods for infectious keratitis pathogen detection.

METHODS: Participants included 86 subjects diagnosed with acute infectious keratitis at Aravind Eye Hospital in Madurai, India. Corneal scrapings from all subjects were evaluated using Gram stain, potassium hydroxide (KOH) smear, culture, and metagenomic deep sequencing (MDS). The sensitivity and specificity of each test were estimated using latent class analysis.

RESULTS: Among 86 participants, clinical diagnostic tests demonstrated varying sensitivity and specificity for bacterial and fungal keratitis. Gram stain exhibited high sensitivity (89%) and specificity (94%) for bacterial detection, whereas KOH smears showed only moderate sensitivity (75%) and specificity (69%) for fungal detection. Culture testing had lower sensitivity for bacterial (68%) and fungal (56%) identification, but high specificity (92% and 88%, respectively). MDS demonstrated the best balance of sensitivity and specificity across pathogen classes, with 100% sensitivity and 90% specificity for bacterial keratitis and 82% sensitivity with 94% specificity for fungal keratitis. MDS detected critical pathogens missed by culture in 29% of cases, including those whose identification is essential for guiding clinical management and preventing vision-threatening complications.

CONCLUSIONS: MDS demonstrated a favorable balance between sensitivity and specificity for both bacterial and fungal keratitis, whereas smears performed well for bacterial but not fungal keratitis and cultures demonstrated high specificity but low sensitivity. Repeated evaluation of diagnostic performance across diverse populations and geographic settings is necessary to validate the reliability and optimize the clinical utility of microbiologic testing for infectious keratitis.},
}

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

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

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

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

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

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

@article {pmid41378921,
year = {2025},
author = {Montini, A and Pellegrini, C and Loddo, G and Ravaioli, F and Baldelli, L and Mainieri, G and Pirazzini, C and Mazzotta, E and Carano, F and Sala, C and De Fanti, S and Bacalini, MG and Provini, F},
title = {Analysis of gut microbiota in Restless Legs Syndrome: searching for a metagenomic signature.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsaf383},
pmid = {41378921},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: We aim to analyse the microbiota composition in RLS patients and its relationship with the different RLS phenotypes.

METHODS: We recruited idiopathic RLS (RLS) and insomnia (INS) patients and healthy subjects (CTRL). Validated questionnaires (PSQI, IRLS, ISI, BDI-II) were administered in the RLS and INS. Fecal microbiota was analysed by 16S rRNA gene sequencing according to Illumina metagenomics standard procedure on MiSeq Platform. Dada2 pipeline was used to process sequencing data, while DESeq2 and Aldex2 tools were used to calculate differential abundance taxa, correcting for age, sex, Body Mass Index, sequencing run and presence of mood disorders.

RESULTS: The sample included 37 RLS (28 females, mean age 64.78 years), 31 INS (22 females, mean age 60.64 years) and 33 CTRL (24 females, mean age 62.54 years). Differential abundance analysis revealed a statistically significant decrease in the abundance of Lachnoclostridium and Flavonifractor genera in RLS compared to CTRL and INS, but not in the INS compared to CTRL. Lachnoclostridium abundance tended to decrease with long disease duration and a predominant motor phenotype. In the RLS group, several genera were identified as significantly associated with IRLS and PSQI scores.

CONCLUSIONS: Although only a few previous studies have reported the presence of small intestinal bacterial overgrowth (SIBO) in RLS, to the best of our knowledge this is the first study to highlight significant differences in the gut microbiota composition of RLS compared to both CTRL and INS, identifying a specific RLS metagenomic signature.},
}

@article {pmid41378915,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf275},
pmid = {41378915},
issn = {1751-7370},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.},
}

@article {pmid41378891,
year = {2025},
author = {Khanal Pokharel, S and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC},
title = {Establishing conserved biosynthetic gene clusters of the phylum Myxococcota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0215125},
doi = {10.1128/aem.02151-25},
pmid = {41378891},
issn = {1098-5336},
abstract = {UNLABELLED: A surge in sequenced myxobacteria catalyzed by advancements in long-read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze 11 genera and 195 sequenced genomes, including 10 newly reported myxobacterial isolates, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to the diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.

IMPORTANCE: Critical contributions to soil nutrient cycles by predatory bacteria, including the Myxococcota, and utility as a resource for the discovery of novel enzymology and metabolism motive continued isolation and characterization of myxobacteria from the environment. Each of these motivating factors involves specialized metabolites produced by myxobacteria and the biosynthetic gene clusters (BGCs) responsible for their assembly. Primarily associated with the predatory lifestyles of myxobacteria, myxobacterial specialized metabolites have been pursued as therapeutic leads for novel antibacterials, antifungals, anthelmintics, and cancer therapies. Despite these efforts and the observation that nearly all genera within the Myxococcota have an extraordinary number of BGCs, there is no consensus view of the conserved BGCs in the phylum. Our study revealed the core BGCs consistently present throughout the phylum. By reporting these core specialized metabolites and their ecological roles, we hope to streamline the discovery and investigation of specialized metabolism in myxobacteria.},
}

@article {pmid41378809,
year = {2025},
author = {Huang, X and Wu, X and Huang, H},
title = {A Case of Tinea Nigra in Southern China.},
journal = {The American Journal of dermatopathology},
volume = {47},
number = {8},
pages = {640-641},
doi = {10.1097/DAD.0000000000002997},
pmid = {41378809},
issn = {1533-0311},
support = {SZSM202311029//Sanming Project of Medicine in Shenzen Municipality/ ; },
mesh = {Humans ; Female ; Adult ; China ; Antifungal Agents/administration & dosage/therapeutic use ; Dermoscopy ; *Tinea/microbiology/drug therapy/pathology/diagnosis ; *Hand Dermatoses/microbiology/drug therapy/pathology/diagnosis ; Treatment Outcome ; },
abstract = {Tinea nigra, a rare superficial fungal infection caused by Hortaea werneckii, is often mistaken for a melanocytic lesion. We report a case in Shenzhen, a city in southern China, involving a 31-year-old woman with slowly enlarging brown patches on her left palm over 15 years. The patches were smooth, asymptomatic, and without scaling or travel history to tropical regions. Dermatological examination revealed a 30 mm × 25-mm brown macule with distinct borders. Dermoscopic analysis showed brownish-gray pigmented strands parallel to skin ridges, differing from the pattern in melanoma. Histopathological examination confirmed fungal hyphae in the upper stratum corneum. The fungus was identified as H. werneckii using metagenomic next-generation sequencing. The lesion resolved completely after an 8-week course of 1% butenafine cream. Accurate diagnosis is crucial to prevent misdiagnosis as malignant melanoma. Dermoscopy and fungal microscopy are key diagnostic tools. Treatment with topical antifungal agents is effective, with symptoms resolving within weeks.},
}

Humans
Female
Adult
China
Antifungal Agents/administration & dosage/therapeutic use
Dermoscopy
*Tinea/microbiology/drug therapy/pathology/diagnosis
*Hand Dermatoses/microbiology/drug therapy/pathology/diagnosis
Treatment Outcome

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

@article {pmid41378133,
year = {2025},
author = {Langwig, MV and Sneed, SL and Rasmussen, A and Seitz, KW and Lee, JA and Anantharaman, K and De Anda, V and Francis, CA and Baker, BJ},
title = {Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf182},
pmid = {41378133},
issn = {2730-6151},
abstract = {Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With intensifying anthropogenic pressures, it is critical to understand the capacity of these communities to maintain essential functions under environmental change. Here, we examined the metabolic functions and redundancy in the microbial community of San Francisco Bay (SFB) sediments, providing the first large-scale, genome-resolved, and spatiotemporally resolved characterization of the estuary. Salinity, iron, phosphorus, sulfur, and total sediment nitrogen were significantly correlated with microbial community composition, suggesting these factors play a key role in structuring SFB communities. In support of this, we identified broad capabilities for iron cycling and key uncultured players that contribute to denitrification, nitrification, and complete nitrification (comammox). We also identified widespread capabilities for sulfur cycling, including understudied lineages capable of rDsr-mediated sulfur oxidation. SFB MAGs exhibited partitioning of multistep metabolisms, or metabolic handoffs, and the rare biosphere broadly encoded key nitrogen and sulfur cycling genes. Despite shifts in community composition across sites and fluctuations in environmental parameters, key nitrogen and sulfur metabolisms were maintained throughout the estuary, especially in nitrate reduction, nitrite reduction, and the Dsr/Sox pathway. The presence of multiple microbial taxa with similar functional roles (functional redundancy) may provide an ecosystem buffer, suggesting these functions could better recover from disturbances and ultimately contribute to the long-term health and sustainability of these vital coastal habitats.},
}

@article {pmid41377518,
year = {2025},
author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S},
title = {Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.26.689816},
pmid = {41377518},
issn = {2692-8205},
abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective curation. We performed comprehensive manual curation and harmonization of clinical metadata from 212,027 samples across 468 studies in two major repositories: curatedMetagenomicData (93 studies, 22,588 samples) and cBioPortal (375 studies, 189,438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into much fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions encountered during large-scale metadata harmonization across two distinct omics domains. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.},
}

@article {pmid41377425,
year = {2025},
author = {Nawaz, S and Nadeem, IA and Talha, M and Irshad, NUN and Imran, SB},
title = {Engineered microbes over immunosuppression: MAGIC as a transformative strategy for vasculitides.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {12},
pages = {9131-9132},
pmid = {41377425},
issn = {2049-0801},
}

@article {pmid41377246,
year = {2025},
author = {Singh, PK and Rathi, D and Shweliya, MA and Farooq, A and Anfaal, Z and Saleem, NUA and Hamza, M and Qadri, M and Rath, S and Hemida, MF and Rani, H and Mahgoub, AMA and Wazir, HU},
title = {The interplay of the microbiome and breast cancer: beyond the gut: a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {87},
number = {12},
pages = {8496-8507},
pmid = {41377246},
issn = {2049-0801},
abstract = {Breast cancer remains a leading cause of morbidity and mortality among women worldwide, with emerging evidence underscoring the microbiota's pivotal role in its etiology, progression, and therapeutic response. This narrative review synthesizes the intricate interplay between the breast tissue, skin, and lung microbiomes in breast cancer pathogenesis, with particular emphasis on inflammatory breast cancer (IBC) and metastatic dissemination. The healthy breast microbiome, dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes, maintains tissue homeostasis through pH regulation, metabolite production, and immune modulation. Dysbiosis disrupts this equilibrium, fostering carcinogenesis via chronic inflammation, estrogen deconjugation, and DNA damage-induced genomic instability, with subtype-specific microbial signatures influencing tumor growth and therapy resistance. In IBC, skin microbiome alterations characterized by overgrowth of pathogens like Pseudomonas aeruginosa and Staphylococcus aureus exacerbate inflammation, epithelial-mesenchymal transition (EMT), and lymphatic invasion, while promoting a pro-tumorigenic microenvironment enriched in regulatory T cells and M2 macrophages. Concurrently, lung microbiota dysbiosis impairs immune surveillance, remodels the extracellular matrix, and facilitates metastatic seeding through neutrophil extracellular traps and cytokine storms. Cross-talk among these microbiomes amplifies systemic effects, highlighting their synergistic contributions to disease aggressiveness. Advanced analytical techniques, including 16S rRNA sequencing, metagenomics, and metabolomics, offer promising microbial biomarkers for early detection and risk stratification. By elucidating these host-microbe dynamics, this review advocates for microbiome-centric interventionssuch as probiotics, fecal microbiota transplantation, and targeted antimicrobials to enhance precision diagnostics and therapies, ultimately improving outcomes in breast cancer management.},
}

@article {pmid41377184,
year = {2025},
author = {Ayilaran, E and McHugh, O and Jung, Y},
title = {Metagenomic sequencing dataset of microbial communities in onion and cabbage microgreens across substrates, Salmonella inoculation, and bacteriophage application.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112297},
pmid = {41377184},
issn = {2352-3409},
abstract = {This dataset comprises shotgun metagenomic sequencing results from edible portion of onion (Allium cepa) and cabbage (Brassica oleracea) microgreens cultivated on soil, biostrate, and jute fiber substrates, with and without Salmonella inoculation and bacteriophage application. Table 1 contains detailed sequencing quality metrics and National Center for Biotechnology Information Sequence Read Archive accession numbers (BioProject: PRJNA1327464) for all 24 samples. Figure 1 provides a species-level (≥5% relative abundance) heatmap highlighting microbial community clustering by seed type. These data can be reused for comparative microbiome analyses, evaluation of pathogen-phage-substrate interactions, and benchmarking of metagenomic workflows.},
}

@article {pmid41377047,
year = {2025},
author = {Lee, SH and Yun, YB and Kim, DS and Park, M and Um, Y and Kang, JW},
title = {Isolation of plant growth-promoting rhizobacteria from wild-simulated ginseng and evaluation of soil health following its application in the field.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682016},
pmid = {41377047},
issn = {1664-302X},
abstract = {Wild-simulated ginseng must be cultivated at natural forest sites without artificial structures, chemical fertilizers, or pesticides to qualify for certification. However, its extended cultivation period makes stable production challenging, necessitating effective strategies to enhance early growth and yield. In this study, we evaluated the ability of five bacterial strains isolated from the rhizosphere of wild-simulated ginseng to promote initial growth and development. The strains exhibited diverse functional traits, including indole-3-acetic acid (IAA) production, phosphate solubilization, siderophore production, and enzymatic activities such as protease and cellulase. Antifungal activity, however, was primarily observed in strains 79 and 81. We inoculated field-grown ginseng plants with each strain at biweekly intervals for a total of seven applications. Inoculation with strain 75 (Pseudomonas frederiksbergensis) significantly increased shoot dry weight by 48.9% and root biomass by 37.0% relative to uninoculated controls (p < 0.05). Strain 81 (Paenibacillus terrae) promoted stem elongation, whereas strain 89 (Paraburkholderia madseniana) reduced leaf size. Soil analysis showed that strain 75 and 77 plots maintained higher organic matter, phosphorus, calcium, and cation exchange capacity, whereas strains 79, 81, and 89 had lower values. Metagenomic analysis revealed a marked enrichment of the order Pseudomonadales and the maintenance or enhancement of bacterial alpha diversity (Chao1 and PD indices), suggesting a stable and resilient microbial ecosystem. Functional profiling revealed enhancements in nitrogen fixation and nutrient cycling pathways. We determined statistical significance using a t-test and one-way ANOVA with Duncan's multiple range test (p < 0.05). In contrast, strains 79 (Paraburkholderia terricola), 81 (Paenibacillus terrae), and 89 (Paraburkholderia madseniana) did not elicit significant growth responses. Our findings indicate that P. frederiksbergensis (strain 75) is a promising plant growth-promoting rhizobacterium for wild-simulated ginseng, offering a biologically based approach for improving early-stage development under forest cultivation conditions.},
}

@article {pmid41377041,
year = {2025},
author = {Zhou, Y and Qi, D and Chen, C and Bi, W and Yu, X and Liu, J and Lan, G and Hou, R and Li, Z and Ma, R},
title = {Divergent gut microbial metabolism supports niche partitioning in giant and red pandas.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698108},
pmid = {41377041},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbiota plays a pivotal role in regulating the host's physiological functions and behavior. The coevolutionary relationship between the host and its gut microbiota facilitates adaptation to specific ecological niches. As obligate bamboo feeders, giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus styani) exhibit distinct feeding preferences: the former primarily consumes bamboo stems and leaves, while the latter feeds mainly on bamboo leaves. This study aims to elucidate how these species adapt metabolically to different parts of bamboo via gut microbial activity.

METHODS: We employed 16S rRNA gene sequencing to analyze the structure and function of fecal microbial communities in giant pandas (GP) and red pandas (RP).

RESULTS: Significant differences in gut microbiota composition were observed between the GP and RP groups. Eight core bacterial taxa constituted over 99.97% of the total microbial composition, with the RP group exhibiting higher species richness but lower overall diversity. At the phylum level, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, and Flavobacteria were significantly enriched in the GP group, whereas Firmicutes dominated in the RP group. At the genus level, Sphingomonas, Methylobacterium, Cryomonas, and Terriglobus were more abundant in the GP group, while Streptococcus and Rhizobium were enriched in the RP group. Functional metabolic analysis indicated that lipid and amino acid metabolism pathways were significantly enriched in the GP group, whereas nucleotide and carbohydrate metabolism pathways were prominent in the RP group. Further analysis revealed that Sphingomonas and Methylobacterium in the GP group positively regulated amino acid and lipid metabolism, while Streptococcus in the RP group enhanced nucleotide and carbohydrate metabolism.

DISCUSSION: These findings suggest that the distinct metabolic pathways of the gut microbiota in giant and red pandas have evolved in concert with their dietary strategies, energy acquisition modes, and ecological niche differentiation, forming a highly coordinated adaptive system.},
}

@article {pmid41376967,
year = {2025},
author = {Liu, H and Ji, S and Xing, F and Wang, C and Sun, W and Shao, H and Hu, C},
title = {Performance of metagenomic next-generation sequencing, Xpert MTB/RIF and acid-fast staining for diagnosing tuberculous pleurisy and empyema.},
journal = {Journal of thoracic disease},
volume = {17},
number = {11},
pages = {10298-10307},
pmid = {41376967},
issn = {2072-1439},
abstract = {BACKGROUND: The detection of Mycobacterium tuberculosis (MTB) is an important basis for the diagnosis of tuberculosis. Detecting fresh tissue, pus, and other samples is challenging. Both metagenomic next-generation sequencing (mNGS) and Xpert MTB/RIF have demonstrated excellent performance in the diagnosis of tuberculosis; however, their research base is still lacking in tissue or pus samples. We hope to explore the detection performance of mNGS and Xpert MTB/RIF in these sample types through this study.

METHODS: This study enrolled 154 patients suspected of having tuberculosis. Fresh tissues, pleural fluid or pus were collected from these patients and performed mNGS, Xpert, and acid-fast staining (AFS) tests. Their detection performance was statistically analyzed and compared.

RESULTS: Overall, the positivity rate of mNGS was 48.05% (74/154), Xpert was 44.44% (44/99), and AFS was 57.34% (82/143). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 55.22%, 100%, 100% and 25%, respectively. The sensitivity, specificity, PPV and NPV of Xpert were 48.35%, 100%, 100%, 18.97%, respectively. The sensitivity, specificity, PPV and NPV of acid-fast stain were 58.59%, 53.33%, 91.46%, 13.11%, respectively. A total of 93 samples underwent all three types of testing, and 45.16% (42/93) were completely consistent in the results of the three tests. The analysis results of these samples showed that the sensitivity, specificity, PPV and NPV of mNGS were 65.88%, 100%, 100%, 21.62%, respectively. The sensitivity, specificity, PPV and NPV of Xpert were 49.41%, 100%, 100%, 15.69%, respectively. The sensitivity, specificity, PPV and NPV of acid-fast stain were 57.65%, 62.50%, 94.23%, 12.20%, respectively. The sensitivity of mNGS was significantly higher than that of Xpert (P=0.01).

CONCLUSIONS: Our research results indicate that mNGS and AFS have higher sensitivity compared to Xpert, while mNGS and Xpert have higher specificity.},
}

@article {pmid41376957,
year = {2025},
author = {Liu, Y and Deng, N and Lu, Y and Peng, J and Yuan, S},
title = {Comparison of metagenomic next-generation sequencing (mNGS) technology with routine laboratory culture for bacterial and fungal detection in bronchoalveolar lavage fluid.},
journal = {Journal of thoracic disease},
volume = {17},
number = {11},
pages = {10036-10044},
pmid = {41376957},
issn = {2072-1439},
abstract = {BACKGROUND: Pulmonary infections continue to threaten human health. Metagenomic next-generation sequencing (mNGS) technology provides a rapid detection method for identifying the pathogens responsible for pulmonary infections, with many advantages compared to traditional culture method. Our objective is to collect and analyze testing data from patients with pulmonary infections at the Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, in order to compare the detection rates of mNGS and traditional culture method.

METHODS: This study conducted a retrospective analysis of bronchoalveolar lavage fluid (BALF) samples from 50 patients with pulmonary infections at the Department of respiratory medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, comparing the differences between mNGS and the traditional "gold standard" culture method.

RESULTS: The detection rate of mNGS for fungi or bacteria was 72.0% (36/50), while that of culture method was 12.0% (6/50). According to the McNemar χ[2] test, there was a statistical significance between the detection results of mNGS and culture method (P<0.0001). In addition, mNGS can detect viruses that cannot be detected by culture method. Only 12.0% (6/50) tested positive for both mNGS and culture, while 60% (30/50) tested positive for mNGS but negative for culture. mNGS results led to treatment modifications for 18 patients. 8 cases added antifungal treatment, 7 cases adjusted antibiotic treatment, 2 cases adjusted both antifungal and antibiotic treatment, and 1 case adjusted antifungal treatment.

CONCLUSIONS: mNGS, as a new diagnostic testing technology, has significant advantages in identifying bacteria, fungi, and virus. The combination of mNGS analysis of BALF and traditional pathogen culture method can improve the efficiency of pathogen detection and facilitate the diagnosis of patients with pulmonary infections, allowing patients to receive targeted treatment as soon as possible.},
}

@article {pmid41376878,
year = {2026},
author = {Sengupta, S and Basak, P and Pramanik, A and Ghosh, P and Mukhopadhyay, M and Sen, A and Bhattacharyya, M},
title = {Altitude-driven variations in soil microbial communities of Himalayan subalpine forests.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {7},
pmid = {41376878},
issn = {2190-572X},
abstract = {UNLABELLED: The Himalayas offer a unique environment for the study of microbial diversity and their response to biotic and abiotic factors, enhancing knowledge on ecological processes under altitudinal control in subalpine forests. This study investigates the impact of altitude on bacterial diversity and soil physico-chemical properties of Himalayan subalpine coniferous forests at four different regions-Sillery Gaon (S1; 1829 m), Gangotri (S2; 3415 m), Kausani (S3; 1890 m) and Gwal Dam (S4; 1940 m). Using 16S rDNA amplicon sequencing, soil microbial diversity of the said subalpine ecosystems were explored. Physico-chemical studies of the soil samples showed that S1 had the highest moisture content (25.66 ± 0.26%) and C:N ratio (136.26 ± 5.4) while S4 had the highest TOC (22.78 ± 1.2%), TKN (0.7373 ± 0.043%) and available phosphate content. Results indicated presence of diverse microflora from various phyla, including Actinomycetota (7.52% in S2, 7.98% in S3), Planctomycetota (53.36% in S1, 51.09% in S3), Proteobacteria (14.3% in S1, 18.28% in S3, 14.96% in S4), and Verrucomicrobiota (18.75% in S2 and 21.88% in S4). Proteobacteria was the dominant phyla in mid (S4) and lower (S1, S3) subalpine forest soils, suggesting enhanced abundance due to human intervention at these altitudes. Multivariate analysis revealed a positive correlation between altitude, precipitation, moisture content, soil pH, organic carbon, nitrogen and phosphate contents with the presence of Proteobacteria and Actinomycetota phyla. The study highlights the connection between microbial communities and soil physicochemical properties, and the intricate interplay of biotic and abiotic factors affecting the microbial community composition in a unique region at different elevations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04608-8.},
}

@article {pmid41376791,
year = {2025},
author = {Liu, Y and Tan, Y and Xia, F and Wu, S and Zou, S and Chen, Q and Liu, J and Song, S and Du, Q and Guo, W and Liang, K},
title = {Diagnostic utility of metagenomic next-generation sequencing for tissue in patients with suspected infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634406},
pmid = {41376791},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Adult ; Retrospective Studies ; *Communicable Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; Aged ; HIV Infections ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; },
abstract = {Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methods because of its comprehensiveness. However, the diagnostic utility of mNGS for tissue hasn't been fully explored, especially for patient with HIV infection. HIV-positive and negative patients with suspected infectious diseases who performed tissue mNGS and conventional microbiological tests (CMTs) were retrospectively enrolled between October, 2020 and May 2024. The microbial spectrum of tissue mNGS and CMTs was analyzed, and the diagnostic accuracy and consistency of mNGS and CMTs for tissue were compared. The related factors of positive rate of mNGS was analyzed. Of 70 patients with suspected infectious diseases, 44 cases were confirmed with the infectious diseases. Among 44 patients with infectious diseases, aerobic bacteria (36.4%) was the most common detected pathogen, followed by mycobacterium tuberculosis (MTB, 18.2%), non-tuberculous mycobacteria (NTM, 13.6%) and fungus (11.4%). The sensitivity of tissue mNGS (72.7%, 95%CI 56.9%-84.5%) was significantly higher than that that in tissue CMTs (29.5%, 95%CI 17.2%-45.4%) (p<0.001), but the specificity was not statistically significant(P = 0.656). mNGS demonstrated higher detection rates than CMTs in the case with single microbial infections (70.0% vs. 30.0%; p<0.01). For the case with multiple microbial infections, the detection rates of mNGS and CMTs was 100.0% and 25.5% (p=1.000), respectively. Both positive mNGS and CMTs were observed in 22.7% patients with infectious diseases, and sole positive mNGS and sole positive CMTs were observed in 50.0% and 6.8% patients, respectively. There were no statistically differences in age, gender, HIV infection, PCT levels, neutrophil counts, CD4[+] lymphocyte count and antibiotic exposure between mNGS positive and mNGS negative groups (P > 0.05). Tissue mNGS could provide a higher sensitivity, more robust and broader method for pathogen identification by comparison with CMTs. However, CMTs shouldn't be ignored since the low consistency between CMTs and mNGS.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Male
*Metagenomics/methods
Female
Middle Aged
Adult
Retrospective Studies
*Communicable Diseases/diagnosis/microbiology
Sensitivity and Specificity
Aged
HIV Infections
Bacteria/genetics/isolation & purification/classification
Young Adult

@article {pmid41376097,
year = {2025},
author = {Jiang, W and Zhang, S and Feng, Z and Dong, Y and Ao, Z and Jia, J and Li, H and Chen, Z and Liu, R and Wen, X},
title = {Microenvironmental Gradients Drive Spatial Stratification of Saccharifying Microbial Communities and Enzyme Activity in Strong-Flavor Daqu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/foods14234160},
pmid = {41376097},
issn = {2304-8158},
abstract = {Daqu, a representative solid-state fermentation product, produces saccharifying enzymes to degrade sorghum starch into fermentable sugars for ethanol synthesis. Spatial heterogeneity in Daqu drives community assembly. However, its regulatory role in enzyme-driven saccharification remains unclear. By integrating metagenomics and PacBio full-length sequencing, this study investigated how microenvironmental gradients across distinct Daqu layers (QP (surface layer), HQ (middle layer), QX (center layer)) shape saccharifying microbiota and activity. Saccharifying activity exhibited a declining surface-to-center gradient (e.g., QP: 870.9 ± 21.2 U/mL > HQ: 631.2 ± 16.4 U/mL > QX: 296.5 ± 16.1 U/mL on day 30, p < 0.05), paralleled by divergence in microenvironments. Metagenomics identified α-amylase and α-glucosidase as key saccharifying enzymes, primarily encoded by fungi; their abundance was inhibited by heat and humidity, yet promoted by acidity. Enzymatic validation confirmed higher saccharifying activity in QP and HQ core microbes (e.g., Lichtheimia ramosa: 43.16 ± 1.97 U/mL) than in QX (e.g., Paecilomyces variotii: 14.27 ± 1.25 U/mL). Network analysis revealed Lactobacillaceae are closely linked with saccharifying communities. This study establishes microenvironmental gradients as critical regulators of spatial saccharification in Daqu, informing strategies to optimize microbial consortia for baijiu production.},
}

@article {pmid41375521,
year = {2025},
author = {Xiao, L and Liang, Y and Hao, S and Wu, K},
title = {Integrative High-Throughput Screening and Microscopic Evidence Implicates Microsporidia as a Potential Pathogen of "Pus Crab" in the Mud Crab (Scylla paramamosain).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233463},
pmid = {41375521},
issn = {2076-2615},
abstract = {The mud crab (Scylla paramamosain), an economically important crustacean aquaculture species in southern China, is susceptible to infections due to its immune system lacking acquired immunity. An emergent disease locally termed "pus crab" has caused severe muscle lesions in pond-farmed crabs, but its etiology remained unclear. Here, we applied an integrated approach, histopathology, electron microscopy, metagenomic sequencing, and experimental infection to identify the pathogen of "pus crab". Histological staining (H&E, Wright-Giemsa, and Masson) revealed muscle fiber dissolution, disordered fiber arrangement, and abundant interstitial spore-like bodies. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) confirmed intracellular spore morphology consistent with microsporidia. Metagenomic profiling showed a pronounced shift in the muscle microbiome, with a marked increase in microsporidian taxa at the genus level and a concurrent decline in bacterial relative abundance. Functional annotation indicated enrichment of pathways related to protein processing, ribosome biogenesis, glycosylation, and the ubiquitin-proteasome system. Isolation of spores from diseased muscle and subsequent injection into healthy crabs reproduced wild-like clinical signs and histopathology, confirming infectivity and implicating microsporidia as the likely etiological agents of "pus crab". These findings establish a multidisciplinary framework for pathogen identification in aquaculture and provide candidate molecular and biochemical markers for early diagnosis and management.},
}

@article {pmid41375452,
year = {2025},
author = {Wang, Z and Yang, C and Li, Y and Dong, B and Song, Q and Bai, H and Jiang, Y and Chang, G and Chen, G},
title = {Multi-Omics Insights into the Relationship Between Intestinal Microbiota and Abdominal Fat Deposition in Meat Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233393},
pmid = {41375452},
issn = {2076-2615},
support = {2023YFD1300301//National Key Research and Development Project of China/ ; 32472890//National Natural Science Foundation/ ; CARS-42-3//China Agriculture Research System of MOF and MARA/ ; },
abstract = {Abdominal fat deposition is an important economic trait in poultry, as excessive accumulation reduces feed efficiency and carcass yield. The gut microbiota is known to influence host energy metabolism and fat storage, suggesting its potential involvement in fat deposition. This study examined the relationship between intestinal microbiota and abdominal fat deposition in an F2 population derived from Cherry Valley Ducks (♂) × Runzhou Crested White Ducks (♀) at 42 days of age. Based on abdominal fat rate, ducks with values of 0-0.75% and 1.5-2.25% were defined as the low (LF) and high (HF) abdominal fat groups, respectively. A combined multi-omics approach was used, including 16S rRNA gene sequencing, metagenomics, and whole transcriptomics, to compare high and low abdominal fat rate groups. 16S rRNA gene sequencing results showed that the cecum had the highest microbial diversity among all intestinal segments (duodenum, jejunum, ileum, and rectum) and was significantly enriched in carbohydrate metabolism pathways, highlighting its key role in nutrient utilization and growth. Therefore, the cecum was selected for further analysis. Metagenomic analysis of the cecum contents revealed significantly different intestinal microbial β diversity between the high and low abdominal fat rate groups (p < 0.05). The low abdominal fat rate group was enriched in beneficial microorganisms such as Paenibacillus, Butyrivibrio, Coprococcus, Ruminococcaceae, Veillonellaceae (Clostridiales), and Firmicutes. Conversely, the high abdominal fat rate group was characterized by an increased abundance of Bacteroidetes, including both beneficial and potentially pathogenic taxa such as Alistipes and Eggerthellales. The integrated analysis of metagenomic and whole transcriptome sequencing showed that Firmicutes and Bacteroidetes were not only related to energy metabolism, lipid metabolism, and amino acid metabolism, but also to the expression of FGF2, FKBP5, PNPLA2, PLIN3, FGFR2, DGAT2, and ACER2. In addition, Firmicutes and Bacteroidetes were also associated with 7 lncRNAs: XR_003493494.1, XR_003492471.1, XR_001190174.3, TCONS_00005095, XR_001190238.3, TCONS_00005095, and XR_003492841.1. In conclusion, this study highlights that the cecal microbiota is closely associated with abdominal fat deposition in ducks, elucidating its potential influence on host metabolism and gene expression. These findings enhance our understanding of the gut microbiota's relationship with obesity and offer new strategies to modulate gut-microbe interactions to reduce abdominal fat accumulation in poultry.},
}

@article {pmid41375438,
year = {2025},
author = {Pacini, MI and Forzan, M and Mazzei, M},
title = {Fecal Sample Surveillance of the Wildlife Virome in Central Italy: Insights from the Foreste Casentinesi National Park.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/ani15233378},
pmid = {41375438},
issn = {2076-2615},
support = {Fondi Ateneo//University of Pisa/ ; },
abstract = {Wildlife can act as both a reservoir and a sentinel for emerging pathogens, but surveillance is often constrained by difficulties in obtaining samples without disturbing animals. This study explored the viral diversity of wild mammals inhabiting the Foreste Casentinesi National Park (Central Italy) using non-invasive fecal sampling. From 2021 to 2022, 99 fecal samples from several species were collected and analyzed by PCR and metagenomic next-generation sequencing. Of 26 pools examined, 10 (38.5%) tested positive for at least one viral target. Astroviruses were the most frequently detected, found in deer, foxes, wolves, small mustelids, and porcupines. Several sequences showed low similarity to known strains, suggesting divergent or novel viral lineages. Metagenomic analysis also identified members of Circoviridae, Anelloviridae, and Picobirnaviridae. While none of these virus families are currently recognized as major zoonotic agents, their widespread occurrence in wildlife and domestic animals underscores the importance of continued surveillance to better assess their ecological roles, host range, and potential implications for both animal and human health. These results provide new insights into the virome of European wildlife, including the first reports of some viruses in certain species. Overall, our study demonstrates that non-invasive surveillance is a valuable tool for monitoring ecosystem health and supports a One Health approach to early detection of viral threats.},
}

@article {pmid41375370,
year = {2025},
author = {Wang, Y and Hang, X and Shao, C and Zhang, Z and Guo, S and Li, R and Shen, Q},
title = {Organic Amendments and Trichoderma Change the Rhizosphere Microbiome and Improve Cucumber Yield and Fusarium Suppression.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/plants14233660},
pmid = {41375370},
issn = {2223-7747},
support = {ZZFH2024-2026QNRC001//the Young Elite Scientists Sponsorship Program by CAST/ ; 42307171//the National Natural Science Foundation of China/ ; 2023M731724//the Postdoctoral Science Foundation of China/ ; },
abstract = {Conventional chemical-based control methods for soil-borne diseases often degrade soil quality. The recycling of organic wastes offers a promising solution to simultaneously alleviate environmental pollution and restore soil health. As a beneficial fungus, Trichoderma plays a crucial role in enhancing plant performance. However, knowledge of the mechanisms through which organic wastes and Trichoderma interact to influence plant performance remains limited. We investigated how the combined application of organic wastes (chitin and straw) and a biocontrol fungus (Trichoderma) influenced the rhizosphere microbiome to improve plant performance. Compared with the control, organic waste alone, and Trichoderma alone treatments, the combined application of organic wastes and Trichoderma significantly (p < 0.05) increased cucumber yield and reduced pathogen density. Increased yield and reduced pathogen density were associated with changes in bacterial and fungal communities induced by this combined application treatment. Indeed, this combined application treatment enabled plants to recruit certain potentially beneficial core bacterial (e.g., Streptomyces and Flavisolibacter) and fungal taxa (e.g., Trichoderma), increasing their positive interactions in the rhizosphere. We demonstrate that the combined application of organic wastes and Trichoderma can shape distinct rhizosphere bacterial and fungal communities, promoting an increase in beneficial microorganisms and their positive interactions, which contribute to enhanced plant performance.},
}

@article {pmid41375040,
year = {2025},
author = {Rogges, E and Bertolazzi, G and Vacca, D and Borro, M and Lopez, G and Simmaco, M and Scattone, A and Firmani, G and Sorotos, M and Santanelli di Pompeo, F and Noccioli, N and Savino, E and Vecchione, A and Di Napoli, A},
title = {High-Throughput Molecular Characterization of the Microbiome in Breast Implant-Associated Anaplastic Large Cell Lymphoma and Peri-Implant Benign Seromas.},
journal = {Cancers},
volume = {17},
number = {23},
pages = {},
doi = {10.3390/cancers17233839},
pmid = {41375040},
issn = {2072-6694},
abstract = {Background: Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is a mature T-cell lymphoma linked to textured breast implants. A leading hypothesis suggests that chronic inflammation, combined with immunological and genetic factors, drives its pathogenesis. Two previous studies investigating bacterial biofilms on breast implant capsules have produced conflicting results, particularly regarding the enrichment of Ralstonia spp. Methods: We analyzed the microbiota profiles in seroma samples from 10 BIA-ALCL patients and 12 patients with non-neoplastic effusion, subclassified into acute-, mixed-, and chronic-type based on cellular composition. We used two metagenomic approaches: 16S rRNA gene sequencing and Nanopore sequencing with the "What's in My Pot?" (WIMP) taxonomic classifier. Our analyses included alpha and beta diversity metrics, as well as comparisons of Gram status and oxygen requirements. Results: Both sequencing methods identified Staphylococcaceae, Propionibacteriaceae, and Bradyrhizobiaceae as the most prevalent bacterial families in both BIA-ALCL and benign seroma samples. Notably, the Burkholderiaceae family was more abundant in some of the benign seromas according to the 16S rRNA sequencing, but Ralstonia spp. were not detected. BIA-ALCL showed higher richness (based on Nanopore data) and higher evenness (based on 16S rRNA data) compared to acute-type seromas, indicating a more homogenous representation of the different taxa identified. BIA-ALCL seromas did not cluster together based on Nanopore data, but they did form a distinct cluster with 16S rRNA data. This cluster was differentiated from the other two clusters by a relatively balanced presence of multiple families without overt dominance. We observed no significant differences in Gram staining between BIA-ALCL and benign samples using either method. However, non-aerobic bacterial families were enriched in BIA-ALCL cases only when analyzed with the Nanopore pipeline. Conclusions: Overall, our findings did not identify a distinctive microbial signature specifically associated with BIA-ALCL.},
}

@article {pmid41374325,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Edrees, HM and Abdelsalam, MH and Aljizani, F and Alqarni, S and Khateeb, E and Alzaben, F and Ibrahem, M and Mousa, AM and Huraysh, N and Abu-Okail, A},
title = {Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {23},
pages = {},
doi = {10.3390/diagnostics15232944},
pmid = {41374325},
issn = {2075-4418},
abstract = {Bloodstream infections and sepsis necessitate rapid, sensitive, and clinically relevant diagnostics to minimize treatment delays and improve clinical outcomes. Next-generation sequencing enables culture-independent pathogen detection, antimicrobial resistance profiling, and genome-informed epidemiology. This narrative review integrates clinical evidence with practical workflows across three complementary approaches. We describe the use of plasma microbial cell-free DNA for broad organism detection and burden monitoring, as well as metagenomic next-generation sequencing of blood or plasma for unbiased pathogen discovery, including culture-negative and polymicrobial infections. Same-day Oxford Nanopore Technologies sequencing of positive blood culture broth is also discussed as a way to accelerate species identification, targeted resistance reporting, and infection-prevention decisions. We outline the sample-to-result steps, typical turnaround time (TAT), and stewardship-aligned decision points. Analytical reliability depends on effective reduction in human DNA background, stringent control of background and reagent-derived nucleic acids in low-biomass samples, and documented and validated bioinformatics workflows that are supported by curated taxonomic and resistance databases. Quantitative reports should adhere to validated thresholds and should be interpreted in the context of internal controls and clinical pretest probability. Ongoing challenges include variable correlation between genotype and phenotype for specific pathogen and antibiotic pairs, interpretation of low-level signals, and inconsistent regulatory and reimbursement environments. Advances in portable sequencing, faster laboratory and analytical workflows, and scaled liquid biopsy strategies may further reduce the TAT and expand access. Integrating these tools within One Health frameworks and global genomic surveillance programs could support early resistance detection and coordinated public health action, which could help to advance sepsis care toward more precise treatment and real-time infection control insights.},
}

@article {pmid41374080,
year = {2025},
author = {Kimble, R and Shannon, OM},
title = {Can Beetroot (Beta vulgaris) Support Brain Health? A Perspective Review on Alzheimer's Disease.},
journal = {Nutrients},
volume = {17},
number = {23},
pages = {},
doi = {10.3390/nu17233790},
pmid = {41374080},
issn = {2072-6643},
mesh = {Humans ; *Alzheimer Disease/prevention & control ; *Beta vulgaris/chemistry ; *Brain/drug effects ; Antioxidants/pharmacology ; Nitrates/pharmacology ; Oxidative Stress/drug effects ; Neuroprotective Agents/pharmacology ; Animals ; Polyphenols/pharmacology ; Betalains/pharmacology ; },
abstract = {Alzheimer's disease (AD), the leading cause of dementia, has limited treatment options despite extensive pharmacological research. This has increased interest in dietary strategies that act across multiple pathological mechanisms. Beetroot (Beta vulgaris), known for its cardiovascular and metabolic benefits, contains a distinctive combination of bioactive compounds including inorganic nitrate, betalains, and polyphenols. Together these constituents influence vascular function, oxidative stress, mitochondrial efficiency, inflammation, and the microbiota. Previous reviews have typically focused on dietary nitrate in dementia prevention or have examined nitrate and betalains separately. In contrast, this review synthesises evidence on beetroot as a combined neuroprotective food. Preclinical data indicate that beetroot and its key constituents enhance antioxidant defences, support neuronal bioenergetics, and modulate cholinergic and inflammatory pathways. Human studies further suggest that nitrate-rich beetroot can improve cerebral blood flow and vascular responsiveness, and that higher intakes of plant-derived nitrate are associated with reduced cognitive decline. However, findings are inconsistent, most trials are small and short in duration, and research directly involving people with AD is scarce. By integrating vascular, antioxidant, and microbiome perspectives, this review identifies beetroot as a promising yet underexplored dietary candidate for AD management. Further mechanistic studies and multidomain approaches combining metagenomics, biomarkers, neuroimaging, and cognitive outcomes are needed.},
}

Humans
*Alzheimer Disease/prevention & control
*Beta vulgaris/chemistry
*Brain/drug effects
Antioxidants/pharmacology
Nitrates/pharmacology
Oxidative Stress/drug effects
Neuroprotective Agents/pharmacology
Animals
Polyphenols/pharmacology
Betalains/pharmacology

@article {pmid41373884,
year = {2025},
author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L},
title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311737},
pmid = {41373884},
issn = {1422-0067},
support = {LF-ST-21-500002//LEO Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.},
}

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

@article {pmid41373816,
year = {2025},
author = {Wang, F and Sun, X and Wang, K and Long, B and Li, F and Xie, D},
title = {Physiological and Multi-Omics Insights into Trichoderma harzianum Alleviating Aged Microplastic Stress in Nicotiana benthamiana.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311667},
pmid = {41373816},
issn = {1422-0067},
support = {2022GDASZH-2022010110//'GDAS' Project of Science and Technology Development/ ; 0525149001//Innovation Capacity Building Project for Provincial Scientific Research Institutions/ ; 2024A1515030175//Guangdong Basic and Applied Basic Research/ ; },
mesh = {*Nicotiana/microbiology/drug effects/metabolism/genetics/growth & development ; *Stress, Physiological/drug effects ; *Microplastics/toxicity ; *Hypocreales/physiology ; Reactive Oxygen Species/metabolism ; Transcriptome ; Gene Expression Regulation, Plant/drug effects ; *Trichoderma ; Multiomics ; },
abstract = {Microplastics derived from biodegradable PBAT film, widely used in agriculture, pose ecological and biological hazards. This study explores how Trichoderma harzianum T4 mitigates this microplastic-induced stress in Nicotiana benthamiana. Using five experimental setup-control (CK), low/high-dose aged microplastics (MP80/MP320), and their co-treatments with T. harzianum T4 (MP80+T4/MP320+T4), multi-omics analyses reveal the microplastic stress-alleviating mechanisms of T. harzianum T4. Aged microplastics significantly inhibit plant growth, promote reactive oxygen species (ROS) and malondialdehyde (MDA) accumulation, and disrupt metabolic homeostasis. Conversely, T. harzianum T4 activates the plant antioxidant defense system, reducing ROS/MDA levels and upregulating superoxide dismutase (SOD)/peroxidase (POD) activities, and promotes biomass. Transcriptomic analysis shows T. harzianum T4 reverses gene expression patterns disrupted by microplastics, particularly in DNA replication and pentose-glucuronic acid pathways. Metagenomic sequencing indicates T. harzianum T4 restores soil microbial diversity, increases the abundance of Bacteroidota and Myxococcota, downregulates antibiotic resistance genes (e.g., tetA5, MDR), and upregulates carbohydrate-active enzymes (CAZys), thereby enhancing carbon metabolism. In conclusion, T. harzianum T4 alleviates microplastic stress through a tripartite mechanism: activating plant stress-response gene networks, reshaping soil microbial communities, and modulating functional gene expression, offering a promising bioremediation strategy.},
}

*Nicotiana/microbiology/drug effects/metabolism/genetics/growth & development
*Stress, Physiological/drug effects
*Microplastics/toxicity
*Hypocreales/physiology
Reactive Oxygen Species/metabolism
Transcriptome
Gene Expression Regulation, Plant/drug effects
*Trichoderma
Multiomics

@article {pmid41373768,
year = {2025},
author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
doi = {10.3390/ijms262311616},
pmid = {41373768},
issn = {1422-0067},
support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation & purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation & purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.},
}

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

@article {pmid41373093,
year = {2025},
author = {Ströher, JA and Flôres, SH and de Freitas, AS and Salazar, MM and da Silva, LFF and Bresciani, L and Sant'Anna, V and Malheiros, PDS},
title = {Consumer Perception, Sensory Acceptance, and Microbial Characterization of Artisanal Milk Kefir During Shelf Life.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70739},
doi = {10.1111/1750-3841.70739},
pmid = {41373093},
issn = {1750-3841},
support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico-CNPq/ ; 140557/2024-5//Secretaria de Inovação, Ciência e Tecnologia do Rio Grande do Sul (SICT)/ ; },
mesh = {*Kefir/microbiology/analysis ; *Consumer Behavior ; Humans ; Food Storage ; Animals ; Taste ; Probiotics/analysis ; Adult ; Food Microbiology ; Bacteria/classification/isolation & purification/genetics ; Female ; Brazil ; Male ; *Milk/microbiology ; Middle Aged ; Young Adult ; Fungi/isolation & purification/classification ; Fermentation ; },
abstract = {Milk kefir is a traditional fermented beverage with a complex microbiota of bacteria and yeasts that contributes to its distinctive sensory profile and functional properties. Artisanal kefir, in particular, preserves this natural microbial diversity but faces challenges related to sensory stability and limited shelf life. This study investigated the physicochemical, microbiological, metagenomic, and sensory characteristics, as well as gastrointestinal survival, of artisanal kefir samples stored for 0, 15, and 30 days. The physicochemical and microbiological parameters remained within the limits established by Brazilian legislation throughout storage. Metagenomic analysis revealed changes in microbial composition, with reductions in certain bacterial species and alterations in the relative abundance of fungal genera over time. Simulated gastrointestinal survival tests confirmed the stability of bacterial populations, indicating the maintenance of probiotic potential. Sensory analysis demonstrated general acceptance of the product, with significant differences detected mainly in texture. The analysis of social representations highlighted associations with health, naturalness, and positive consumer perceptions. Together, these findings show that artisanal kefir remains safe, microbiologically stable, and acceptable to consumers for at least 30 days, providing insights that can guide future standardization and commercial development strategies. PRACTICAL APPLICATIONS: Artisanal kefir showed physicochemical, microbiological, and sensory stability for up to 30 days, maintaining its probiotic potential and consumer acceptance. These findings contribute to strategies for standardization, increased shelf life, and strengthened commercial development of the product.},
}

*Kefir/microbiology/analysis
*Consumer Behavior
Humans
Food Storage
Animals
Taste
Probiotics/analysis
Adult
Food Microbiology
Bacteria/classification/isolation & purification/genetics
Female
Brazil
Male
*Milk/microbiology
Middle Aged
Young Adult
Fungi/isolation & purification/classification
Fermentation

@article {pmid41373036,
year = {2025},
author = {Fidler, DB and George, PBL and Le Brun, LJ and Griffiths, RI and Jones, DL and McDonald, JE},
title = {Soil microbial adaptation to carbon deprivation: shifts in lignocellulolytic gene profiles following long-term plant exclusion.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00810-6},
pmid = {41373036},
issn = {2524-6372},
support = {NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; NE/M009106/1//Natural Environment Research Council/ ; },
abstract = {BACKGROUND: Lignocellulose represents a primary input of organic carbon (C) into soils, yet the identity of specific microorganisms and genes which drive lignocellulose turnover in soils remains poorly understood. To address this knowledge gap, we used a 10-year grassland plant-exclusion experiment to investigate how reduced plant C inputs affect microbial communities and their lignocellulolytic potential using a combination of metagenomic sequencing and untargeted metabolomics. We specifically tested the hypothesis that microbial community function in bare fallow plots would transition towards microbiota with genes for recalcitrant biomass degradation (i.e., lignocellulose), when compared to grassland plots with high labile C inputs.

RESULTS: Long-term plant exclusion lowered soil C and nitrogen (N) and reduced cellulose content, whilst hemicellulose and lignin were unchanged. Similarly soil microbiomes were highly distinct in long-term bare soils, along with soil extracellular enzyme profiles, though short-term plant-removal effects were less apparent. Plant exclusion resulted in a general enrichment of Firmicutes, Thaumarchaeota, Acidobacteria, Fusobacteria, and Ascomycota, with a general reduction in Actinobacteria. However, changes in bare soil lignocellulose degradation genes were more associated with discrete taxa from diverse lineages, particularly the Proteobacteria. Grouping of lignocellulose-degrading genes into broad substrate classes (cellulases, hemicellulases and lignases) revealed a possible increase in lignin degradation genes under plant exclusion confirming our hypothesis, although all other changes were at the level of the carbohydrate-active enzyme (CAZy) family. Intriguingly, untargeted metabolome profiles were highly responsive to plant exclusion, even after only one year. Bare soils were depleted in oligosaccharides and enriched in monosaccharides, fatty and carboxylic acids, supporting emerging evidence of long-term persistent C being within simple compounds.

CONCLUSIONS: Together our data show that extracellular lignin degrading enzymes increase under long-term plant exclusion. There is now a need for increased focus on the microbial metabolic mechanisms which regulate the processing and persistence of enzymatically released compounds, particularly in energy limited soils.},
}

@article {pmid41373015,
year = {2025},
author = {Duvivier, M and Moumen, B and Héchard, Y and Moulin, L and Delafont, V and Wurtzer, S},
title = {Implementation and comparison of two concentration methods to detect and characterize bacteriophages and bacterial hosts from large drinking water samples.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00818-y},
pmid = {41373015},
issn = {2524-6372},
abstract = {Drinking water distribution systems (DWDS) are low biomass biomes harboring a large variety of microorganisms. Much of the attention has been focused on bacteria, whose diversity and abundance in DWDS were repeatedly shown to be influenced by abiotic factors such as pH, temperature, growth inhibitors and water sources. However, little is known about biotic factors, such as bacteriophage presence, even though they are known to be present in DWDS and to influence bacterial dynamics. While bacteriophage impact has been assessed in natural environments such as oceans, little is known about the way they shape DWDS bacterial communities. To fill this knowledge gap and accessing bacteriophage diversity from such low biomass environment, the present study aimed to propose and compare two methods based on ultrafiltration and adsorption/elution methods, already used for the concentration of bacteria and virus from water. To this end, both methods were compared with a weekly sample collection, for one month, on the DWDS of Paris, France. Metagenomic sequencing was performed on concentrated samples to investigate the presence and diversity of bacteriophages, using a coupling of complementary bioinformatic prediction tools. Though viral fractions represented a minority of recovered contigs (1.5 to 2.5%), most were associated with Caudoviricetes class. The predicted bacterial hosts matched with the observed bacterial diversity, highlighting the robustness of host prediction tool. A total of 437 putative phages were present in all samples, constituting a core phage diversity. Among those, 380 viral contigs contained sequences showing significant non-viral matches. We leveraged this information to further refine the inference of bioinformatics pairs of bacterial hosts and their phages. In conclusion, we propose a method to simultaneously concentrate bacteriophages with bacteria from low-biomass environment. Through metagenomics, this study showed that an optimized bioinformatic pipeline could provide an overview of DWDS phage diversity. Moreover, this method allowed to detect sequence similarities between phages and bacteria, suggesting potential genetic exchanges and providing clues for host spectrum. Altogether, this study highlights the tight interactions between bacteria and bacteriophages in drinking water and the possibility to study both phages and potential hosts to better grasp their intricate interplay.},
}

@article {pmid41372802,
year = {2025},
author = {Almas, S and Carpenter, RE and Tamrakar, VK and Singh, A and Sharma, A and Sharma, R},
title = {Precision metagenomics reveals microbial landscape in acute upper respiratory infections: a comprehensive dataset.},
journal = {BMC research notes},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13104-025-07519-2},
pmid = {41372802},
issn = {1756-0500},
abstract = {OBJECTIVES: The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina[®]/IDbyDNA Respiratory Pathogen ID/AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance.

DATA DESCRIPTION: This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial resistance detection, and therapeutic interventions. Its potential for reuse and integration with other omics datasets enhances its significance. The comprehensive nature of the data facilitates research into relationships between the respiratory microbiota and host factors, including clinical outcomes, immune responses, or genetic predispositions. Moreover, the article underscores the interdisciplinary potential by advocating for the integration of this dataset with other relevant datasets such as transcriptomics or metabolomics, enabling a deeper understanding of the intricate interactions in acute upper respiratory infections. The presented dataset contributes to the expanding knowledge in precision metagenomics and holds the promise to propel research and clinical practices in the field of respiratory diseases.},
}

@article {pmid41372750,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04560-w},
pmid = {41372750},
issn = {1471-2180},
abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.

METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.

RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37 µg/L), chromium (1.89 µg/L), and nickel (4.93 µg/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P < 0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P < 0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P < 0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.

CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.},
}

@article {pmid41310458,
year = {2025},
author = {Li, Q and Chen, T and Hu, B and Guo, L and Dou, Z and Feng, W and Ning, X and Xiao, H and Liu, G},
title = {Clinical characteristics and management of Listeria monocytogenes meningitis in children beyond the neonatal stage: a 10 years retrospective study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1708},
pmid = {41310458},
issn = {1471-2334},
abstract = {INTRODUCTION: The data of Listeria monocytogenes (LM) meningitis in children beyond the neonatal stage has been limited. We aimed to summarize the clinical characteristics, management, and risk factors of neurological complications in LM meningitis children beyond the neonatal stage.

METHODS: We retrospectively reviewed LM meningitis cases from January 2013 to December 2022 at Beijing Children’s Hospital. Clinical characteristics, pathogen detection results and management were analyzed.

RESULTS: There were 41 LM meningitis patients at our center, with a median age of 2.3 years (ranging from 6 months to 9 years). Most patients (97.6%) were immunocompetent. Fourteen patients (34.1%) had a history of suspected food contamination. The most common symptom was fever (100%), and 29.2% of patients presented with diarrhea in the early stages of the disease. About 61% of patients showed monocyte predominance in their cerebrospinal fluid (CSF). Thirteen patients (31.7%) experienced neurological complications. Multivariate analysis indicated that a diagnosis delay of more than one week and a CRP level of 50 mg/L or higher were significant risk factors for these neurological complications (p < 0.05). CSF culture rates were much higher before hospital admission (85.7%) compared to after (31.7%, p < 0.05). Metagenomic next-generation sequencing (mNGS) identified pathogens in 3 culture-negative cases. In total, 97.5% of patients received meropenem, either alone or with other antibiotics, and all children recorded a Glasgow Outcome Scale (GOS) score of 5.

CONCLUSION: LM meningitis can affect immunocompetent children. Strengthening food hygiene and safety education is crucial to prevent LM infection. Penicillin or ampicillin are the preferred treatments, while meropenem may be considered as an alternative treatment.},
}

@article {pmid41270835,
year = {2025},
author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L},
title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.},
journal = {Virus research},
volume = {362},
number = {},
pages = {199666},
pmid = {41270835},
issn = {1872-7492},
mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; },
abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.},
}

Animals
Dogs
*Feces/virology
China
*Virome
*Viruses/classification/genetics/isolation & purification
Metagenomics
Dog Diseases/virology
Phylogeny
Pooled Testing

@article {pmid41372637,
year = {2025},
author = {Kosmopoulos, JC and Pallier, W and Malik, AA and Anantharaman, K},
title = {Ecosystem health shapes viral ecology in peatland soils.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41372637},
issn = {2058-5276},
support = {DBI2047598//National Science Foundation (NSF)/ ; 2137424//National Science Foundation (NSF)/ ; },
abstract = {Peatlands hold up to one-third of Earth's soil carbon but are increasingly turning from being carbon sinks to becoming carbon sources due to human impacts. Restoration efforts aim to reverse this trend, but viral influences on peatland recovery remain unclear, despite viruses being potent regulators of microbiomes and ecosystem function. Here we sequenced soil metagenomes to study viral communities across seven UK peatlands, each encompassing areas representing three peatland ecosystem health statuses: natural, damaged and restored. We found that viral diversity and community structure were shaped by both geography and ecosystem health. Viruses were geographically widespread, yet exhibited ecosystem health-specific endemism and functional adaptation, highlighting their sensitivity to restoration. Virus-host dynamics ranged from stable 'piggyback-the-winner' relationships to decoupled dynamics in those infecting keystone aerobes, sulfate reducers, carbohydrate degraders and fermenters. These findings position viruses as dynamic drivers of peatland ecosystem recovery and could unlock pathways to bolster carbon retention and accelerate climate mitigation.},
}

@article {pmid41372407,
year = {2025},
author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N},
title = {Gut micro-organisms associated with health, nutrition and dietary interventions.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41372407},
issn = {1476-4687},
abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.},
}

@article {pmid41371202,
year = {2025},
author = {Xu, B and Zhang, H and Li, M and Lin, H and Wang, C},
title = {Application of metagenomic next-generation sequencing in diagnose the pulmonary infections caused by Aureobasidium melanogenum: A case report and review of the literature.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117213},
doi = {10.1016/j.diagmicrobio.2025.117213},
pmid = {41371202},
issn = {1879-0070},
abstract = {Aureobasidium melanogenum (A. melanogenum) is a black-yeast-like fungus widely present in nature that rarely causes human infections. We report a case of pulmonary infection caused by A. melanogenum in a 60-year-old male farmer, who initially presented with severe paroxysmal coughing and right-sided chest pain and was initially misdiagnosed with tuberculosis or lung cancer. While sputum cultures were negative, metagenomic next-generation sequencing (mNGS) detected A. melanogenum in bronchoalveolar lavage fluid, which was confirmed by PCR-Sanger sequencing. Susceptibility thresholds for Aureobasidium have not been established, and the optimal treatment requires further investigation. This case highlights that A. melanogenum infection should be considered even when lung lesions cannot be diagnosed by conventional methods. mNGS demonstrates potential advantages in detecting this pathogen, underscoring its value in diagnosing such rare fungal pulmonary infections.},
}

@article {pmid41371154,
year = {2025},
author = {Tervo, S and Zalewski, A and Vauhkonen, H and Nieoczym, M and Kołodziej-Sobocińska, M and Lehikoinen, S and Aaltonen, K and Smura, T and Sironen, T and Pettersson, J},
title = {Virus circulation in native, introduced, and farmed mustelids in Poland.},
journal = {Virology},
volume = {615},
number = {},
pages = {110771},
doi = {10.1016/j.virol.2025.110771},
pmid = {41371154},
issn = {1096-0341},
abstract = {American mink (Neogale vison) are known carriers of various viruses, including many zoonoses. Their susceptibility to a wide range of pathogens and anatomical similarities to human lungs raise concerns about their potential role in facilitating interspecies transmission. Here we analysed viruses detected in tissue samples of native mustelids, and feral and farmed mink in Poland (2019-2022). The species included American mink, pine and stone marten (Martes martes, Martes foina), weasel (Mustela nivalis), European badger (Meles meles), European polecat (Mustela putorius), and Eurasian otter (Lutra lutra). Blood samples were tested for antibodies against SARS-CoV-2 (n = 270), and lung samples were subjected to genetic studies by PCR (n = 129) or metagenomics (n = 37). No evidence of SARS-CoV-2 was found in feral or wild populations, although two farmed mink tested positive for SARS-CoV-2 by PCR. Aleutian mink disease virus (AMDV) and mink Torque teno neovison virus (mTTV) were identified by metagenomics, and PCR analyses revealed frequent co-infection. AMDV was most prevalent in mink, while other mustelids showed serological evidence but were PCR-negative suggesting viral clearance. AMDV-DNA was found in 26.4 % and mTTV-DNA in 87.8 % of tissue samples. Two animals were co-infected with AMDV, mTTV, and SARS-CoV-2. Phylogenetic analysis revealed both local persistence and inter-farm transmission of AMDV, including transmission between feral and farmed mink. mTTV showed mixing of strains between Poland and China. The findings stress the need for improved surveillance and biosafety to monitor zoonotic threats and cross-species transmission.},
}

@article {pmid41371144,
year = {2025},
author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y},
title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140716},
doi = {10.1016/j.jhazmat.2025.140716},
pmid = {41371144},
issn = {1873-3336},
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.},
}

@article {pmid41371128,
year = {2025},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}

@article {pmid41370957,
year = {2025},
author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G},
title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.},
journal = {Environment international},
volume = {207},
number = {},
pages = {109971},
doi = {10.1016/j.envint.2025.109971},
pmid = {41370957},
issn = {1873-6750},
abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.},
}

@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97751},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}

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

@article {pmid41369685,
year = {2025},
author = {Mohammadi, R and Morovati, H and Safari, F},
title = {The human mycobiome: a critical yet understudied component of health and disease.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001631},
pmid = {41369685},
issn = {1465-2080},
mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; },
abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.},
}

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

@article {pmid41369293,
year = {2025},
author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L},
title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf273},
pmid = {41369293},
issn = {1751-7370},
abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.},
}

@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
doi = {10.1099/mic.0.001632},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation & purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}

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

@article {pmid41369016,
year = {2025},
author = {Southwood, LL and Long, A and Perez, J and Daniel, S and Bittinger, K and Aitken, M and Redding, L},
title = {Effect of surgical antimicrobial prophylaxis duration for colic surgery on complications and resistome.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1002/evj.70137},
pmid = {41369016},
issn = {2042-3306},
support = {//Raymond Firestone Research Foundation/ ; },
abstract = {BACKGROUND: Based on human studies, surgical antimicrobial (AMD) prophylaxis (SAP) beyond 24 h is unnecessary and potentially detrimental.

OBJECTIVE: To compare clinical and microbiological outcomes in patients receiving 24- or 72-h of SAP for colic surgery.

STUDY DESIGN: Prospective randomised clinical trial.

METHODS: Horses that recovered from colic surgery were considered. Exclusion criteria were (1) age <2 years; (2) Miniature Horses, pony, and draught breeds; (3) azotaemia; (4) recent hospitalisation, colic surgery, or AMDs; (5) local AMD administration. Eligible horses were randomly assigned to receive SAP with potassium penicillin and gentamicin for 24- or 72-h. Clinical data and complications were compared between SAP groups. Admission and discharge faecal samples from a subset of horses (N = 49) underwent shotgun metagenomic sequencing on an Illumina platform. Host reads were filtered by aligning to reference genomes using the Burrows-Wheeler Aligner, and taxonomic classification was performed with kraken2. Sequencing reads were aligned to the Comprehensive Antimicrobial Resistance Database (CARD)5 and characterised using the AMR++ pipeline. The microbiome/resistome was characterised and compared between SAP groups over time.

RESULTS: One hundred and forty horses completed the study (24-h N = 71 and 72-h N = 69). The only clinical variable that was different between SAP groups was age (24-h median age 16 [IQR 9, 20] and 72-h 12 [6, 18] years, p = 0.03). There was no significant difference between groups for any complications including incisional infection (24-h 17 [95% CI 10-27]% and 72-h 16 [9-26]%, p = 0.9). Time was the main driver of changes in the microbiome/resistome: alpha diversity decreased while AMD resistance genes associated with administered AMD increased between admission and discharge. Discharge beta-lactam resistance genes were significantly higher in the 72-h than the 24-h group.

MAIN LIMITATIONS: Single hospital, small numbers for complications, clinicians not blinded to SAP group.

CONCLUSIONS: SAP for 24-h is recommended for horses undergoing colic surgery.},
}

@article {pmid41368664,
year = {2025},
author = {Diaz, AJ and Centurioni, DA and Lasek-Nesselquist, E and Lapierre, P and Egan, CT and Perry, MJ},
title = {Whole genome sequencing of neurotoxin-producing Clostridium species in New York state to bolster epidemiological investigations and reveal patterns of diversity and distribution.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1651032},
pmid = {41368664},
issn = {2296-2565},
mesh = {New York/epidemiology ; *Whole Genome Sequencing ; Humans ; *Clostridium/genetics/isolation & purification/classification ; Phylogeny ; Polymorphism, Single Nucleotide ; Botulism/epidemiology ; *Neurotoxins ; Retrospective Studies ; Botulinum Toxins/genetics ; },
abstract = {Clostridia that produce neurotoxins are highly relevant organisms to public health. While cases of botulism [caused by C. botulinum and other organisms that produce botulinum neurotoxin (BoNT)] are rare, the severity of this disease necessitates robust epidemiologic surveillance to promptly identify and mitigate outbreaks. Next generation sequencing (NGS) can provide additional support to these investigations through single nucleotide polymorphism (SNP)-based analysis, phylogenetic reconstruction, toxin subtyping, and structural analysis. Until recently, testing for this disease was restricted to traditional culture or molecular methods such as polymerase chain reaction (PCR) to detect bont genes, while mouse bioassay and endopeptidase-mass spectrometry (Endopep-MS) methods confirmed the presence of enzymatically active toxin. The New York State Department of Health (NYSDOH) Wadsworth Center Biodefense Laboratory performed a retrospective whole genome sequence (WGS) analysis of approximately 240 Clostridium spp. isolates from the past 40 years to supplement traditional test results and further characterize these organisms. Genomic analyses identified seven BoNT serotypes/serotype combinations, including A4(B5), A5(B2'), and B5F2 that were uncharacteristic of samples typically received. Additionally, SNP-based analysis and de novo genome assemblies retrospectively validated several epidemiology links or differentiated samples previously tested with only traditional methods. Our work highlights the clinical utility of supplementing conventional data with NGS to further characterize BoNT-producing organisms and underscores the importance of incorporating WGS into laboratory workflows to support epidemiologic investigations. However, several obstacles still exist which may prevent implementation. These include the expertise needed to execute bioinformatic analyses and interpret the resulting data, a lack of standardized bioinformatic workflows, and difficulty in determining SNP-based thresholds to identify linked samples without incorporation of additional data and analyses. Supplementing or replacing short-read sequencing with long-read sequencing (LRS) and the use of metagenomic or capture-based enrichment for analysis of primary specimens could increase the leverage obtained from WGS in epidemiological investigations.},
}

New York/epidemiology
*Whole Genome Sequencing
Humans
*Clostridium/genetics/isolation & purification/classification
Phylogeny
Polymorphism, Single Nucleotide
Botulism/epidemiology
*Neurotoxins
Retrospective Studies
Botulinum Toxins/genetics

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

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

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

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

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

@article {pmid41368505,
year = {2025},
author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D},
title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20328},
pmid = {41368505},
issn = {2167-8359},
mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; },
abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.},
}

*Software
Reproducibility of Results
Workflow
*Transcriptome
*Computational Biology/methods
*Molecular Sequence Annotation/methods
*Metagenomics/methods

@article {pmid41368072,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Geers, A and , and Busi, SB and Battin, TI},
title = {Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf076},
pmid = {41368072},
issn = {2730-6151},
abstract = {The factors and processes that shape microbial genomes and determine the success of microbes in different environments have long attracted scientific interest. Here, leveraging 2855 metagenome-assembled genomes sampled by the Vanishing Glacier Project from glacier-fed streams (GFSs), we shed light on the genomic architecture of the benthic microbiome in these harsh ecosystems-now vanishing because of climate change. Owing to glacial influence, the GFS benthic habitat is unstable, notoriously cold, and ultra-oligotrophic. Along gradients of glacial influence and concomitant variation in benthic algal biomass across 149 GFSs draining Earth's major mountain ranges, we show how genomes of GFS bacteria vary in terms of size, coding density, gene redundancy, and translational machinery. We develop a novel, phylogeny-rooted analytical framework that allows pinpointing the phylogenetic depth at which patterns in genomic trends occur. These analyses reveal both deep- and shallow-rooting phylogenetic patterns in genomic features associated with key GFS taxa and functional potential relevant to live in these ecosystems. Additionally, we highlight the role of several clades of Gammaproteobacteria in shaping community-level genomic architecture. Our work shows how genome architecture is shaped by selective environmental constraints in an extreme environment. These insights are important as they reveal putatively important adaptations to the GFS environment which is now changing at rapid pace due to climate change.},
}

@article {pmid41367710,
year = {2026},
author = {He, M and Chen, F and Xian, X and Guo, Z},
title = {Diagnosis and treatment of invasive fungal disease in children with hematological malignancies after chemotherapy: Challenges and strategies (Review).},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {1},
pages = {21},
pmid = {41367710},
issn = {1792-1015},
abstract = {Invasive fungal disease (IFD) has a high incidence rate in pediatric patients with hematological malignancies and hematopoietic stem cell transplantation, markedly elevating mortality rates. Major pathogens include Aspergillus, Candida and emerging non-Aspergillus molds. Clinical manifestations such as persistent fever and dyspnea are frequently non-specific, complicating early diagnosis. Invasive candidiasis typically manifests as candidemia or hepatosplenic infection, whereas invasive aspergillosis predominantly involves the lower respiratory tract. Prophylactic antifungal therapy reduces IFD risk but may lead to breakthrough IFD, particularly during prolonged neutropenia (>14 days). Treatment strategies require individualized selection between monotherapy and combination regimens, incorporating patient status, local epidemiology, prior antifungal exposure, drug metabolism and socioeconomic factors; however, treatment strategies can be hindered by diagnostic challenges including age-specific biomarker thresholds. Emerging techniques such as metagenomic next-generation sequencing show promise for rapid pathogen identification. Central nervous system involvement occurs in a certain proportion of pediatric cases and requires multimodal intervention. Early diagnosis through optimized imaging and timely initiation of targeted therapy are key to overcome clinical challenges and improving prognosis in this vulnerable population. The present review aimed to systematically review the epidemiological characteristics, diagnostic challenges and therapeutic strategies of IFD in pediatric hematological malignancies post-chemotherapy. By collating current clinical evidence, the present review provides an evidence-based framework for optimizing management in this high-risk population.},
}

@article {pmid41367425,
year = {2025},
author = {An, Y and Xu, M and Kang, Y and Fang, J and Zhang, X},
title = {Tripartite exacerbation stratification in AECOPD suggests a gradient of lower airway dysbiosis: a metagenomic transition from commensal taxa to pseudomonadota dominance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588029},
pmid = {41367425},
issn = {1664-302X},
abstract = {BACKGROUND: The frequency of acute exacerbations (AECOPD) is a critical predictor of disease progression in chronic obstructive pulmonary disease (COPD). However, the dynamics of the lower respiratory microbiome across a spectrum of exacerbation frequency remain poorly characterized, limiting insights into microbial drivers of susceptibility.

METHODS: We conducted a cross-sectional study of 39 hospitalized AECOPD patients, stratified into non-frequent (NFE, ≤ 1 event/year, n = 11), moderate (ME, 2 events/year, n = 13), and frequent exacerbators (FE, ≥3 events/year, n = 15). Metagenomic next-generation sequencing (mNGS) was performed on bronchoalveolar lavage fluid (BALF) to profile the airway microbiome.

RESULTS: Microbial alpha diversity exhibited a significant, graded decline from NFE to FE groups (e.g., Shannon index: NFE 3.68 ± 0.34, ME 3.02 ± 1.02, FE 0.84 ± 0.54; p < 0.05). Beta diversity analysis revealed distinct community clustering by exacerbation phenotype (PERMANOVA R[2] = 0.19, p = 0.001). The FE group was characterized by a striking dominance of Pseudomonadota (relative abundance: 72.25%), which correlated positively with exacerbation frequency (r = 0.536, p < 0.001). In contrast, commensal taxa including Streptococcus (r = -0.814, p < 0.0001) and others within the Bacillota and Bacteroidota phyla were depleted in FE and were negatively associated with exacerbation frequency. Twelve exacerbation-resilient taxa (83.3% belonging to Bacillota/Bacteroidota) were positively correlated with FEV1% predicted (r = 0.322-0.483, p < 0.05). Alpha diversity indices showed a strong inverse association with exacerbation frequency (r = -0.84 to -0.86, p < 0.001) but not spirometric measures.

CONCLUSION: Our findings delineate a gradient of airway microbial dysbiosis along the exacerbation frequency spectrum in COPD. The exacerbation-prone phenotype is defined by a loss of microbial diversity, expansion of Pseudomonadota, and depletion of potentially protective commensals. These microbiome features represent promising biomarkers for identifying high-risk patients and may inform future microbiome-targeted therapeutic strategies.},
}

@article {pmid41367410,
year = {2025},
author = {Tansirichaiya, S and Songsomboon, K and Wigand, J and Winje, E and Chaianant, N and Leartsiwawinyu, W and Al-Haroni, M},
title = {Geographic signatures in the oral resistome: a comparative metagenomic analysis of healthy individuals from Thailand and Norway.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589656},
pmid = {41367410},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is an important yet understudied reservoir of antimicrobial resistance genes (ARGs), potentially shaped by geographic variation in antibiotic usage.

OBJECTIVE: To compare the oral resistomes of healthy adults from Thailand and Norway, two countries with contrasting antimicrobial use practices, using shotgun metagenomic sequencing.

DESIGN: Stimulated saliva samples were collected from healthy adults in Thailand (n = 43) and Norway (n = 50). ARGs were identified with AMRPlusPlus against the MEGARes database, and microbial taxonomy was profiled with KrakenUniq. Diversity metrics, ordination, and clustering analyses assessed resistome and microbiome structures.

RESULTS: Thai samples exhibited significantly greater ARG richness, evenness, and diversity (p < 0.001), driven by higher abundances of multi-biocide, nucleoside, and copper resistance genes. Norwegian samples were enriched in aminoglycoside, sulfonamide, and quaternary ammonium compound resistance genes. Both cohorts shared core oral genera, but Thai samples showed greater taxonomic richness without differences in overall microbiome diversity. Non-metric multidimensional scaling and PERMANOVA revealed stronger geographic separation for resistomes (R² = 0.639) than microbiomes (R² = 0.382). Co-occurrence networks highlighted structured associations between ARG groups and bacterial genera, suggesting ecological influences beyond taxonomic composition.

CONCLUSIONS: These results reveal distinct geographic signatures in the oral resistome that are not fully explained by microbiome structure, reflecting the influence of local ecological and societal factors, including antimicrobial exposure. The findings highlight the oral cavity as a dynamic ARG reservoir and support its inclusion in regional antimicrobial resistance surveillance to inform public health strategies.},
}

@article {pmid41367394,
year = {2025},
author = {Oke, OE and Fasasi, LO and Opowoye, IO and Akosile, OA},
title = {The role of gut microbiota-derived metabolites in modulating poultry immunometabolism.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1700406},
pmid = {41367394},
issn = {1664-042X},
abstract = {The poultry sector is crucial to global food security, but it faces increasing challenges from heat stress, viral diseases, and restrictions on antibiotic use. These stressors highlight immunometabolism, the junction of immune function and metabolic pathways, as a crucial factor in determining the productivity and health of poultry. There is growing evidence that the gut microbiota is a dynamic metabolic organ that produces a diverse range of bioactive metabolites in addition to its function in nutritional digestion. The immunometabolism of poultry is significantly influenced by these microbiota-derived metabolites, including short-chain fatty acids, bile acid derivatives, amino acid catabolites, vitamins, and polyamines. Disease resistance, vaccination responsiveness, and stress adaptability are shaped by their modulation of intestinal barrier integrity, energy balance, oxidative stress resilience, and immune cell activation. This review summarises what is currently known about the functional diversity and composition of the gut microbiota in poultry, describes the concept of immunometabolism in birds, and assesses the mechanisms by which microbial metabolites regulate metabolic and immunological crosstalk. Prebiotics, probiotics, synbiotics, postbiotics, phytochemicals, and other nutritional and managerial interventions that improve advantageous metabolite profiles are given particular consideration. Applications to enhance poultry health, alleviate heat stress, reduce reliance on antibiotics, and promote sustainable production are also discussed. For mapping metabolite-immune interactions, emerging methods such as germ-free models, metabolomics, metagenomics, and systems biology approaches are emphasised as revolutionary. Metabolites produced by the gut microbiota are crucial to poultry immunometabolism and offer promising opportunities for precision nutrition and healthcare. Bridging the existing research gaps using integrative, multidisciplinary methods to promote sustainable and resilient poultry production is needed. This review centres on the mechanistic axis linking gut microbiota-derived metabolites to host immunometabolic regulation, tracing the pathway from metabolite generation through receptor activation and immune-metabolic reprogramming to measurable phenotypic outcomes in poultry.},
}

@article {pmid41367385,
year = {2025},
author = {Cavenaghi, A and Mallah, NEZ and Navarro, L and Martinón-Torres, F and Gómez-Carballa, A and Salas, A},
title = {Decoding the peripheral transcriptomic and meta-genomic response to music in autism spectrum disorder via saliva-based RNA sequencing.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1696704},
pmid = {41367385},
issn = {2296-889X},
abstract = {INTRODUCTION: Behavioral interventions for autism spectrum disorder show variable outcomes, highlighting the need for complementary therapies. Music-based interventions are promising, yet their molecular mechanisms remain unclear. Saliva-based RNA sequencing (RNA-seq) provides a non-invasive framework to monitor neuroimmune and metabolic dynamics, but its application in autism remains underexplored.

METHODS: We explored the buccal transcriptional effects of music exposure in five individuals with autism (8-37 years; 60% female). To overcome saliva-specific limitations, we combined Poly-A selection and Human-Enriched protocols preparation methods to enhance human transcript detection and reproducibility while capturing microbial signals.

RESULTS: Individually, each dataset revealed a few differentially expressed genes, but integrated analysis improved biological resolution. Consistently modulated genes included HERC6, TSPAN5, and REM2, involved in neurodevelopmental and immune functions. Enrichment analyses highlighted pathways associated with immune regulation, oxidative phosphorylation, and epithelial differentiation, hallmarks of autism, such as immune dysregulation and mitochondrial dysfunction. Co-expression network analysis identified modules correlated with music exposure. The AKNA module, previously linked to autism, was downregulated and enriched for Ras-related GTPase and immune pathways, suggesting modulation of intracellular signaling and inflammation. Conversely, upregulation of the UBE2D3 module indicated activation of endoplasmic reticulum stress responses, a contributor to autism. Exploratory metagenomics identified 15 microbial species responsive to music exposure, including Acidipropionibacterium acidipropionici and Propionibacterium freudenreichii, producers of propionic acid, a metabolite associated with autism-like behaviors and neuroinflammation.

CONCLUSION: Saliva-based RNA-seq can stably capture transcriptomic and microbial responses to behavioral stimuli. Music exposure modulates neuroimmune pathways relevant to autism, supporting the biological plausibility of music therapy and demonstrating saliva-based RNA-seq as a viable, non-invasive tool for monitoring intervention outcomes.},
}

@article {pmid41366867,
year = {2025},
author = {Khaengraeng, C and Mhuantong, W and Chaiprom, U and Bunkoed, W and Kuncharoen, N and Kasem, S and Chatnaparat, T and Suwannarat, S},
title = {Fungal and Bacterial Communities Associated with Northern Corn Leaf Blight in Resistant and Susceptible Sweet Corn.},
journal = {The plant pathology journal},
volume = {41},
number = {6},
pages = {736-754},
doi = {10.5423/PPJ.OA.05.2025.0060},
pmid = {41366867},
issn = {1598-2254},
support = {FF(KU)2.66//Kasetsart University Research and Development Institute/ ; },
abstract = {Northern corn leaf blight (NCLB), caused by Exserohilum turcicum (Setosphaeria turcica), is a major disease that negatively impacts the yield and quality of sweet corn. Plant-associated microbes hold great potential for enhancing crop productivity and sustainability. This study investigated the fungal and bacterial communities associated with NCLB in resistant and susceptible sweet corn cultivars using amplicon metagenomic sequencing. The structural composition and diversity of the fungal community in symptomatic NCLB-susceptible cultivars differed significantly from those in asymptomatic NCLB-resistant cultivars. In contrast, the bacterial communities showed no significant differences between resistant and susceptible cultivars in both the phyllosphere and rhizosphere. Exserohilum and Alternaria were significantly more abundant in the phyllosphere of symptomatic NCLB-susceptible plants, while fungal genera such as Sporobolomyces and Aureobasidium, along with the order Dothideales and the bacteria Bacillus, were significantly more abundant in the phyllosphere of asymptomatic NCLB-resistant cultivars. Microbial metabolic functions related to sugar metabolism-including sucrose biosynthesis and the degradation of glucose and xylose, compounds abundant in plant cell walls-were enriched in the phyllosphere of symptomatic NCLB-susceptible plants. In contrast, functions associated with detoxification and defense responses to plant phenolic compounds were enriched in microbes from asymptomatic NCLB-resistant cultivars. Additionally, Bacillus, identified ash part of the core microbiome, and the epiphytic yeast Sporobolomyces, identified as a hub in the microbial network, exhibited antimicrobial activity that may suppress E. turcicum. These findings offer valuable insights into the role of microbial communities in plant health and disease resistance, with promising implications for developing microbiome-based strategies to manage NCLB.},
}

@article {pmid41366832,
year = {2025},
author = {Wu, X and Yang, C and Qing, L and Yang, W and Zhou, K and Lu, G},
title = {Metagenomic Next-generation Sequencing Aids Diagnosis of Leishmania donovani-associated Hemophagocytic Lymphohistiocytosis in Infants: Case Report and Systematic Review.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005078},
pmid = {41366832},
issn = {1532-0987},
abstract = {Diagnosing hemophagocytic lymphohistiocytosis (HLH) triggers in infants is challenging. In a 9-month-old boy with unresponsive fever and pancytopenia, conventional tests were negative. Metagenomic next-generation sequencing detected Leishmania donovani, confirming Leishmania donovani-associated HLH. Targeted antiparasitic therapy replaced empiric immunosuppression, leading to rapid recovery. This case demonstrates that metagenomic next-generation sequencing is crucial for rapid pathogen identification in critically ill infants with HLH of unknown cause.},
}

@article {pmid41366711,
year = {2025},
author = {Rey Redondo, E and Xu, W and Xu, Y and Sun, R and Wan, SH and Leung, SKK and Yung, CCM},
title = {Multi-domain temporal patterns reveal stable community membership but dynamic interactions in the coastal microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00803-5},
pmid = {41366711},
issn = {2524-6372},
support = {Hong Kong PhD Fellowship Scheme//Research Grants Council of Hong Kong/ ; 16102024//Research Grants Council of Hong Kong/ ; },
abstract = {BACKGROUND: Marine microbial communities drive global biogeochemical cycles and oceanic food webs, yet our understanding of their holistic temporal dynamics remains limited, particularly in the South China Sea. Most studies have focused on specific taxonomic groups or single temporal scales, leaving a gap in comprehensive, multi-domain, and multi-timescale analyses.

RESULTS: Using an integrated multi-omics approach that combined metagenomic, metatranscriptomic, and metaviromic analyses, we conducted time-series sampling over 48-h periods during winter and summer to investigate microbial community dynamics in the coastal South China Sea. Seasonal transitions were identified as the primary drivers of community shifts, with diel variations playing a secondary role across all taxonomic domains. Within seasons, diel changes followed a progressive trajectory rather than recurring cyclic patterns. Eukaryotic communities exhibited the most pronounced temporal fluctuations, while prokaryotic and viral communities displayed remarkable stability. Unlike previous coastal studies, viral communities maintained high similarity between seasons, suggesting the presence of a persistent viral reservoir in this region. Gene expression analysis revealed dynamic population shifts in photosynthetic microorganisms, with Mamiellophyceae green algae and their associated Prasinovirus displaying pronounced seasonal and diel rhythmicity.

CONCLUSIONS: This study provides novel insights into the temporal dynamics of microbial communities and host-virus interactions in the South China Sea. The stability of viral communities, coupled with synchronised host-virus activities, highlights potential mechanisms supporting ecosystem resilience in this coastal region. These findings enhance our understanding of marine ecosystem processes and establish a robust framework for exploring microbial responses to environmental changes on both diel and seasonal scales.},
}

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

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

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

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

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

@article {pmid41366253,
year = {2025},
author = {Breselge, S and de Paula Dias Moreira, L and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Porcellato, D and Cotter, PD},
title = {Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {265},
pmid = {41366253},
issn = {2396-8370},
support = {818368//European Union's Horizon 2020/ ; 818368//European Union's Horizon 2020/ ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; USIRL-2019-1//HRB/SFI/ ; USIRL-2019-1//HRB/SFI/ ; SFI/16/RC/3835//Irish Department of Agriculture, Food and the Marine/ ; TC/2018/0025//Food for Health Ireland/ ; NA-AGFOODDEVELAUTH20201216//Institute for the Advancement of Food and Nutritional Sciences/ ; 101060218//European Union's Horizon Europe/ ; },
abstract = {Water kefir (WK) is a fermented beverage produced by a complex symbiotic community of microbes, including yeasts, lactic acid bacteria (LAB), and acetic acid bacteria (AAB). Here, we combined shotgun metagenomics, NMR metabolomics, GC-MS volatile organic compound (VOC) analysis, and metaproteomics to investigate microbial succession, functional dynamics, and the roles of yeasts and Zymomonas in WK fermentations representative of two WK types, i.e., one dominated by yeast-LAB-AAB and another by Zymomonas. Metagenomic profiling revealed that yeast-LAB-AAB communities exhibited dynamic microbial succession, whereas Zymomonas-dominated communities remained stable. Despite differing microbial compositions, both fermentations maintained consistent global metabolic functions, although specialized metabolic pathways and VOC profiles diverged. Metaproteomic analysis revealed a strong underappreciation of yeast contributions in metagenomic datasets, with yeasts representing a larger fraction of the proteome than predicted by DNA-based abundance. Lentilactobacillus hilgardii was enriched on WK grains, suggesting a specialized niche role. Our findings highlight the value of integrating multi-omics approaches to uncover microbial activity and community function in fermented foods and offer insights for the design of tailored WK starter cultures.},
}

@article {pmid41366061,
year = {2025},
author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY},
title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41366061},
issn = {1532-1827},
support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.

METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.

RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC = 0.95, 95% CI = 0.92-0.98).

CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.},
}

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

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

@article {pmid41279710,
year = {2025},
author = {Joshi, B and Zulk, JJ and Serchejian, C and Hameed, ZA and Larson, AB and Terwilliger, AL and Kumar, D and Mysorekar, IU and Britton, RA and Maresso, AW and Patras, KA},
title = {Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279710},
issn = {2692-8205},
abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, ΦHP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage significantly inhibited UPEC growth in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal ΦHP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed to uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable treatment option for UTI prevention.},
}

@article {pmid41055130,
year = {2025},
author = {Henson, LH and Christensen, KA and Sutherland, BJG and Johnson, HA and vonHoldt, B and Stronen, AV and Paquet, PC and Moody, J and Koop, BF and Darimont, CT},
title = {Grizzly bear population genomics across a coastal-interior ecotone in British Columbia, Canada.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {12},
pages = {},
doi = {10.1093/g3journal/jkaf237},
pmid = {41055130},
issn = {2160-1836},
support = {GEN013//Genome BC GeneSolve/ ; //LHH/ ; IT07676//MITACS Accelerate/ ; //Raincoast Chair of Applied Conservation Science/ ; },
mesh = {Animals ; British Columbia ; *Ursidae/genetics ; Polymorphism, Single Nucleotide ; *Genetics, Population ; *Metagenomics/methods ; Genotype ; *Ecosystem ; *Genomics/methods ; },
abstract = {Local adaptation research often focuses on discrete populations without extensive gene flow that are under differential selective pressures. By contrast, grizzly bears Ursus arctos in British Columbia (BC) are wide-ranging omnivores that span an environmental and resource ecotone from the coastal, salmon-enriched rainforest to dry interior plateau. This ecotone has been associated with local adaptation in other species and the different regions to morphological variation in grizzly bears. To understand genome-wide population genetic patterns across the ecotone and to identify loci or genomic regions associated with these different environments, here we use whole-genome resequencing to characterize 3.9 M SNPs in 31 grizzly bears spanning from central to northern latitudes in coastal and interior regions (to the west and east of the coastal mountain range [CMR], respectively). Clustering grizzly samples by genotypes identified 3 groups that generally correspond to the source geographic regions, with the greatest variation occurring from north to south. The data were best explained by a single ancestry cluster, but K = 3 recovered the 3 geographic groupings and were used to identify putative nonmigrant individuals. The presence of individuals with mixed ancestry (using K = 3) provides evidence for travel across the CMR, but significant differentiation between clusters (mean FST = 0.015 to 0.036) suggests some genetic separation between the regions, supporting an isolation-by-distance or clinal variation model. Putative close-kin were identified and removed, then multiple supervised outlier SNP detection methods were applied to identify regions of the genome consistently segregating between coastal and interior regions. Several associated genomic regions and candidate genes were identified, including a consistently identified outlier region near the gene creatine kinase, m-type. This work provides the first genome-wide analysis of grizzly bears in the studied region. These findings will be useful for connectivity planning and research on the adaptability of coastal and interior grizzlies to future climate change scenarios.},
}

Animals
British Columbia
*Ursidae/genetics
Polymorphism, Single Nucleotide
*Genetics, Population
*Metagenomics/methods
Genotype
*Ecosystem
*Genomics/methods

@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
doi = {10.1111/1758-2229.70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}

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

@article {pmid41365463,
year = {2025},
author = {Xi, L and Chen, J and Chen, Y and Lai, K and Xu, S},
title = {Nonthyroidal illness syndrome and diagnostic utility of CSF mNGS: insights from a case series of neurological scrub typhus.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108291},
doi = {10.1016/j.ijid.2025.108291},
pmid = {41365463},
issn = {1878-3511},
abstract = {We describe five cases of neurological scrub typhus that highlight two critical, underrecognized aspects of this disease. First, cerebrospinal fluid metagenomic next-generation sequencing (CSF mNGS) accurately identified Orientia tsutsugamushi in all three patients tested, while the conventional Weil-Felix test was negative in every case, establishing mNGS as a pivotal diagnostic tool. Second, we uncovered a high prevalence of thyroid dysfunction, with nonthyroidal illness syndrome (NTIS) present in three of four patients tested, a novel systemic complication linked to severe inflammatory stress. Additional notable findings included frequent hypokalemia, at times severe enough to mimic periodic paralysis, and urban acquisition in two cases, suggesting an expanding epidemiological footprint. All patients improved on doxycycline-based regimens. This series underscores the diagnostic superiority of CSF mNGS and reveals NTIS as a key endocrine manifestation in neurological scrub typhus, urging greater clinical vigilance.},
}

@article {pmid41365368,
year = {2025},
author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X},
title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133782},
doi = {10.1016/j.biortech.2025.133782},
pmid = {41365368},
issn = {1873-2976},
abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.},
}

@article {pmid41365245,
year = {2025},
author = {De Koch, MD and Kraberger, S and Fielding, R and Smith, K and Schiavone, K and Hall, KR and Reid, VS and Boyea, D and Smith, EL and Schmidlin, K and Fontenele, RS and Martin, DP and Krupovic, M and Varsani, A},
title = {Novel circoviruses identified in short-finned pilot whale and orca from the North Atlantic Ocean.},
journal = {Virology},
volume = {615},
number = {},
pages = {110768},
doi = {10.1016/j.virol.2025.110768},
pmid = {41365245},
issn = {1096-0341},
abstract = {The family Circoviridae comprises viruses with small single-stranded DNA genomes that are known to infect various animals, resulting in considerable morbidity and mortality in some hosts. Circoviruses have been recently identified through metagenomic sequencing in diverse terrestrial vertebrate species, but their distribution and diversity in marine vertebrates remains underexplored. Here, we use high-throughput sequencing (HTS) to identify circoviruses from archived tissue samples of delphinids (order Artiodactyla, infraorder Cetacea, family Delphinidae). Based on the HTS data, we designed specific abutting primer pairs to recover seven complete circovirus genomes from individual delphinid hosts, namely, the short-finned pilot whale (Globicephala macrorhynchus, n = 5) and the orca (Orcinus orca, n = 2). The circoviruses from the two delphinid species share <65.4 % genome-wide pairwise nucleotide identity with all classified circovirus representative sequences and 66 % amongst themselves. Accordingly, these viruses, which we have named shofin circovirus and orcin circovirus, respectively, represent two novel species. This report also marks the first detection of cetacean circoviruses in the North Atlantic Ocean (near St. Vincent, Caribbean). Notably, analysis of the capsid protein sequences and structures of the delphinid circoviruses revealed notable elaborations within the surface exposed loops that have been previously shown to be a major antigenic epitope in porcine circovirus 2. Collectively, the delphinid circovirus genomes expand the known diversity of circoviruses of marine vertebrates and suggest similar evolutionary pressures exerted by the immune systems of cetacean and suina hosts, both members of the order Artiodactyla.},
}

@article {pmid41365225,
year = {2025},
author = {Jin, W and Zhang, Y and Li, Y and Li, R and Su, X and Jing, S and Wang, R and Qiu, Y and Xie, X and Guo, Z and Zhao, X},
title = {Polyethylene microplastics induce microbial functional reprogramming via rhizosphere network disruption, accelerating soil decline.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128236},
doi = {10.1016/j.jenvman.2025.128236},
pmid = {41365225},
issn = {1095-8630},
abstract = {Polyethylene microplastics (PE-MPs) are emerging soil pollutants with unclear mechanisms of impact on rhizosphere ecosystem functions. Using Angelica sinensis, a medicinal plant valued for its root use, as a model, this study integrated untargeted metabolomics, metagenomic sequencing, and PLS-PM modeling to investigate rhizosphere responses to different PE-MPs concentrations (250, 500, 1000 mg/kg). With increasing PE-MPs dosage, rhizosphere metabolic pathways shifted toward stress adaptation, featuring functional homeostasis and energy reprogramming. Exposure to PE-MPs significantly altered microbial community structure: bacterial and viral shannon, richness, and pielou evenness indices increased, fungal dominance and reduced evenness were observed, and archaeal diversity indices declined. Microbial network stability and functional redundancy weakened, increasing ecosystem sensitivity. Metabolite-microbe association analysis revealed synergistic enrichment patterns, suggesting that plants may recruit beneficial microbes through metabolite regulation. The PLS-PM modeling results indicated that metabolite changes regulate the expression of C/N/S/P cycling functional genes through shifts in bacterial and viral community compositions, where bacteria serve as the primary regulatory hubs and viruses play a key role in amplifying microbial signaling by influencing the microbial community. The expression of these functional genes was negatively correlated with the Soil Quality Index (SQI), indicating that PE-MPs-induced metabolic stress accelerates soil functional degradation. This study provides new insights into microplastic-driven rhizosphere disruption and offers a theoretical basis and biomarkers for microbial regulation and soil ecological restoration.},
}

@article {pmid41365051,
year = {2025},
author = {Wang, H and Congzhu, and Wang, J and Lin, X and Guo, Y and Kiani, FA and Zhou, X and Ding, Y},
title = {Clostridium perfringens can promote the formation of fatty liver in cows.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110826},
doi = {10.1016/j.vetmic.2025.110826},
pmid = {41365051},
issn = {1873-2542},
abstract = {During the periparturient period, reduced feed intake often causes negative energy balance in dairy cows, leading to fat mobilization, hepatic lipid accumulation, and fatty liver disease (FLD), ultimately compromising health and milk production. This study investigated the association between FLD and gut microbiota dysbiosis, with a particular focus on the role of Clostridium perfringens within the gut-liver axis. Metagenomic sequencing of ileal contents revealed a marked decrease in microbial diversity in cows with FLD, along with increased abundances of potential pathogens such as C. perfringens, Enterobacter cloacae, and Vibrio alginolyticus. Functional annotation indicated elevated expression of virulence factors (e.g., Hsp60, flagella, mu-toxin), antibiotic resistance genes (e.g., otrA, lsaC), and pathways related to lipopolysaccharide (LPS) biosynthesis and mitogen-activated protein kinase (MAPK) signaling pathways, suggesting enhanced pro-inflammatory potential. qPCR analysis of ileal tissue demonstrated reduced expression of tight junction proteins (zona occludens 1 (ZO-1), Claudin-1, and Occludin) and increased levels of pro-inflammatory cytokines (Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumour necrosis factor-alpha (TNF-α)), alongside a decrease in the anti-inflammatory cytokine interleukin-10 (IL-10), indicating compromised intestinal barrier function and local inflammation. Given the significant enrichment of C. perfringens in the ileum of FLD cows, we hypothesized its involvement in disease pathogenesis. To test this, C. perfringens was isolated and orally administered to antibiotic-pretreated mice fed a high-fat diet. These mice developed exacerbated hepatic steatosis, metabolic disturbances, and heightened inflammatory responses. Moreover, Western blot analysis revealed reduced expression of intestinal tight junction proteins (ZO-1, Claudin-1, Occludin), indicating increased intestinal permeability. Quantitative PCR confirmed upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and downregulation of IL-10 in both intestinal and hepatic tissues. These findings indicate that C. perfringens may promote FLD by impairing gut barrier integrity and enhancing inflammatory responses. In conclusion, our findings suggest that C. perfringens may contribute to the development of FLD in dairy cows by impairing intestinal barrier integrity and promoting systemic inflammation.},
}

@article {pmid41364992,
year = {2025},
author = {Alharbi, M and Nguyen-Dinh, T and Wong, WW and Leung, PM and Kessler, AJ and Greening, C and Cook, PLM},
title = {Dissimilatory nitrate reduction to ammonium driven by iron tolerant Lutibacter in coastal sediments.},
journal = {The Science of the total environment},
volume = {1010},
number = {},
pages = {181095},
doi = {10.1016/j.scitotenv.2025.181095},
pmid = {41364992},
issn = {1879-1026},
abstract = {The processes of denitrification and dissimilatory NO3[-] reduction to ammonium (DNRA) occupy a competing pivotal point in the nitrogen cycle. Denitrification leads to a loss of fixed nitrogen, while DNRA recycles NO3[-] as bioavailable ammonium. Iron (II) is known to enhance DNRA, by acting as an electron donor, however, the organisms responsible for iron driven DNRA remain poorly understood. Here we undertook incubations of sediment with NO3[-] and Fe[2+] additions followed by process measurements and metagenomic analysis to measure DNRA and microbial community structure. Addition of Fe[2+] stimulated DNRA, and greatly increased the relative abundance of flavobacteria (Lutibacter) in slurries over a period of 12-24 days compared to controls. We isolated a strain of Lutibacter from these slurries which mediated organotrophic and mixotrophic DNRA (while oxidising sulphide). No genes capable of Fe[2+] oxidation were detected in agreement with experiments that showed this strain had no ability to oxidise Fe[2+]. The addition of Fe[2+] to pure cultures had no significant effect on DNRA, suggesting these bacteria are not stimulated nor inhibited by the presence of Fe[2+]. As such, in contrast to previous studies, we find Fe[2+] addition to sediments enhances DNRA by favouring Fe tolerant Lutibacter and is uncoupled Fe[2+] oxidation in coastal sediments. This has implications for how pollutants such as higher Fe[2+] concentrations and disturbance can lead to bacterial community shifts that enhance nitrogen retention within ecosystems. Isolates of these robust bacteria have the potential to help recover NO3[-] as NH4[+] in novel water treatment systems.},
}

@article {pmid41364990,
year = {2025},
author = {Shen, S and Shimotori, K and Tsuchiya, K and Shigeta, S and Sueyoshi, M and Matsuda, T and Shimizu, Y},
title = {Carrier-resolved metagenomics suggests the dual "filter-hub" function of a large freshwater lake toward incoming antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {1010},
number = {},
pages = {181145},
doi = {10.1016/j.scitotenv.2025.181145},
pmid = {41364990},
issn = {1879-1026},
abstract = {Rivers and wastewater-treatment plants (WWTPs) convey antibiotic resistance genes (ARGs) to lakes. Studies simultaneously profiling ARGs and their carriers and tracking their persistence in lakes remain scarce. We collected cell- and virus-size fractions from Lake Biwa, Japan, 11 in-flowing rivers, and one WWTP for shotgun metagenomic sequencing. We reconstructed 326 bacterial metagenome-assembled genomes, 7917 plasmid contigs (472 harboring conjugation genes), and 32,375 viral contigs. The chromosomes contained 1502 ARGs (predominantly fluoroquinolone and glycopeptide resistance). The plasmids encoded efflux- and target-alteration determinants spanning 25 drug classes. Only 3.6 % of the viral genomes carried ARGs, chiefly qnr and dfr. ARG class composition differed among carriers, forming a spatial mosaic unrelated to land use or livestock density. Of the ARG-carrying cells and viruses, 85-97 % were undetectable in the lake, suggesting dilution and adaptation failure. Chromosome comparison identified 1809 putative horizontal gene transfer events, 2.1 % of which bridged lake-resident and external taxa. ARG profiles differed according to carrier type. Thus, Lake Biwa might function simultaneously as a filter, removing incoming ARG-carrying cells and viral particles, and as a "silent hub," potentially integrating external ARGs into lake-resident bacteria through horizontal gene transfer. These data provide a foundation for assessing and managing antimicrobial resistance in large freshwater ecosystems.},
}

@article {pmid41364878,
year = {2025},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B cell lymphoma.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016858},
pmid = {41364878},
issn = {2473-9537},
abstract = {CD19 CAR T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (RR-DLBCL), but challenges like post-treatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from RR-DLBCL patients were analyzed at apheresis (47 samples) and one month post-infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly diagnosed DLBCL, RR-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders to treatment had higher levels of Bacteroides fragilis, while non-responders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs, and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in RR-DLBCL.},
}

@article {pmid41364497,
year = {2025},
author = {Saroff, MJ and Haile, AA and Baniel, A and Kraberger, S and Regney, M and Harrach, B and Kaján, GL and Lu, A and Beehner, JC and Bergman, TJ and Snyder-Mackler, N and Varsani, A and Schneider-Crease, IA},
title = {Early-life infection dynamics and genomic diversity of adenoviruses in a wild primate (Theropithecus gelada).},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001595},
pmid = {41364497},
issn = {2057-5858},
mesh = {Animals ; Feces/virology ; *Theropithecus/virology ; Ethiopia ; *Adenoviridae Infections/virology/veterinary ; Phylogeny ; Genome, Viral ; *Adenoviruses, Simian/genetics/classification ; *Adenoviridae/genetics/classification ; Genetic Variation ; Female ; Male ; },
abstract = {In humans, adenoviruses (AdVs) are frequently associated with respiratory illnesses, posing risks to children with developing immune systems and immunocompromised individuals. Outbreaks and epidemics are generally centred in close-contact settings, such as childcare facilities, and transmission occurs through faecal-oral and airborne pathways. AdVs have coevolved across the primate lineage, but very little is known about whether the early-life dynamics in non-human primates mirror those in humans. Here, we leverage longitudinal data collected on a population of geladas (Theropithecus gelada) in the Simien Mountains National Park, Ethiopia, to evaluate AdV dynamics across the gelada lifespan. We identified ten coding-complete AdV genomes representing seven unique simian adenovirus (SAdV) types, four of which are adequately different from the known ones to establish new species. We assessed behavioural and seasonal drivers of SAdV presence and richness across repeated faecal samples from known individuals. Contrary to our expectation that the highest risk would occur after the initiation of play behaviour in infancy (~6 months of age), when peer-to-peer transmission risk is expected to increase, SAdV likelihood was highest in infants under 6 months of age. Risk and richness declined over the lifespan, with very few adults infected, and higher minimum temperatures were weakly but significantly negatively associated with richness. Our results suggest that, unlike in humans, SAdV exposure occurs prior to the initiation of close-contact play behaviours and likely results from the close spatial proximity of conspecifics throughout the dependent period. Like AdVs in humans, SAdVs in geladas maintain low levels in adulthood, with early infections potentially conferring life-long immunity.},
}

Animals
Feces/virology
*Theropithecus/virology
Ethiopia
*Adenoviridae Infections/virology/veterinary
Phylogeny
Genome, Viral
*Adenoviruses, Simian/genetics/classification
*Adenoviridae/genetics/classification
Genetic Variation
Female
Male

@article {pmid41364398,
year = {2025},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Strain-level dynamics of Akkermansia muciniphila in the human gut microbiota.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-01982-7},
pmid = {41364398},
issn = {2191-0855},
support = {2018YFC1200100//National Key Research and Development Program of China/ ; },
abstract = {Akkermansia muciniphila (Akk), a mucin-degrading bacterium residing in the human gut, plays a pivotal role in intestinal health. This study investigated its temporal dynamics, strain-level diversity, and cross-regional transmission using longitudinal metagenomic data from the Chinese Microbiome Project (CMP). We observed significant fluctuations in Akk relative abundance across 52 time points in 7 healthy individuals, with detection rates of 56.9% (16S rRNA gene sequencing) and 33.3% (whole-genome sequencing, WGS). Notably, "short-term blooms"--rapid increases followed by declines in relative abundance--were identified in multiple subjects. Genomic analysis of 39 Akkermansia metagenome-assembled genomes (MAGs), combined with 89 publicly available strains with complete genome, revealed phylogenetically distinct clusters (average nucleotide identity, ANI < 98% between clusters). Strikingly, individuals harbored different clusters at varying time points (e.g., AmII replaced by AmIb and later AmIa in subject P4), suggesting strain replacement and recurrent colonization. Furthermore, high-similarity strains (ANI > 99%) were shared between individuals with close contact (e.g., cohabiting subjects P2 and P4) and across geographically distant regions (China, South Korea, and the United States), implicating human-mediated or environmental transmission pathways. These findings underscore the dynamic nature of Akk within the gut microbiota and highlight the need to explore factors driving its colonization, strain competition, and ecological dissemination.},
}

@article {pmid41363757,
year = {2025},
author = {Li, J and Pang, Y and Yu, H},
title = {Robot-Assisted Stereotactic Aspiration of a Parietal Brain Abscess With Metagenomic Identification of Fusobacterium nucleatum.},
journal = {The Journal of craniofacial surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SCS.0000000000012287},
pmid = {41363757},
issn = {1536-3732},
abstract = {Robot-assisted stereotactic aspiration offers a minimally invasive approach to brain abscesses near the eloquent cortex. We report a rare case of a left parietal abscess caused by Fusobacterium nucleatum in an immunocompetent adult, managed successfully with this approach. The patient, a 52-year-old man, presented with right-sided limb numbness. MRI and contrast-enhanced CT revealed a cystic, ring-enhancing lesion with diffusion restriction in the left parietal lobe. Despite empiric broad-spectrum antibiotics, neurological deterioration occurred due to progressive mass effect. Robot-assisted stereotactic aspiration enabled single-stage, precise drainage of the abscess. Metagenomic next-generation sequencing identified F. nucleatum, prompting adjustment of antibiotics to ceftriaxone plus metronidazole, followed by metronidazole monotherapy. The patient improved clinically, and a 6-month MRI confirmed complete resolution, underscoring the precision of robotic stereotaxy for eloquent-region abscesses and highlighting the diagnostic value of metagenomic sequencing in detecting anaerobic pathogens.},
}

@article {pmid41363534,
year = {2025},
author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y},
title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0053925},
doi = {10.1128/msphere.00539-25},
pmid = {41363534},
issn = {2379-5042},
abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.},
}

@article {pmid41362850,
year = {2025},
author = {Shu, H and Li, X and Chen, Y and Wang, W},
title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis in an HIV-negative patient: A case of misdiagnosis.},
journal = {Medical mycology case reports},
volume = {50},
number = {},
pages = {100752},
pmid = {41362850},
issn = {2211-7539},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to disseminated histoplasmosis (DH) is rare and often misdiagnosed, especially in non-endemic areas. We present a case of a 70-year-old Chinese man who was admitted with fever, nausea, and vomiting, initially misdiagnosed with pulmonary tuberculosis. The use of metagenomic next-generation sequencing (mNGS) played a crucial role in the early and accurate diagnosis, highlighting its potential as a valuable diagnostic tool for rare infections.},
}

@article {pmid41362398,
year = {2025},
author = {Xu, X and Li, J and Pan, L and Yu, H and Huang, J},
title = {Gastropleural Fistula Following Combined TACE, Immunotherapy, and Bevacizumab in HCC: A Case Report.},
journal = {Journal of hepatocellular carcinoma},
volume = {12},
number = {},
pages = {2671-2677},
pmid = {41362398},
issn = {2253-5969},
abstract = {Gastropleural fistula (GPF) is an extremely rare complication after treatment for liver cancer. We report a case of a 54-year-old man with hepatitis B virus (HBV)-related liver cancer who developed a GPF after multiple sessions of transarterial chemoembolization (TACE) combined with immunotherapy and targeted therapy. During the third treatment, because of arterial remodeling and changes in tumor vascular supply, the embolization route was changed to the left inferior phrenic artery. After the procedure, the patient presented with abdominal pain, chest pain, and fever. Metagenomic next-generation sequencing (mNGS) of the pleural effusion identified Porphyromonas endodontalis, and Pneumocystis jirovecii was also detected in the sputum. Upper gastrointestinal endoscopy and water-soluble contrast radiography confirmed a gastric fundus perforation with a fistulous communication to the pleural cavity. After multidisciplinary evaluation, the patient underwent laparoscopic fistula repair and had a favorable postoperative recovery. This case highlights that, while the combination of TACE, immunotherapy, and targeted agents may provide synergistic antitumor benefits, it also carries a potential risk of serious gastric complications.},
}

@article {pmid41362143,
year = {2025},
author = {Gao, WJ and Wan, YQ and Bian, WJ and Sun, KK and Gao, ZC},
title = {[A case of pulmonary alveolar proteinosis secondary to GATA2 deficiency combined with splenic M. kansasii infection and literature review].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {12},
pages = {1153-1161},
doi = {10.3760/cma.j.cn112147-20250527-00287},
pmid = {41362143},
issn = {1001-0939},
mesh = {Humans ; *Pulmonary Alveolar Proteinosis/etiology ; Male ; *Mycobacterium Infections, Nontuberculous/complications ; *GATA2 Deficiency/complications ; Young Adult ; *GATA2 Transcription Factor/genetics/deficiency ; Mycobacterium kansasii ; Spleen/microbiology ; },
abstract = {Objective: To enhance the understanding of the rare disease GATA2 deficiency syndrome leading to pulmonary alveolar proteinosis (PAP) and non-tuberculous mycobacterial (NTM) disease. Methods: The clinical data of a patient with GATA2 deficiency-associated PAP and splenic M. kansasii disease admitted to Peking University People's Hospital were summarized. Relevant literature from January 1, 2010 to March 31, 2025 was retrieved and reviewed through Wanfang Data, China National Knowledge Infrastructure, and the National Center for Biotechnology Information database. Results: The patient was a 19-year-old male. The clinical manifestations included recurrent fever for 7 years. The peripheral blood routine test showed peripheral blood pancytopenia accompanied by monocytopenia. The serum granulocyte-macrophage colony-stimulating factor (GM-CSF) antibody was negative. Chest CT revealed diffuse interstitial lung changes, while [18]F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG PET-CT) demonstrated splenomegaly with multiple focal FDG-avid lesions. Bone marrow biopsy indicated marrow failure. Histopathological examination of lung biopsy specimens was consistent with alveolar proteinosis, whereas histopathology of the spleen biopsy revealed granuloma and patellar necrosis. Metagenomic next-generation sequencing (mNGS) of the splenic specimen detected M. kansasii, and genetic testing identified a germline GATA2 mutation(c.1128del, p.Y377fs). Based on these findings, a diagnosis of GATA2 deficiency with secondary PAP and splenic M. kansasii infection was established. Following anti-NTM treatment, the patient's infection was controlled; however, hematopoietic stem cell transplantation was planned due to bone marrow failure. Literature search revealed 4 cases of GATA2 deficiency syndrome with bone marrow dysplasia. Three cases developed PAP. All 4 cases had NTM infection, including 1 case with disseminated NTM infection in the lungs, spleen, and bone marrow. GATA2 deficiency syndrome patients are prone to decreased numbers and functional defects of cells such as monocytes and NK cells, resulting in immune dysfunction and pulmonary alveolar macrophage dysfunction, reduced ability to resist NTM, leading to the patient being prone to NTM infection, namely MonoMAC syndrome, and can cause secondary PAP. Early identification and timely completion of genetic testing are beneficial for clear diagnosis and establishment of precise intervention strategies. Conclusion: GATA2 deficiency is a rare autosomal dominant genetic disorder caused by mutations in the GATA2 gene. Patients with cytopenia, GM-CSF antibody-negative PAP accompanied by NTM infection should be considered to have the possibility of this disease. Those patients should undergo GATA2 gene screening. Hematopoietic stem cell transplantation is currently the only possible method for curing GATA2 deficiency.},
}

Humans
*Pulmonary Alveolar Proteinosis/etiology
Male
*Mycobacterium Infections, Nontuberculous/complications
*GATA2 Deficiency/complications
Young Adult
*GATA2 Transcription Factor/genetics/deficiency
Mycobacterium kansasii
Spleen/microbiology

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

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

@article {pmid41361265,
year = {2025},
author = {Wang, C and Wang, C and Chen, S and Shi, K and Yu, J and Ding, Y and Yue, Y and Hua, Y and Wang, H and Chen, J},
title = {Global landscape of antibiotic resistance genes in the human gut microbiome metagenome-assembled genomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04586-0},
pmid = {41361265},
issn = {1471-2180},
support = {No.202524//the Scientific Research Program of the Bozhou University/ ; No. W2412100//International Cooperation and Exchanges NSFC-ASRT/ ; No. 42276137//National Natural Science Foundation of China/ ; No. 2022YFC2804205//National Key Research and Development Program of China/ ; No. 2022YFC2804104//National Key Research and Development Program of China/ ; },
}

@article {pmid41361202,
year = {2025},
author = {Korzekwa, K and Lepionka, T and Bisak, A and Obuch-Woszczatyńska, O and Bylińska, K and Kauc, A and Skuza, K and Zaborski, B and Krzyżowska, M},
title = {Long-term biological surveillance of SARS-CoV-2 in critical points for municipal sewage catchment in light of wastewater-based epidemiology, public health and environmental hygiene.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43320},
pmid = {41361202},
issn = {2045-2322},
support = {National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; National Health Program for 2021-2025" no 357/2021/DA//Ministry of National Defence, Poland/ ; },
mesh = {*SARS-CoV-2/genetics/isolation & purification ; *Sewage/virology ; *COVID-19/epidemiology/virology ; Humans ; *Wastewater/virology ; Public Health ; *Wastewater-Based Epidemiological Monitoring ; Poland/epidemiology ; Hygiene ; Environmental Monitoring ; },
abstract = {Routine monitoring and wastewater-based bio-surveillance represents a strong supporting tool for following and understanding SARS-CoV-2 endemicity or epidemic dynamics in society. The main objective of the research was a two-year qualitative and quantitative monitoring program of SARS-CoV-2 in sewage in a model urban agglomeration (the capital city), including the development of an algorithm for action in this area and a joint evaluation of procedures with a water and sewage company (public administration sector). To resolve problems, we continuously investigated inflows and outflows of four wastewater treatment plants and raw sewage of the whole catchment (including healthcare units, airport and military areas) within the Warsaw capital city for SARS-CoV-2, during two waves of COVID-19 in 2023 and 2024. The screening was performed by RT-qPCR (N1, N2, E probes) and NGS metagenomics analysis. The average cumulative load of the virus in sewage for the whole tested period was 3.5 × 10[5] genomic copies per litre. The highest load was found for wastewater inflows and the lowest one was found for housing estates and wastewater outflows. Higher viral concentrations in the wastewater than expected in medical records suggested a higher number of undiagnosed COVID-19 infections within the community. The obtained genotypes segregated within 11 clades (21I to 24 F), making '23 and '24 waves distinguishable. We consider our results and methodological approaches hold significant potential for public health, with particular emphasis on the needs of the Directive (EU) 2024/3019 of the European Parliament and of the Council.},
}

*SARS-CoV-2/genetics/isolation & purification
*Sewage/virology
*COVID-19/epidemiology/virology
Humans
*Wastewater/virology
Public Health
*Wastewater-Based Epidemiological Monitoring
Poland/epidemiology
Hygiene
Environmental Monitoring

@article {pmid41360901,
year = {2025},
author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R},
title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30604-2},
pmid = {41360901},
issn = {2045-2322},
support = {BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10045515//Innovate UK/ ; },
abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.},
}

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

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