@article {pmid41315421,
year = {2025},
author = {Thystrup, C and Gobena, T and Salvador, EM and Fayemi, OE and Kumburu, H and Buys, EM and Gichure, J and Moiane, BT and Belina, D and Hugho, EA and Faife, S and Ogunbiyi, TS and Akanni, G and Ayolabi, CI and Mmbaga, B and Thomas, KM and Pires, SM and Njage, PMK and Hald, T},
title = {Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66400-9},
pmid = {41315421},
issn = {2041-1723},
support = {OPP1195617//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
abstract = {Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.},
}

@article {pmid41315331,
year = {2025},
author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S},
title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {223},
pmid = {41315331},
issn = {2055-5008},
support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; },
mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; },
abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.},
}

Humans
*Microbiota/genetics
Saliva/microbiology
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Mouth Neoplasms/microbiology
Dental Caries/microbiology
*Host Microbial Interactions
*Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing/methods
Child
Child, Preschool

@article {pmid41315266,
year = {2025},
author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P},
title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10777},
pmid = {41315266},
issn = {2041-1723},
support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Zea mays/microbiology/genetics/growth & development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; },
abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.},
}

*Zea mays/microbiology/genetics/growth & development/metabolism
*Hybrid Vigor/genetics
*Plant Roots/microbiology/genetics
Soil Microbiology
Biomass
Microbiota/genetics
Flavonoids/metabolism
Metabolomics
Rhizosphere

@article {pmid41315190,
year = {2025},
author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and , and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M},
title = {Unveiling the global urban virome through wastewater metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10707},
pmid = {41315190},
issn = {2041-1723},
support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; },
mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; Cities ; Animals ; Metagenome ; },
abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.},
}

*Wastewater/virology
*Metagenomics/methods
*Virome/genetics
Humans
*Viruses/genetics/classification/isolation & purification
Cities
Animals
Metagenome

@article {pmid41314968,
year = {2025},
author = {Li, YX and Wang, RY},
title = {Autoimmune glial fibrillary acidic protein astrocytopathy following human herpesvirus-7 infection: a case report.},
journal = {Brain injury},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/02699052.2025.2596225},
pmid = {41314968},
issn = {1362-301X},
abstract = {OBJECTIVE: Human herpesvirus-7 encephalitis (HHV7E) is exceedingly rare in immunocompetent adults, and the subsequent development of autoimmune glial fibrillary acidic protein astrocytopathy (GFAP-A) following HHV7E is even rarer. We present the inaugural Chinese case of GFAP-A triggered by HHV7E, confirmed via metagenomic next-generation sequencing (mNGS).

RESULTS: A 37-year-old male initially presented with fever and significant memory impairment. Brain magnetic resonance imaging (MRI) revealed T2/fluid-attenuated inversion recovery (FLAIR) hyperintensity in the right temporal lobe. The diagnosis of HHV7E was confirmed by the detection of HHV7 in the cerebrospinal fluid (CSF) via mNGS. His symptoms improved significantly following acyclovir treatment. However, five weeks post-discharge, he experienced acute neurological deterioration, with symptoms including bifrontal headaches, vomiting, memory impairment, and visual hallucinations. Repeat brain MRI revealed new bilateral punctate and patchy T2/FLAIR hyperintensities in the periventricular white matter. Contrast-enhanced MRI demonstrated bilateral linear radial perivascular enhancements. A cell-based assay detected GFAP antibodies in CSF at a titer of 1:100, establishing a diagnosis of postinfectious GFAP-A. The patient responded well to combined intravenous steroid and immunoglobulin therapy.

CONCLUSIONS: This case highlights the importance of considering autoimmune encephalitis in patients with new or recurrent neurological symptoms after HHV7E recovery. Systematic mNGS and neuronal antibody testing are essential for timely diagnosis, and early aggressive immunotherapy may improve outcomes in post-HHV7E GFAP-A.},
}

@article {pmid41314430,
year = {2025},
author = {Gabbay, U and Carmi, D},
title = {The Paradox of Rapid and Synchronized Propagation of Seasonal Influenza 'A' Outbreaks in Contrast with COVID-19: a Testable Hypothesis.},
journal = {Virus research},
volume = {},
number = {},
pages = {199670},
doi = {10.1016/j.virusres.2025.199670},
pmid = {41314430},
issn = {1872-7492},
abstract = {Seasonal influenza A virus (SIAV) apparently exhibits a paradoxical pattern: despite a lower basic reproduction number (R0) than SARS-CoV-2, it propagates across the Northern Hemisphere with remarkable speed and synchronicity. We propose a testable hypothesis, developed in two conceptual steps to explain this phenomenon. First, we discuss what may explain the rapid, near-synchronous propagation of SIAV seasonal outbreak. We suggest that it may result from parallel seeding from multiple sources, rather than emerging from a singular origin, as observed with COVID-19. Second, we examined potential mechanisms for parallel seeding. The hypothesis is testable through genomic and metagenomic methods. Sequencing viruses from humans and migratory birds across regions may be evaluated to reveal identical viral lineages. The hypothesis may highlight the potential role of ecological reservoirs in global influenza propagation dynamics. If validated, this framework would advance understanding of influenza seasonality and may guide integrated surveillance strategies linking avian ecology with human epidemiology.},
}

@article {pmid41314145,
year = {2025},
author = {Li, X and Lin, X and Dong, Z and Zhou, R and Niu, Q},
title = {Biomass ratio regulates methane conversion and carbon fixation in a methanotrophs-microalgae symbiotic system: Efficiency optimization and mechanisms driven by co-metabolism.},
journal = {Water research},
volume = {290},
number = {},
pages = {125016},
doi = {10.1016/j.watres.2025.125016},
pmid = {41314145},
issn = {1879-2448},
abstract = {The methanotrophs-microalgae symbiotic system for greenhouse gas treatment is a novel biological carbon fixation technology. However, practical applications are limited by low conversion efficiency, which arises from metabolic heterogeneity in growth rates and carbon-nitrogen resource utilization within the system. To improve metabolic stability of such symbiotic systems, this study systematically assessed CH4 metabolic fluxes by regulating the methanotrophs-microalgae biomass ratio, and further revealed synergistic mechanisms that enhance system stability. Experimental results indicated that at a methanotrophs to microalgae ratio of 1:5, the CH4 consumption rate peaked at 1.1 L CH4/d/g biomass. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the laser confocal revealed that the co-aggregation force of methanotrophs and microalgae was significantly enhanced at the optimal ratio. This enhancement was crucial for regulating the spatial mutualistic growth and metabolic interactions within the methanotrophs-microalgae symbiotic community. Structural equation modeling (SEM) indicated that poly-β-hydroxybutyrate (PHB) exerts a significant negative effect on methane consumption (-0.68***). Metagenomics results indicated that at the optimal methanotrophs-microalgae ratio, the relative abundance of genes associated with the methane oxidation center metabolic pathway increased by 1.38 times. This significantly enriched Type I methanotrophs (1.89 times) and Type II methanotrophs (1.51 times), while the relative abundance of genes involved in the PHB production pathway decreased by 16 %. This change accelerated the conversion and assimilation of methane carbon, ultimately improving the carbon fixation efficiency by 16 %. This study provided theoretical foundations and technical support for advancing the engineering application of methanotrophs and microalgae symbionts to achieve efficient, stable methane conversion and simultaneous carbon sequestration.},
}

@article {pmid41314069,
year = {2025},
author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK},
title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181062},
doi = {10.1016/j.scitotenv.2025.181062},
pmid = {41314069},
issn = {1879-1026},
abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.},
}

@article {pmid41313993,
year = {2025},
author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y},
title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128135},
doi = {10.1016/j.jenvman.2025.128135},
pmid = {41313993},
issn = {1095-8630},
abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.},
}

@article {pmid41313912,
year = {2025},
author = {Li, Y and Tang, C and Qin, X and Qin, W and Fu, Y and Shi, D and Lan, W and Tang, Y and Wu, R and Yu, F},
title = {Rhizosphere nutrient dynamics and physiological responses of Oryza sativa L. under polyethylene terephthalate microplastic stress.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt E},
pages = {110797},
doi = {10.1016/j.plaphy.2025.110797},
pmid = {41313912},
issn = {1873-2690},
abstract = {Polyethylene terephthalate microplastics (PET-MPs), as emerging environmental contaminants, pose growing threats to agricultural ecosystems. This study investigated the impacts of PET-MPs on key physiological traits of Oryza sativa L. and the abundance of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling within rhizosphere soils. Results demonstrated that PET-MPs were absorbed by rice roots and translocated to aerial tissues, significantly inhibiting chlorophyll biosynthesis (p < 0.05). Exposure to PET-MPs induced oxidative stress, with the 2.5 g kg[-1] treatment elevating root malondialdehyde levels by 175.3 %, and reducing plant height and biomass by 15.8 % and 44.6 %, respectively. Metagenomic analysis revealed a marked increase in the denitrification gene narI, while genes associated with C fixation (korB, korA), methanogenesis (mch), organic N metabolism (glnA), and P transport (ugpC) were significantly suppressed, indicating disruptions to soil nutrient cycling. Actinomycetota and Pseudomonadota were identified as predominant microbial hosts of these functional genes. Pearson correlation analysis showed significant positive associations (p < 0.05) between plant growth parameters and the abundance of korA, korB, IDH1, mch, glnA, and ugpC. These findings advance our understanding of the ecological risks posed by PET-MPs in terrestrial environments and underscore their potential to compromise soil fertility and sustainable rice production.},
}

@article {pmid41313659,
year = {2025},
author = {Sun, W and Pan, J and Gao, X},
title = {Research on the influence mechanism of low-temperature storage on nitrifying bacteria.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {10},
pages = {1426-1440},
pmid = {41313659},
issn = {0273-1223},
support = {2022JH1/10800006//Science and Technology Program of Guizhou Province/ ; },
mesh = {*Nitrification ; *Bacteria/metabolism/genetics ; Sewage/microbiology ; *Cold Temperature ; Nitrites/metabolism ; Ammonia/metabolism ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; },
abstract = {To develop a more cost-effective nitrogen removal strategy, this study investigated the impact of low-temperature storage methods on nitrifying bacterial activity. Sludge was stored under laboratory-scale static batch conditions in three media: (1) distilled water, (2) nutrient solution, and (3) nutrient solution supplemented with hydroxylamine (NH2OH). Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) activity, sludge properties, and microbial characteristics were examined. Results revealed that all storage methods inhibited both AOB and NOB activity. Notably, nutrient solution storage demonstrated the most significant effect: it suppressed NOB activity by 86.6% and reduced its relative abundance by 20%, while maintaining high extracellular polymeric substance content (43.5 mg/g VSS) and AOB relative abundance (0.18%). This method substantially shortened the required storage duration (from 8 months to 60 days) and better preserved AOB activity and sludge stability. Metagenomic analysis indicated strong inhibition of the NOB functional gene nitrite oxidoreductase across all methods, while nutrient solution storage specifically elevated the abundance of the AMO gene. Although NH2OH supplementation exhibited inhibitory effects on microorganisms, the concurrent addition of nutrient solution effectively mitigated this impact. Consequently, sludge properties and functional microbiota abundance showed no significant difference between the NH2OH-supplemented nutrient solution method and distilled water storage.},
}

*Nitrification
*Bacteria/metabolism/genetics
Sewage/microbiology
*Cold Temperature
Nitrites/metabolism
Ammonia/metabolism
Waste Disposal, Fluid/methods
Oxidation-Reduction

@article {pmid41313651,
year = {2025},
author = {Zhang, Q and Jiang, X and Xi, Y and Ma, X and Zhang, W},
title = {Complete genome sequences of two Cressdnaviricota viruses identified in respiratory tract samples from forest musk deer in China.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063225},
doi = {10.1128/mra.00632-25},
pmid = {41313651},
issn = {2576-098X},
abstract = {We identified two circular single-stranded DNA viruses from forest musk deer in China through metagenomic analysis. Phylogenetic results suggest they represent unclassified Cressdnaviricota lineages. This study highlights the diversity of the deer's respiratory virome and underscores the importance of wildlife virus surveillance for conservation and public health.},
}

@article {pmid41313537,
year = {2025},
author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS},
title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41313537},
issn = {1867-1314},
abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.},
}

@article {pmid41313246,
year = {2025},
author = {Rigonato, J and Lozano, JC and Vergé, V and Jaillon, O and Bouget, FY},
title = {Latitudinal Diversity in Circadian and Light-Sensing Genes in an Ecologically Vital Group of Marine Picoeukaryote Algae.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf263},
pmid = {41313246},
issn = {1751-7370},
abstract = {Organismal life cycles are influenced by Earth's rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms' ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.},
}

@article {pmid41313177,
year = {2025},
author = {Hoque, MN and Rahman, MS},
title = {Bacteriome and resistome dysbiosis in subclinical mastitis and antibiotic-treated milk of dairy cows.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0107025},
doi = {10.1128/mra.01070-25},
pmid = {41313177},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct bacteriome profiles in subclinical mastitis, antibiotic-treated, and healthy cow milk, with enriched resistance repertoires in diseased and treated samples. Findings highlighted the need for better diagnostics, precision antimicrobial use, and antibiotic alternatives to ensure milk safety and address antimicrobial resistance in dairy farming.},
}

@article {pmid41313018,
year = {2025},
author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0086225},
doi = {10.1128/msystems.00862-25},
pmid = {41313018},
issn = {2379-5077},
abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.

IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.},
}

@article {pmid41313013,
year = {2025},
author = {Babb, PL and Akhund-Zade, J and Spacek, D and Brick, K and Christians, FC and Portnoy, V and Tsai, M-S and Jarman, KH and Bercovici, S and Vilfan, ID and Blauwkamp, TA},
title = {In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/jcm.00944-25},
pmid = {41313013},
issn = {1098-660X},
abstract = {Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel microbial biomarkers for disease. However, widespread implementation of this approach is limited by lengthy and complex workflows, high host background cfDNA leading to high sequencing costs, and prevalent environmental DNA contamination risks. Addressing these barriers is critical for scalable deployment in both centralized and decentralized settings. To overcome these limitations, we developed Karius Helion-4 Chemistry (Helion-4), an in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, to serve as a platform for mcfDNA sequencing applications in infectious disease, microbiome analyses, and disease biomarker discovery. We compared Helion-4 to two widely used metagenomic extraction-based sequencing workflows, as well as to the prior Karius chemistry platform (Digital Culture-3), using 36 clinical plasma specimens. Helion-4 enables end-to-end sequencing library construction for up to 96 samples in 5.25-6.1 h, including setup and final quality control evaluation, with 2.25 h of hands-on time when using automated liquid handling robots. Compared to the other methods, Helion-4 recovered 58-fold to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating 1.8-fold to 6-fold lower exogenous background DNA contamination, likely due to the absence of DNA extraction. The fraction of mcfDNA reads among total reads was enriched by 60-fold to 164-fold for Helion-4 compared to current state-of-the-art methods, significantly lowering sequencing costs required for applications built on the Helion-4 platform vs other platforms. Collectively, these advances enable routine processing of small specimen volumes and provide a simple, efficient, and scalable approach for mcfDNA sequencing applications.IMPORTANCEMetagenomic sequencing of microbial cell-free DNA (mcfDNA) enables the identification and quantification of diverse pathogens from blood and other biofluids, providing minimally invasive and rapid diagnosis of deep-seated infectious disease. However, widespread implementation of this approach is limited by complex workflows, high sequencing costs, and prevalent contamination risks. Karius Helion-4 Chemistry, the first in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, overcomes these limitations. Compared to the other methods, Helion-4 is faster, cleaner, and more sensitive. Helion-4 recovered up to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating up to sixfold lower exogenous background DNA contamination. The fraction of mcfDNA reads among total reads was enriched by up to 164-fold for Helion-4, lowering sequencing costs. These advances by Helion-4 technology enable a simple, efficient, and scalable approach for mcfDNA sequencing applications and bring us closer to widespread, high-resolution, and real-time microbial profiling across diverse healthcare settings.},
}

@article {pmid41312992,
year = {2025},
author = {D'Amico González, G and Rodríguez, MM and Penzotti, P and Brunetti, F and Ghiglione, B and Moe, LA and Centrón, D and Gutkind, G and Gao, L and Haider, S and Powers, RA and Klinke, S and Power, P},
title = {Proposal of metagenomic-origin LRA-5 as a precursor of active β-lactamases through Tyr69Gln and Val166Glu amino acid substitutions: a functional and structural analysis.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0067525},
doi = {10.1128/aac.00675-25},
pmid = {41312992},
issn = {1098-6596},
abstract = {Wild-type LRA-5, recovered from Alaskan soil samples, shares no more than 33% amino acid sequence identity with enzymes from pathogens like PER β-lactamases. Recombinant E. coli expressing wild-type LRA-5 and its engineered variants LRA-5[Y69Q] and LRA-5[V166E] showed MIC values equivalent to control strains. However, LRA-5[Y69Q/V166E] displayed MICs above the resistant breakpoint for some β-lactams. Kinetic parameters correlated with the MICs, showing that the catalytic efficiency of LRA-5[Y69Q/V166E] was comparable to those from class A β-lactamases, such as CTX-M-15, PER-2, and KPC-2. LRA-5[Y69Q/V166E] exhibited kcat/Km values up to 11,000-fold higher compared to wild-type LRA-5, which is associated with the presence of Glu166. The X-ray crystallographic structure of wild-type LRA-5 (1.80 Å; PDB 8EO5) shows that the lack of both Glu166 and a deacylation water molecule contributes to a biologically insignificant activity. Interactions observed between LRA-5 and ceftazidime (2.35 Å; PDB 8EO6) show structural conservation with other β-lactamases. In contrast, the crystallographic structure of LRA-5[Y69Q/V166E] (2.15 Å; PDB 8EO7) bears a deacylation water molecule that is associated with the increase in catalytic activity compared to the wild-type variant. Circular dichroism results confirm that amino acid substitutions in LRA-5 do not affect the overall content of the secondary/tertiary structures. Evidence suggests that alternative evolutionary paths could have occurred for β-lactamases like LRA-5, produced by environmental microorganisms: (i) proteins having similar structural features than active β-lactamases may accumulate a small number of mutations (e.g., Y69Q/V166E) to yield active enzymes and (ii) the β-lactamase fold may have lost key residues in the absence of antibiotics.},
}

@article {pmid41312680,
year = {2025},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}

@article {pmid41312645,
year = {2025},
author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC},
title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1283},
pmid = {41312645},
issn = {1362-4962},
support = {DE-AC02-05CH11231//US DOE/ ; FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Hellenic Foundation for Research and Innovation/ ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; },
abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.},
}

@article {pmid41312456,
year = {2025},
author = {Huang, W and Ran, X and Zhang, Z and Yang, L and Yin, J and Lv, S and Liu, G and Pei, Y},
title = {Multiple brain abscesses caused by Nocardia asiatica co-infection with Torque teno virus in an "immunocompetent" patient: a rare case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1661345},
pmid = {41312456},
issn = {2296-858X},
abstract = {Brain abscess is a suppurative infection of brain tissue caused by one or more pathogens under specific susceptible conditions and is associated with a high clinical fatality rate. Beyond surgical intervention, the identification of pathogens is key to clinical antimicrobial therapy, yet this remains a challenge. Nocardia is a ubiquitous bacterium that typically manifests as an opportunistic infection, primarily affecting immunocompromised individuals. Pulmonary involvement, characterized by suppurative inflammation, commonly occurs following inhalation, with subsequent hematogenous dissemination potentially leading to widespread infection. To our knowledge, central nervous system (CNS) infection by Nocardia asiatica (N. asiatica) resulting in brain abscess has hitherto rarely been reported. We present a rare case of multiple brain abscesses caused by N. asiatica co-infection with Torque teno virus (TTV) in an immunocompetent patient with suspected multiple organ involvement. The patient was admitted to our hospital, presenting with a headache, and imaging revealed brain abscess-like lesions. A robot-assisted stereotactic puncture and drainage were used for abscess removal. N. asiatica and TTV were identified by metagenomic next-generation sequencing (mNGS) of the brain abscess aspirate, with N. asiatica subsequently confirmed by mass spectrometry of the cultured organism. A disseminated Nocardia infection was suspected based on the patient's skin trauma history, pulmonary inflammatory changes, and imaging findings (liver cysts, subcutaneous nodules). However, etiological confirmation was not obtained prior to his death. While this is not the first reported instance of Nocardia and TTV co-infection in brain abscesses, our case is notable for its occurrence in an immunocompetent patient. This report highlights the significance and value of TTV in the context of brain abscesses and warrants a re-evaluation of Nocardia and TTV co-infection. Given that the diagnosis of intracranial infection depends on the detection of pathogens, we advocate for the routine and early implementation of mNGS testing in patients with brain abscesses. Moreover, systemic nutritional support and immunomodulatory therapies should be considered in the early stage of treatment for complex cases. Earlier diagnosis and treatment in this case might have altered the patient's outcome.},
}

@article {pmid41312302,
year = {2025},
author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {450},
pmid = {41312302},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).},
}

@article {pmid41312195,
year = {2025},
author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W},
title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5191656},
pmid = {41312195},
issn = {1865-1682},
mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; },
abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.},
}

Animals
Swine
Tibet/epidemiology
*Virome
Phylogeny
*Swine Diseases/virology/epidemiology
Feces/virology
*Viruses/classification/genetics/isolation & purification
Metagenomics
Genetic Variation
*Gastrointestinal Microbiome

@article {pmid41312164,
year = {2025},
author = {Onohuean, H and Nnolum-Orji, NF and Naik Bukke, SP and Abass, KS and Alagbonsi, AI and Choonara, YE},
title = {Non-alcoholic fatty pancreas disease (NAFPD) as a pre-neoplastic niche: Metabolic and inflammatory Gateways to pancreatic ductal adenocarcinoma.},
journal = {Journal of clinical & translational endocrinology},
volume = {42},
number = {},
pages = {100424},
pmid = {41312164},
issn = {2214-6237},
abstract = {Non-alcoholic fatty pancreas disease (NAFPD), marked by ectopic triglyceride accumulation in the exocrine pancreas, is increasingly observed yet its recognition as a cancer-predisposing condition remains limited. We synthesize evidence supporting NAFPD as an early and modifiable niche for pancreatic ductal adenocarcinoma (PDAC), using a PRISMA-ScR-guided framework. The findings were synthesized into three domains: epidemiological risk, metabolic-inflammatory signaling, and immune-stromal remodeling. Mechanisms include palmitate-induced ER stress, ROS-driven NLRP3-IL-1β and STAT5 signaling, and KRAS^G12D-mediated lipotoxicity. Lipid-laden stellate cells promote fibrosis, immunosuppression, and epithelial-mesenchymal transition. NAFPD may represent an early, modifiable PDAC niche, warranting further imaging-omic studies and targeted prevention trials.},
}

@article {pmid41311850,
year = {2025},
author = {Aditya, C and Bukke, SPN and Anitha, K and Meeraraje, P and Goruntla, N and Yadesa, TM and Onohuean, H},
title = {A comprehensive review on diabetic foot ulcer addressing vascular insufficiency, impaired immune response, and delayed wound healing mechanisms.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1622055},
pmid = {41311850},
issn = {1663-9812},
abstract = {Diabetic foot ulcers (DFUs) continue to represent one of the most significant and costly complications related to diabetes mellitus, posing serious challenges to healthcare systems and resulting in considerable morbidity rates. This narrative review explores the complex pathophysiology of DFUs, focusing on the interplay between peripheral neuropathy, vascular insufficiency, and a weakened immune response, all of which contribute to delayed wound healing. Neuropathy leads to a loss of protective sensation, causing unnoticed repetitive injuries, while both microvascular and macrovascular complications reduce tissue perfusion and hinder angiogenesis. Additionally, immune dysfunction and exaggerated inflammatory responses raise the occurrence of infection and negatively affect the healing process. The clinical manifestation, progression, and key risk factors of DFUs were discussed in this review, emphasizing the importance of early detection, careful foot care, and routine screening in individuals who are at risk. Numerous therapeutic approaches are reviewed, including wound debridement, sophisticated wound dressings, offloading techniques, glycemic control, and adjuvant therapies such as growth factor administration, hyperbaric oxygen therapy, and negative pressure wound therapy. For optimal results, a multidisciplinary team combining of vascular surgeons, podiatrists, endocrinologists, and wound care specialists was included. The analysis also points out that promising advancements in bioengineered skin substitutes, intelligent dressings, and regenerative medicine hold promise for the treatment of DFU in the future. Self-monitoring, appropriate footwear, and patient education are all important components of prevention, which remains a fundamental strategy. In the clinical management of DFUs, this narrative review incorporates the most recent research and highlights the value of proactive, customized, and multidisciplinary approaches.},
}

@article {pmid41311501,
year = {2025},
author = {Wu, Q and Hu, S and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Liu, Y and Chen, Y and Gan, M and Zhu, L},
title = {Age-related gut microbiota succession in Neijiang pigs: insights for precision feeding and productivity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698169},
pmid = {41311501},
issn = {1664-302X},
abstract = {OBJECTIVE: To characterize age-related gut microbiota succession in Neijiang pigs and translate these dynamics into actionable insights for precision feeding and productivity improvement.

METHODS: Growth data from 0 to 180 days (n = 16, 780 weight records) were fitted with three non-linear models to determine the optimal growth curve and partition physiological stages. Fresh feces were collected at 25, 70, 110, and 150 days (n = 6/stage). 16S rRNA V3-V4 amplicon sequencing was used to profile microbiota composition and diversity; PICRUSt2 was employed to predict metagenome functions against the KEGG database.

RESULTS: The Gompertz model best described growth (R [2] = 0.996) with an inflection point at 84.2 days (25.9 kg). Microbial alpha-diversity (Shannon, Chao1) increased with age and plateaued after 110 days. Firmicutes and Bacteroidota dominated (>90% relative abundance), whereas Spirochaetota and Euryarchaeota expanded significantly in finishing pigs. LEfSe identified 45 stage-specific biomarkers: Prevotella_9, Collinsella and Blautia characterized suckling-weaning stages; Faecalibacterium and Clostridium_sensu_stricto_1 peaked at 70 days; Lactobacillus was dominant at 110 days; Treponema, Streptococcus and Bacteroides defined the 150-day microbiome. Functional prediction revealed a metabolic shift from basal biosynthesis and DNA repair in early life toward enhanced ABC transporters, bacterial motility proteins, oxidative phosphorylation and methane metabolism in finishing pigs.

CONCLUSION: Our data provide a temporal blueprint of gut microbiota maturation that mirrors host nutrient requirements across growth phases. These microbial indicators and functional signatures can guide stage-specific dietary formulations and microbiota-targeted interventions to improve feed efficiency, reduce environmental emissions and enhance the productivity of indigenous pig breeds.},
}

@article {pmid41311499,
year = {2025},
author = {Wang, J and Su, W and Chen, Q and Zhou, J and Wang, X and Jiang, R and Li, J and Xing, P},
title = {Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1669172},
pmid = {41311499},
issn = {1664-302X},
abstract = {BACKGROUND: Recent studies indicate that microorganisms significantly influence lung cancer pathogenesis. This research explores the variations in microbiota and metabolites in the lower respiratory tract between lung cancer patients and individuals with benign pulmonary lesions to identify potential diagnostic biomarkers.

METHODS: Two hundred eight patients undergoing bronchoscopy at Tianjin Cancer Institute & Hospital and Tianjin Chest Hospital from October 2022 to October 2023 were screened. Ninety-five bronchoalveolar lavage fluid (BALF) was collected for metagenomic sequencing and untargeted metabolomic analysis. Comparisons of microbial diversity, taxonomic composition, and metabolite profiles were conducted between groups with lung cancer and benign lung conditions.

RESULTS: The cohort comprised 70 patients with lung cancer and 25 with benign lung lesions. Patients with lung cancer showed significantly reduced β-diversity (p = 0.005). Predominant microbes in lung cancer cases included Streptococcus, Haemophilus influenzae, and Veillonella parvula. A microbial-based diagnostic model differentiated lung cancer from benign lesions with an AUC of 0.931 (95%CI: 0.916-0.946). Metabolites increased in lung cancer were Citric acid, N-Acetylneuraminic acid, Oxoglutaric acid, and Neopterin, whereas L-Tryptophan, Uridine, 3-Hydroxybutyric acid decreased. The KEGG pathways suggest a significant link between microbial presence and both tumorigenesis and progression.

CONCLUSION: Specific microbial patterns in the lower respiratory tract of lung cancer patients could assist in the auxiliary diagnosis of the disease. The notably altered microorganisms and metabolites in the BALF from lung cancer patients, as opposed to those with benign conditions, correlate with cancer initiation and advancement.},
}

@article {pmid41311484,
year = {2025},
author = {Xu, J and Yao, Y and Pan, L and Zhang, N and Li, D and Chen, X},
title = {Pea-cucumber crop rotation suppresses Fusarium pathogens by reshaping soil microbial communities and enhancing nutrient availability.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1697343},
pmid = {41311484},
issn = {1664-302X},
abstract = {INTRODUCTION: Pea-cucumber rotation combined with straw return as green manure is an environmentally friendly management strategy to suppress cucumber (Cucumis sativus L.) Fusarium wilt (FW) and alleviate continuous cropping obstacles.

METHODS: We evaluated the variations in soil microbial compositions and nutrient levels between long-term cucumber monocropping and pea-cucumber rotation patterns via metagenomic sequencing and determination of soil properties.

RESULTS: The study found that the bacterial communities exhibited marked diversity, whereas the α-diversity of fungal communities was significantly reduced. Based on the relative abundance of differential fungi and bacteria at the genus level, the genus Bacillus showed the highest abundance, with a two-fold increase, whereas Fusarium species exhibited a 4.9-fold reduction following the pea-cucumber rotation. Additionally, the contents of available nitrogen, potassium, and phosphorus in the soil increased by more than 1.3-fold after the rotation. Correlation analysis revealed that the genus Bacillus and available potassium were significantly and negatively correlated with Fusarium pathogens. Notably, the isolated B. pumilus and B. safensis strains significantly suppressed the growth of cucumber FW pathogens.

DISCUSSION: These findings provide valuable insights for optimizing the combination of soil Bacillus populations and nutrient availability to maintain soil ecosystem health and improve cucumber growth and yield.},
}

@article {pmid41311478,
year = {2025},
author = {Zhong, Y and Li, R and E, J and Chi, H and Cao, N and Bai, Z and Du, X and Wang, L},
title = {Effects of maize straw and corncob return on the soil quality and on the soil microbial structures and functions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675172},
pmid = {41311478},
issn = {1664-302X},
abstract = {Straw return is an effective agricultural strategy for incorporating organic carbon into soil organic matter pools through microbial decomposition. This process modifies soil physicochemical properties, thereby altering microbial habitats and resource availability, which can influence the structure and function of soil microbial communities. However, the changes of soil physicochemical properties and microbial communities under different straw incorporation forms remain poorly understood. And how these straw return materials alter soil physicochemical properties and microbial communities within a single cycle. In this study, we conducted straw returning experiments in a maize-producing region of Jilin Province, China, comparing the impact of two distinct maize-derived residues (crushed maize straw and crushed corncob) on soil quality and microbial communities. Our results demonstrated that corncob return more effectively improved key soil physicochemical properties compared to maize straw return. While neither residue significantly alters microbial alpha diversity, both induced shifts in beta diversity. We identified distinct correlations between dominant microbial taxa and key soil physicochemical parameters. Furthermore, KEGG and GO analyses revealed that both of the residues altered microbial functional hierarchies, with corncob return inducing more pronounced changes than maize straw return. These findings provide a mechanistic basis for optimizing straw management strategies to enhance microbial-mediated soil fertility.},
}

@article {pmid41311042,
year = {2025},
author = {Choi, JH and Oh, S and Yi, MH and Kang, D and Choi, DY and Chavarria, X and Shatta, A and Cho, YH and Choe, S and Lee, SH and Kim, JY},
title = {Detection of intestinal parasites in leopard cat fecal samples using shotgun metagenomics.},
journal = {Parasites, hosts and diseases},
volume = {63},
number = {4},
pages = {349-353},
doi = {10.3347/PHD.25032},
pmid = {41311042},
issn = {2982-6799},
support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; RS-2023-KH139971//Ministry of Health and Welfare/ ; },
mesh = {Animals ; *Feces/parasitology ; *Metagenomics/methods ; *Intestinal Diseases, Parasitic/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 18S/genetics ; *Panthera/parasitology ; *Parasites/isolation & purification/genetics/classification ; *Felidae/parasitology ; Cats ; },
abstract = {The leopard cat (Prionailurus bengalensis) is a wild felid species that serves as a reservoir of zoonotic parasites. In this study, we investigated intestinal parasite taxa by reanalyzing previously published shotgun metagenomic sequencing data from fecal samples of wild leopard cats using a custom 18S rRNA gene reference database constructed from the NCBI nucleotide database. Among 11 metagenomic samples, 5 parasite species were identified: Toxoplasma gondii, Clonorchis sinensis, Strongyloides planiceps, Cylicospirura petrowi, and Pharyngostomum cordatum. These findings demonstrate that shotgun metagenomic analysis of fecal samples can be a useful tool for monitoring zoonotic parasite infections in this species and for investigating parasite life cycles. However, this approach is limited by its dependence on existing reference databases and requires experimental validation of the findings.},
}

Animals
*Feces/parasitology
*Metagenomics/methods
*Intestinal Diseases, Parasitic/veterinary/parasitology/diagnosis
RNA, Ribosomal, 18S/genetics
*Panthera/parasitology
*Parasites/isolation & purification/genetics/classification
*Felidae/parasitology
Cats

@article {pmid41310806,
year = {2025},
author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J},
title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {248},
pmid = {41310806},
issn = {2049-2618},
support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.

RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.

CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology
*Gastrointestinal Microbiome
Metagenomics/methods
Metagenome
*Bacteroides/metabolism/genetics/classification
*Bacteria/classification/metabolism/genetics
Fatty Acids, Volatile/metabolism
Escherichia coli/metabolism/genetics

@article {pmid41310797,
year = {2025},
author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.},
journal = {Radiation oncology (London, England)},
volume = {20},
number = {1},
pages = {179},
pmid = {41310797},
issn = {1748-717X},
support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; },
mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; },
abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.

METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72 h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.

RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p < 0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4 + T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5⁺ intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.

CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.},
}

Animals
Mice
Female
Mice, Inbred C57BL
*Colonic Neoplasms/radiotherapy/pathology
*Intestines/radiation effects
X-Rays
Metabolomics/methods
Gastrointestinal Microbiome/radiation effects
Multiomics

@article {pmid41310780,
year = {2025},
author = {Liu, Y and Brinkhoff, T and Simon, M},
title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {247},
pmid = {41310780},
issn = {2049-2618},
support = {TRR51//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Roseobacter/genetics/classification/isolation & purification ; Phylogeny ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; Phylogeography ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA ; Genome, Bacterial ; },
abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.

RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for ~ 70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of < 2.9 Mbp and G + C contents of < 40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.

CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.},
}

*Roseobacter/genetics/classification/isolation & purification
Phylogeny
Oceans and Seas
RNA, Ribosomal, 16S/genetics
*Seawater/microbiology
Phylogeography
DNA, Bacterial/genetics
Metagenomics/methods
Sequence Analysis, DNA
Genome, Bacterial

@article {pmid41310694,
year = {2025},
author = {Liu, P and Deng, Z and Wang, Y and Wu, F and Peng, J and Huang, P and Wang, Y and Lao, J},
title = {Application of Probe-Capture metagenomics in rabies diagnosis.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-025-03029-6},
pmid = {41310694},
issn = {1743-422X},
support = {82460480//National Natural Science Foundation of China/ ; 20223638//Qinzhou Scientific Research and Technology Development Program/ ; 2024GXNSFAA010067//Guangxi Natural Science Foundation/ ; },
abstract = {BACKGROUND: Rabies, a lethal viral encephalitis caused by Rabies virus (RabV), is transmitted via bites, scratches, or mucosal contact with infected animals, as well as through inhalation of aerosolized particles, ingestion of contaminated raw animal products, or transplantation of infected organs. It's near-universal fatality, diverse transmission routes, and marked clinical variability significantly impede timely diagnosis, highlighting the demand for a rapid and precise diagnostic approach.

METHODS: Single-center retrospective case series.

RESULTS: This series reported three rabies cases admitted to the First People's Hospital of Qinzhou: one without identifiable exposure and two with confirmed exposure histories. Clinical presentations were highly variable and diagnostically misleading. Application of Probe-Capture Metagenomics (pc-mNGS) to cerebrospinal fluid and blood samples enabled direct identification of RabV and concurrent detection of coexisting pathogens.

CONCLUSION: pc-mNGS demonstrates potential as a rapid, economical diagnostic tool capable of detecting RabV in specimens with low viral loads-such as blood and cerebrospinal fluid-from both exposed and unexposed individuals. Simultaneous identification of additional pathogens further supports its diagnostic utility.},
}

@article {pmid41310465,
year = {2025},
author = {Bae, J and Han, JW and Song, JY and Nam, SH and Sung, JS and Ko, HC and Kim, SH and Lee, YJ},
title = {Targeted elimination of latent endophytes improves cryopreservation success in in vitro grapevine (Vitis vinifera) cultures.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07821-y},
pmid = {41310465},
issn = {1471-2229},
support = {PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; },
abstract = {BACKGROUND: Latent endophytic bacteria are common in grapevine in vitro cultures and, while not always causing visible culture decline, can negatively affect downstream applications such as cryopreservation by reducing post-thaw recovery. While antibiotic treatments are widely used for microbial control, their efficacy varies with bacterial species, plant genotype, and application conditions. Few studies have directly linked targeted elimination of identified endophytes with improved post-cryopreservation recovery.

RESULTS: In this study, we identified Leifsonia poae in 'Ruby Seedless' and Curtobacterium oceanosedimentum in 'Merlot' using 16 S rRNA sequencing. Species-specific antibiotic susceptibility testing revealed rifampicin (minimum bactericidal concentration, MBC = 31 µg mL⁻¹) as effective against L. poae, and cefotaxime (MBC = 1000 µg mL⁻¹) as effective against C. oceanosedimentum. In vitro application of these antibiotics eliminated the respective endophytes without significant phytotoxic effects at optimal concentrations. Amplicon-based 16 S metagenomic profiling confirmed complete removal of the target bacteria and revealed substantial shifts in community composition, with reduced abundance of dominant taxa but maintenance of overall endophytic diversity. Cryopreservation experiments in 'Ruby Seedless' showed that removal of endophytes increased post-thaw survival from 31.8 to 70.9% and eliminated variability in regrowth across replicates.

CONCLUSIONS: This study demonstrates that targeted antibiotic elimination of dominant endophytes can restructure the in vitro microbial community and substantially improve cryopreservation outcomes in grapevine. The approach offers a reproducible sanitation strategy for clonal crops vulnerable to endophyte-related culture failures and can be readily adapted for germplasm conservation programs.},
}

@article {pmid41310455,
year = {2025},
author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X},
title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04562-8},
pmid = {41310455},
issn = {1471-2180},
support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; 20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; },
abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.},
}

@article {pmid41310063,
year = {2025},
author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM},
title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29138-4},
pmid = {41310063},
issn = {2045-2322},
support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; },
abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.},
}

@article {pmid41309890,
year = {2025},
author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E},
title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42423},
pmid = {41309890},
issn = {2045-2322},
support = {100217/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; },
abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Metagenomics/methods
Feces/microbiology
Metagenome
Male
*Bacteria/genetics/classification
Female
Adult

@article {pmid41309644,
year = {2025},
author = {Qiu, D and Wang, Y and Xu, N and Chen, B and Zhu, Y and Zhang, Z and Zhang, Q and Lu, T and Dong, H and Shou, J and Qian, H},
title = {Global variation in plant-beneficial bacteria in soil under pesticide stress.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10685},
pmid = {41309644},
issn = {2041-1723},
support = {42377107//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22376187//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Soil/chemistry ; *Soil Pollutants/toxicity ; Agriculture ; Metagenomics ; Crops, Agricultural/microbiology/growth & development ; },
abstract = {The presence of plant-beneficial bacteria (PBB) in soil significantly affects crop production. Excessive agrochemical use in intensive agriculture causes substantial soil residue accumulation, compromising soil health, crop quality, and human health. Understanding changes in beneficial bacteria under pesticide pollution is crucial for guiding sustainable agricultural practices and promoting soil health. We analyze metagenomic data from 1919 soil samples to identify 364 PBBs. We find higher PBB diversity in agricultural soils than in non-agricultural soils; however, pesticide pollution negatively affects the abundance of PBB, particularly those with plant growth-promoting traits. Pesticides not only reduce PBB diversity as individual factors, but they also exert synergistic negative effects with other anthropogenic factors, as determined by Hedges'd effect size and 95% confidence intervals, further accelerating the decline in PBB diversity. Increased pesticide risk also leads to a loss of functional gene diversity in PBB about carbon and nitrogen cycling within essential nutrient cycles, and a reduction in specific amino acid and vitamin synthesis. Artificial application of specific amino acids and vitamins could be an effective strategy to restore PBB in high-pesticide-risk soils. This study provides guidance for regulating pesticide use to mitigate their negative effects on soil PBB and suggests potential remedial measures.},
}

*Soil Microbiology
*Pesticides/toxicity
*Bacteria/genetics/drug effects/classification/isolation & purification
Soil/chemistry
*Soil Pollutants/toxicity
Agriculture
Metagenomics
Crops, Agricultural/microbiology/growth & development

@article {pmid41309591,
year = {2025},
author = {Zhou, N and Li, Q and Liang, Z and Yu, K and Zhang, C and Wang, H and Li, P and He, Z and Wang, S},
title = {Microbially-mediated halogenation and dehalogenation cycling of organohalides in the ocean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10670},
pmid = {41309591},
issn = {2041-1723},
mesh = {*Halogenation ; Oceans and Seas ; *Seawater/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Phylogeny ; Archaea/genetics/metabolism/classification ; Molecular Docking Simulation ; *Hydrocarbons, Halogenated/metabolism ; },
abstract = {Microbially mediated organohalide cycling in the ocean has profound implications for global biogeochemical cycles and climate, but the geographic distribution and diversity of the halogenation-dehalogenation cycling microorganisms remain unknown. Here, we constructed an organohalide-cycling gene database (HaloCycDB) to explore the global atlas of halogenation-dehalogenation cycling microorganisms and genes from 1473 marine metagenomes. Strikingly, 6204 out of 15,252 metagenome-assembled genomes (MAGs) carry organohalide-cycling genes, of which 84.30% are dehalogenating populations. Microorganisms of Pseudomonadota with even spatial distribution dominate both halogenation and dehalogenation potentials in the ocean, in contrast to lineages of Asgardarchaeota and Thermoproteota solely mediating dehalogenation in the Northern hemisphere. Notably, 80.91% of reductive dehalogenase (RDase) genes and 91.35% of RDase-containing prokaryotes represent uncharacterized lineages, substantially expanding known dehalogenation diversity. Further integration of microbial cultivation, protein structure prediction, and molecular docking revealed four unique "microorganism-RDase-organohalide" patterns for marine dehalogenation and its coupling with carbon/sulfur cycles, being distinctively different from their terrestrial patterns. These results advance our understanding of microbial organohalide cycling by providing insights into the halogenation-dehalogenation microbiomes in the ocean.},
}

*Halogenation
Oceans and Seas
*Seawater/microbiology
Metagenome
*Bacteria/genetics/metabolism/classification
Phylogeny
Archaea/genetics/metabolism/classification
Molecular Docking Simulation
*Hydrocarbons, Halogenated/metabolism

@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
doi = {10.4014/jmb.2506.06014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}

*Probiotics/pharmacology
*Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Humans
Fermentation
*Feces/microbiology
*Metabolome
Inflammatory Bowel Diseases/microbiology
Bifidobacterium/metabolism
Lactobacillus/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Streptococcus/metabolism

@article {pmid41309042,
year = {2025},
author = {Lin, QB and Xiao, S and Sheng, YZ and Shen, YX and He, Y and Liu, HY and Ye, YW and Chen, SD},
title = {Case report: Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma with eosinophilia diagnosed via exclusion using metagenomic next-generation sequencing.},
journal = {The Journal of international medical research},
volume = {53},
number = {11},
pages = {3000605251399037},
doi = {10.1177/03000605251399037},
pmid = {41309042},
issn = {1473-2300},
mesh = {Humans ; Male ; *Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology ; *High-Throughput Nucleotide Sequencing ; *Lung Neoplasms/diagnosis/genetics/pathology/complications ; Adult ; *Eosinophilia/diagnosis/genetics/complications/pathology ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Bronchoscopy ; Bronchoalveolar Lavage Fluid ; },
abstract = {Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma (MALToma) is a slow-growing lymphoma often misdiagnosed or undiagnosed due to its nonspecific clinical symptoms. A man in his late 30s initially presented with cough, sputum production, and chest pain, which improved after antibiotic treatment. A definitive diagnosis of pulmonary MALToma was established via bronchoscopic biopsy. Following the exclusion of alternative diagnoses through metagenomic next-generation sequencing of bronchoalveolar lavage fluid, the marked eosinophilia and diverse chest computed tomography findings highlight the need for clinical awareness of this disease.},
}

Humans
Male
*Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology
*High-Throughput Nucleotide Sequencing
*Lung Neoplasms/diagnosis/genetics/pathology/complications
Adult
*Eosinophilia/diagnosis/genetics/complications/pathology
*Metagenomics/methods
Tomography, X-Ray Computed
Bronchoscopy
Bronchoalveolar Lavage Fluid

@article {pmid41308933,
year = {2025},
author = {Yue, J and Han, X and Yu, J},
title = {Multi-omics insights into ultra-rapid formation of aerobic granular sludge in 9 % salinity wastewater by filling of halotolerant loose mycelial pellets.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133705},
doi = {10.1016/j.biortech.2025.133705},
pmid = {41308933},
issn = {1873-2976},
abstract = {Salt-tolerant aerobic granular sludge (SAGS) had great potential in ultra-hypersaline wastewater treatment while slow and unstable formation hindered its application. Mycelial pellets (MPs) inoculation strategy could accelerate SAGS formation but collapse or peeling commonly occurred due to dense hyphal structures hindering microbial colonization in the connection layer between the shell and core. Besides, no MPs were reported to maintain structure under ultra-hypersaline environment. Herein, a novel strategy using newly-isolated ultra-high salt tolerant fungi Penicillium steckii NCSL-JXA6 with a loose MPs structure was applied for AGS start-up in 9 % salinity wastewater. Granulation completed on Day 1 and maintained stable for 97 days (D10 & D50 > 200 μm, SVI30/SVI5 = 1), which was the fastest under similar salinity. SEM and stained cross-sectional slides showed the loose MPs structure allowed early inner microbial colonization and dense connection layer and core formed before hyphae collapsed, enabling stable transition within 27 days without fragmentation or peeling. Extracellular polymeric substances (EPS) and acyl-homoserine lactone signals (AHLs) (mainly PN, C8-HSL, C12-HSL) increased during transition period, supporting rapid microbial colonization. High TOC and TN removal (∼93 % and ∼ 82 %, respectively) was obtained within only 5 days. Metaproteomic analysis identified Penicillium as module hub of community. Integrative metagenomics and metaproteomics revealed upregulated colonization-related pathways and further confirmed that Penicillium steckii NCSL-JXA6 probably facilitated microbial colonization through metabolic complementarity, adhesion sites, and a loose hyphal structure easily enabling bacterial sensing, motility, adhesion, and biofilm construction. This study proposed a novel loose MPs inoculation theory and achieved the fastest SAGS formation in ultra-hypersaline wastewater.},
}

@article {pmid41308930,
year = {2025},
author = {Wang, S and Dai, B and Wang, Z and Yang, S and Xia, S and Rittmann, BE},
title = {S[0] powder as biofilm carrier and electron donor enhances autotrophic nitrogen removal in sulfur-driven partial denitrification coupled with anammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133707},
doi = {10.1016/j.biortech.2025.133707},
pmid = {41308930},
issn = {1873-2976},
abstract = {Sulfur-driven partial denitrification coupled with anammox (SPD/A) has been proposed as an innovative strategy for nitrogen removal from wastewater. This study proposes a novel strategy that integrates 20-μm S[0] powders with anammox granules to establish S[0]-driven partial denitrification coupled with anammox (i.e., S[0]PD/A) for the simultaneous removal of NH4[+] and NO3[-] from wastewater. When the influent concentrations of NH4[+] and NO3[-] were maintained at 31 and 52 mg-N/L, respectively, the efficiency of total-nitrogen removal reached 92 %, with anammox, S[0]-driven denitrification, and sulfammox accounting for 71 %, 27.4 %, and 1.6 %, respectively. Microbial community analysis revealed that anammox bacteria and sulfur-oxidizing bacteria were dominant functional genera involved in the S[0]PD/A. Anammox bacteria were enriched in anammox granules, and sulfur-oxidizing bacteria were enriched in microgranules of S[0] powders and Candidatus Brocadia. These findings highlight distinct microbial niche differentiation, elucidate nitrogen-sulfur metabolic interactions, and offer insights into an autotrophic process for total-nitrogen removal.},
}

@article {pmid41308739,
year = {2025},
author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S},
title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.056},
pmid = {41308739},
issn = {2090-1224},
abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.

OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.

METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography‒mass spectrometry (LC‒MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.

RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-κB/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.

CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-κB/NLRP3 signaling pathway and inhibiting acinar cell inflammation.},
}

@article {pmid41308447,
year = {2025},
author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H},
title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140613},
doi = {10.1016/j.jhazmat.2025.140613},
pmid = {41308447},
issn = {1873-3336},
abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.},
}

@article {pmid41308344,
year = {2025},
author = {Mao, YL and Hu, Y and Wu, ZP and Sun, YP and Hou, J and Cui, HL},
title = {Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126680},
doi = {10.1016/j.syapm.2025.126680},
pmid = {41308344},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains, DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T], were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus Natronorubrum judged by 16S rRNA gene and rpoB' gene sequence similarities, and formed tight clusters with current Natronorubrum species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and rpoB' genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus Natronorubrum were 76.8-92.7 %, 22.8-52.7 %, and 73.4-94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7-3.1 M NaCl, 37 °C, and pH 7.0-9.5. Strain WLHS9[T] was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9[T] was identical to that of the current neutrophilic species of Natronorubrum. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T] represent four novel species within the genus, namely, Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., respectively.},
}

@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02595-0},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}

@article {pmid41307551,
year = {2025},
author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H},
title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf212},
pmid = {41307551},
issn = {1745-1701},
support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.

STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.

STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.

CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.},
}

@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.

METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3 months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.

RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.

CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

@article {pmid41306993,
year = {2025},
author = {Cai, X and Yi, H and Chen, K and Dai, J and Yi, J and Tu, B and Wang, Y and Li, J and Zhuang, J},
title = {Meta-Analysis of the Application Value of Metagenomic Next-Generation Sequencing Technology in the Diagnosis of Infectious Diseases of the Spine.},
journal = {JOR spine},
volume = {8},
number = {4},
pages = {e70134},
pmid = {41306993},
issn = {2572-1143},
abstract = {OBJECTIVE: To evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in infectious diseases of the spine (IDS).

METHODS: Systematic literature on the application of mNGS in the diagnosis of IDS was retrieved by two independent researchers from databases including Pubmed, China National Knowledge Infrastructure (CNKI), Wanfang, and VIP from the inception to 30 November 2024. Meta-analysis was conducted using Meta-Disc 1.4 and Stata 18.0 software.

RESULTS: The initial search identified 314 articles. After applying predefined inclusion and exclusion criteria, 15 studies were included, encompassing 1236 patients, of which 835 had confirmed IDS. Meta-analysis revealed that the pooled sensitivity and specificity of mNGS for IDS diagnosis were 0.95 (95% CI: 0.88-0.98) and 0.60 (95% CI: 0.48-0.71), respectively. The positive likelihood ratio was 2.3 (95% CI: 1.7-3.2), and the negative likelihood ratio was 0.09 (95% CI: 0.04-0.22). The pooled diagnostic odds ratio was 26 (95% CI: 9-75), with an area under the summary receiver operating characteristic curve of 0.85 (95% CI: 0.82-0.88).

CONCLUSION: The primary diagnostic value of mNGS lies in its ability to serve as a rapid screening tool for disease exclusion. However, for diagnosing IDS, it is essential to integrate other clinical indicators for a comprehensive assessment to confirm the diagnosis.},
}

@article {pmid41306730,
year = {2025},
author = {Nielsen, AB and Kvist-Hansen, A and Todberg, T and Zachariae, C and Pedersen, O and Skov, L},
title = {Dysbiosis of the Saliva Microbiota in Patients with Psoriasis: A Case-Control Study.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16315-16330},
pmid = {41306730},
issn = {1178-7031},
abstract = {PURPOSE: Accumulating evidence supports the association between altered salivary microbiota and inflammatory diseases. The existing literature on the salivary microbiota in patients with psoriasis is limited. However, differences in the prevalence of Candida species and abundance of several bacterial taxa in saliva have been found between patients and controls. This study aimed to investigate the differences in the composition and functional potential of salivary microbiota in patients with psoriasis compared to their cohabiting partners and healthy controls.

PATIENTS AND METHODS: Samples from 115 of 123 individuals qualified for statistical analysis: patients with psoriasis who did not receive systemic anti-psoriatic treatment (n=47); cohabiting partners (n=21); and age-, sex-, and BMI-matched healthy controls (n=47). One saliva sample was collected from each participant and analysed by shotgun metagenomic sequencing.

RESULTS: A difference in the α-diversity of bacterial species was observed exclusively between patients and controls, with a lower diversity in patients (p=0.041). Variation in bacterial composition (β-diversity) was influenced by smoking (p=0.001) and diet (p=0.025) but not by group status. Using a linear regression model adjusted for smoking and diet, we identified four bacterial classes and five species that were significantly different between the patient, partner, and control groups. One Kyoto Encyclopedia of Genes and Genomes module differed significantly between patients with psoriasis and their partners. No differences in Candida species or abundance were found among the three groups.

CONCLUSION: Comparison of salivary microbiota at the levels of bacterial diversity, composition, and predicted function indicated that psoriasis cases are characterised by dysbiosis.},
}

@article {pmid41306593,
year = {2025},
author = {Xu, H and Xu, Y and Gu, J and Wang, X and Liao, B and Zhou, P and Wu, S and Tao, R and Fu, Y},
title = {Clinical characteristics of Treponema denticola-associated lung abscess diagnosed by metagenomic next-generation sequencing: a case series analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688498},
pmid = {41306593},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Treponema denticola/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing ; *Lung Abscess/microbiology/diagnosis/drug therapy ; Retrospective Studies ; Female ; Aged ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; *Treponemal Infections/diagnosis/microbiology/drug therapy ; Adult ; },
abstract = {INTRODUCTION: Treponema denticola is an oral anaerobic bacterium commonly associated with periodontitis, but its role in lower respiratory tract infections (e.g., lung abscess) has long been overlooked. For bacteria that grow anaerobically, traditional culture methods exhibit low detection rates, which directly lead to the mis-diagnosis of anaerobic infection. With the ultilization of metagenomic next-generation sequencing (mNGS) in clinical practice, we studied the clinical features and treatment strategies of T. denticola-associated lung abscess.

METHODS: A retrospective analysis was conducted on patients confirmed with T. denticola lung abscess by mNGS from October 2023 to October 2024. Routine aerobic bacterial culture and stains were used. Histopathological analysis and Warthin-Starry silver staining was completed on samples from lung tissue. A literature review was performed using PubMed and CNKI (up to June 2025).

RESULTS: Seven patients were diagnosed with T. denticola lung abscess under mNGS. The cohort predominantly comprised elderly males (mean age 62.3 years), all of whom had underlying oral diseases. Clinical manifestations featured chronic cough (mean symptom duration 3.6 months) and frequent hemoptysis (85.7%), with notably mild systemic inflammation (only one febrile case). Characteristic CT findings included mass-like lesions with necrosis (100%) and cavitation (71.4%), without air-fluid levels. Conventional cultures were overwhelmingly negative, whereas mNGS detected T. denticola in all seven cases. Among the seven patients, one showed clinical improvement after two months of amoxicillin-clavulanate therapy, and another responded well to seven months of doxycycline treatment. The remaining five patients initially treated with levofloxacin or moxifloxacin demonstrated poor responses, with three cases ultimately requiring surgical resection of the lesions.

DISCUSSION: T. denticola lung abscess is most commonly seen in individuals with poor oral hygiene. It presents as an indolent, chronic course and a high incidence of hemoptysis. Typical CT findings include a mass-like lesion with cavitation but no air-fluid level. Traditional microbiological detection often yield false negative results, making mNGS a critical diagnostic tool. First-line therapy should include β-lactams or tetracyclines, and surgery is warranted for refractory cases or massive hemoptysis.},
}

Humans
Male
Middle Aged
*Treponema denticola/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing
*Lung Abscess/microbiology/diagnosis/drug therapy
Retrospective Studies
Female
Aged
Metagenomics/methods
Anti-Bacterial Agents/therapeutic use
*Treponemal Infections/diagnosis/microbiology/drug therapy
Adult

@article {pmid41306589,
year = {2025},
author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H},
title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1708266},
pmid = {41306589},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation & purification ; *Murinae/microbiology ; },
abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.

METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.

RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.

CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.},
}

Animals
*Enterocytozoon
*Gastrointestinal Microbiome/genetics
Metagenomics
*Microsporidiosis/microbiology/veterinary
Feces/microbiology
Mice
China
Animals, Wild/microbiology
Virome
Bacteria/classification/genetics/isolation & purification
*Murinae/microbiology

@article {pmid41306406,
year = {2025},
author = {Hongbin, W and Jing, X and Xianwei, W and Hui, G and Xutao, F},
title = {Successful Treatment of Escherichia coli-Related Spondylitis With an Extended Meropenem Infusion Time for a 72-Year-Old Woman: A Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71531},
pmid = {41306406},
issn = {2050-0904},
abstract = {Escherichia coli (E. coli) causes spinal infections relatively rarely and is often closely associated with parenteral infections. E. coli spondylitis can cause fever and local pain and, in severe cases, can lead to bone destruction, abscess formation, and even the risk of high paraplegia. Therefore, timely and precise diagnosis and effective treatment are crucial. We report successful conservative management of E. coli spondylitis in a 72-year-old female using metagenomic sequencing-guided prolonged meropenem infusion. Extending the infusion time of meropenem achieved clinical resolution without surgery, demonstrating this strategy's efficacy for carbapenem-sensitive spinal infections.},
}

@article {pmid41306274,
year = {2025},
author = {Xue, N and Xia, M and Hu, B and Gong, X and Wang, Z and Zhao, X},
title = {Factors influencing the spatial distributions of river microbial communities at the watershed scale: a case study involving the Wuding River Basin.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667966},
pmid = {41306274},
issn = {1664-302X},
abstract = {Microbial communities regulate water quality and biogeochemical cycling in rivers, but their responses to geomorphological factors remain unclear. Water samples were collected in August 2024 (summer wet season) from the Wuding River, and metagenomic sequencing was used to investigate microbial community changes and the influences of geomorphological factors. Environment (nutrients, etc.,) exhibited significant spatial heterogeneity with temperature (p < 0.01), total organic carbon (TOC, p < 0.001), dissolved organic carbon (DOC, p < 0.001), chemical oxygen demand (COD, p < 0.05), total phosphorus (TP, p < 0.001) and suspended solids (SS, p < 0.001), which were significantly higher downstream than upstream. Pseudomonadota, Cyanobacteriota, and Actinomycetota were the most important microbial phyla, and Cyanobacteriota (p = 0.016) was significantly more abundant upstream than downstream. The linear discriminant analysis effect size (LEfSe) revealed 8 and 10 biomarkers upstream and downstream, respectively. Upstream microbial communities were adapted to oligotrophic and high-light environments, whereas heterotrophic, carbon-metabolizing communities occurred downstream. Significantly higher ACE (p < 0.05), Chao1 (p < 0.05), Shannon (p < 0.001), and Pielou's evenness (p < 0.001) indices were observed downstream than upstream. The relative abundance of genes associated with carbon cycling (the methane metabolism pathway, TCA cycle, and rTCA cycle) was greater downstream than upstream, as was the relative abundance of nitrogen functional genes. Elevation affected the upstream microbial communities, whereas temperature, TP, TOC, and nitrate nitrogen (NO3-N) affected the downstream communities. The results improve our understanding of how geomorphology drives the environmental factors and then governs the microbial community and their carbon and nitrogen cycling pathways.},
}

@article {pmid41306264,
year = {2025},
author = {Shi, Y and Wang, X and Mao, X and Mi, L and Liu, W and Wang, N},
title = {Severe mitral valve papillary muscle rupture of isolated Whipple's endocarditis: a case report and review of the literature.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1669997},
pmid = {41306264},
issn = {2297-055X},
abstract = {BACKGROUND: Tropheryma whipplei endocarditis (TWE) is rarely reported. Diagnosis is particularly challenging when it occurs as isolated TWE without classical manifestations of Whipple's disease.

CASE PRESENTATION: A 35-year-old Asian female with systemic lupus erythematosus presented with acute heart failure secondary to mitral valve papillary muscle rupture as her sole symptom, requiring emergent veno-arterial extracorporeal membrane oxygenation support and urgent valve replacement. Intraoperative absence of vegetations and negative conventional microbiological examination preliminarily ruled out infective endocarditis. However, on postoperative day (POD) 3, her condition rapidly deteriorated into septic shock. Follow-up chest CT revealed bilateral asymmetric pulmonary infiltrates inconsistent with cardiogenic pulmonary edema alone. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected T. whipplei, providing a crucial diagnostic breakthrough. Subsequent periodic acid-Schiff staining of the resected valve confirmed the definitive diagnosis of isolated TWE. Targeted meropenem therapy for 5 days resulted in significant improvement in both pneumonia and septic shock, permitting ECMO discontinuation. The patient was successfully extubated by POD 12 and discharged on POD 22 with oral co-trimoxazole and doxycycline in a stable condition.

CONCLUSION: We present the first case of isolated TWE in a young Asian female, notable for its atypical clinical presentation, fulminant progression, and profound diagnostic challenges. Clinicians should maintain a high vigilance for blood culture-negative endocarditis. Timely diagnosis and appropriate treatment are crucial for improving prognosis. mNGS analysis of samples from suspected disseminated sites may yield crucial diagnostic breakthrough.},
}

@article {pmid41305954,
year = {2025},
author = {Osei Sekyere, J},
title = {Next-Generation Sequencing in Infectious-Disease Diagnostics: Economic, Regulatory, and Clinical Pathways to Adoption.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70104},
doi = {10.1002/mbo3.70104},
pmid = {41305954},
issn = {2045-8827},
support = {//The author received no specific funding for this study./ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/economics/methods ; *Communicable Diseases/diagnosis ; *Molecular Diagnostic Techniques/economics/methods ; Whole Genome Sequencing/economics/methods ; Polymerase Chain Reaction/economics/methods ; },
abstract = {Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well-established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS-based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole-genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent-only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130-600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near-term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious-disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype-phenotype limits while leveraging multiplexing and centralized reference workflows.},
}

Humans
*High-Throughput Nucleotide Sequencing/economics/methods
*Communicable Diseases/diagnosis
*Molecular Diagnostic Techniques/economics/methods
Whole Genome Sequencing/economics/methods
Polymerase Chain Reaction/economics/methods

@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}

Humans
*Saliva/microbiology
*Obesity/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
*Mouth/microbiology
Male
Female
Biomarkers/analysis
Middle Aged
Adult
Dental Plaque/microbiology
*Bacteria/isolation & purification/classification/genetics
Metagenome

@article {pmid41305529,
year = {2025},
author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W},
title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111508},
pmid = {41305529},
issn = {1999-4915},
support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; },
abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Metagenomics
*Crows/virology
*Gastrointestinal Microbiome
*Virome
*Birds/virology
Genome, Viral
Tibet
Genetic Variation

@article {pmid41305512,
year = {2025},
author = {Storms, S and Lim, A and Savard, C and Olivera, YR and Kayastha, S and Wang, L},
title = {Identification of Hunnivirus in Bovine and Caprine Samples in North America.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111491},
pmid = {41305512},
issn = {1999-4915},
support = {1U18FD006673//Food and Drug Administration Veterinary Laboratory Investigation and Response Network/ ; },
mesh = {Animals ; Cattle ; Goats/virology ; Phylogeny ; Feces/virology ; Genome, Viral ; *Cattle Diseases/virology ; North America/epidemiology ; *Goat Diseases/virology ; High-Throughput Nucleotide Sequencing ; *Diarrhea/veterinary/virology ; Sheep ; Metagenomics ; },
abstract = {Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D[pol] RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D[po] region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants.},
}

Animals
Cattle
Goats/virology
Phylogeny
Feces/virology
Genome, Viral
*Cattle Diseases/virology
North America/epidemiology
*Goat Diseases/virology
High-Throughput Nucleotide Sequencing
*Diarrhea/veterinary/virology
Sheep
Metagenomics

@article {pmid41305373,
year = {2025},
author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH},
title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111136},
pmid = {41305373},
issn = {2076-0817},
support = {ĐTĐLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation & purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; },
abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
*Diarrhea/microbiology
Male
Female
Feces/microbiology
Child, Preschool
RNA, Ribosomal, 16S/genetics
Prospective Studies
*Bacteria/classification/genetics/isolation & purification
Vietnam
Biodiversity
DNA, Bacterial/genetics
Metagenomics/methods
Southeast Asian People

@article {pmid41304932,
year = {2025},
author = {Hasan, GM and Mohammad, T and Shamsi, A and Sohal, SS and Hassan, MI},
title = {Applications of Genome Sequencing in Infectious Diseases: From Pathogen Identification to Precision Medicine.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/ph18111687},
pmid = {41304932},
issn = {1424-8247},
support = {PSAU/2025/RV/7//Prince Sattam Bin Abdulaziz University/ ; },
abstract = {Background: Genome sequencing is transforming infectious-disease diagnostics, surveillance, and precision therapy by enabling rapid, high-resolution pathogen identification, transmission tracking, and genomic-informed antimicrobial stewardship. Methods: We review contemporary sequencing platforms (short- and long-read), targeted and metagenomic approaches, and operational workflows that connect laboratory outputs to clinical and public health decision-making. We highlight strengths and limitations of genomic AMR prediction, the role of plasmids and mobile elements in resistance and virulence, and practical steps for clinical translation, including validation, reporting standards, and integration with electronic health records. Results: Comparative and population genomics reveal virulence determinants and host-pathogen interactions that correlate with clinical outcomes, improving risk stratification for high-risk infections. Integrating sequencing with epidemiological and clinical metadata enhances surveillance, uncovers cryptic transmission pathways, and supports infection control policies. Despite these advances, clinical implementation faces technical and interpretative barriers, as well as challenges related to turnaround time, data quality, bioinformatic complexity, cost, and ethical considerations. These issues must be addressed to realize routine, point-of-care sequencing. Conclusions: Emerging solutions, including portable sequencing devices, standardized pipelines, and machine-learning models, promise faster, more actionable results and tighter integration with electronic health records. The widespread adoption of sequencing in clinical workflows has the potential to shift infectious disease management toward precision medicine, thereby improving diagnostics, treatment selection, and public health responses.},
}

@article {pmid41304632,
year = {2025},
author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z},
title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223480},
pmid = {41304632},
issn = {2223-7747},
support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; },
abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.},
}

@article {pmid41304493,
year = {2025},
author = {Sun, H and Li, J and Zhuang, L and Zhang, Y and Zhou, Z and Sun, J and Wang, D and Ren, Y and Xu, X and He, J and Xue, Y},
title = {Ultrasonic Cavitation Transforms Organic Matter to Achieve Reduction of Excess Sludge and Recycling of Carbon Sources.},
journal = {Toxics},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/toxics13110941},
pmid = {41304493},
issn = {2305-6304},
support = {BK20240983//Natural Science Foundation of Jiangsu Province/ ; 52500021//National Natural Science Foundation of China/ ; SJCX24_1645//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Reducing the generation of excess sludge and achieving resource recovery are crucial for enhancing the economic efficiency and environmental sustainability of wastewater treatment plants (WWTPs). This study utilizes ultrasonic cavitation technology to transform organic matter into excess sludge to achieve sludge reduction and carbon source recovery. To this end, we systematically investigated the effects of various ultrasonic cavitation conditions on sludge reduction, organic matter conversion, and denitrification efficiency. The results showed that the optimal sludge reduction effect occurs at an original mixed liquid suspended solids (MLSS) of 10 g/L, under neutral and non-aerated conditions, reaching 15.07%. Ultrasonic cavitation treatment significantly enhanced the conversion efficiency of organic matter in the sludge, greatly increasing the concentration of organic matter in the supernatant, with soluble chemical oxygen demand (SCOD) maintained around 900 mg/L, thereby significantly improving the denitrification process. Furthermore, through magnetic-nanoparticle mediated isolation (MMI) and metagenomic sequencing analysis, the dominant denitrifying bacteria and their functional genes that utilize organic matter in the supernatant of ultrasonically treated sludge as a carbon source were identified. Finally, long-term pilot-scale operations further validated the practical application potential of ultrasonic cavitation technology for excess sludge reduction and resource utilization.},
}

@article {pmid41304327,
year = {2025},
author = {Li, X and Ma, X and Wu, L and Mo, Z and Chen, Z and Zhang, R and Xing, M},
title = {Metagenomic Analysis of Gut Microbiota Structure and Function in Adults with Subclinical Hypothyroidism: A Cross-Sectional Study in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112643},
pmid = {41304327},
issn = {2076-2607},
support = {2025JK158//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK151//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025KY758//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 2024KY910//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 25TJYX05//Research Project of Zhejiang Provincial Bureau of Statistics/ ; 2025ZL254//Zhejiang Province Traditional Chinese Medicine Science and Technology Plan Project/ ; 2023-B-04//Zhejiang CDC Science and Technology Talent Incubation Project/ ; },
abstract = {Subclinical hypothyroidism (SCH) is a condition characterized by thyroid hormone dysregulation, often associated with subtle clinical symptoms and metabolic disturbances. Emerging evidence suggests that the gut microbiota plays a crucial role in modulating thyroid function, but the microbiota-thyroid axis in SCH remains poorly understood. This study systematically investigates the gut microbiota composition, functional characteristics, and their correlation with thyroid hormone profiles in SCH patients. Using metagenomic sequencing and thyroid function assessments, we identified significant alterations in the gut microbiota of SCH patients, including a depletion of beneficial microbes such as Blautia and Bifidobacterium, and an enrichment of opportunistic pathogens like Bacteroides and Escherichia. Notably, Blautia depletion was negatively correlated with TSH levels, while Bacteroides abundance positively correlated with TSH levels, further highlighting the role of gut microbiota in thyroid dysfunction. Moreover, functional gene analysis revealed significant alterations in microbial metabolic pathways, with key pathways demonstrating correlations with thyroid hormone levels (free triiodothyronine (FT3) and triiodothyronine (T3)). Our findings suggest that gut microbial dysbiosis is closely associated with SCH. The study provides novel insights into the gut-thyroid axis and its role in SCH, offering new targets for early diagnosis, risk stratification, and intervention strategies in thyroid diseases.},
}

@article {pmid41304325,
year = {2025},
author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV},
title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112641},
pmid = {41304325},
issn = {2076-2607},
support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.},
}

@article {pmid41304316,
year = {2025},
author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG},
title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112632},
pmid = {41304316},
issn = {2076-2607},
abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304302,
year = {2025},
author = {Xiao, H and Jing, Y and Ma, K and Wang, Y and Xu, C and Yu, X},
title = {Spring Rest-Grazing Time Influenced Soil Phosphorus Fractions by Altering the Abundance of Genes Involved in Phosphorus Cycling in a Subalpine Meadow.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112618},
pmid = {41304302},
issn = {2076-2607},
support = {GAU-KYQD-2021-01//Scientific Research Start-up Funds for Openly-recruited Doctors, China/ ; GSAU-DKZY-2025-004//China Agricultural University Collaborative Research Support Fund, China/ ; 32460356, 32301509//National Natural Science Foundation of China/ ; },
abstract = {Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but its effects on soil P availability and the microbial processes driving P transformation remain poorly understood. To address this, a long-term field experiment was conducted with five different spring rest-grazing periods, where soil P fractions were examined and metagenomic sequencing was employed to assess the functional profiles of microbial genes involved in P cycling. Early spring rest-grazing led to higher concentrations of labile P fractions (Resin-P and NaHCO3-Pi), indicating improved soil P availability. Moreover, rest-grazing in early spring significantly reduced HCl-Pi concentration while increased the concentration of conc. HCl-Po. Metagenomic analysis revealed that early spring rest-grazing may have contributed to a higher relative abundance of the organic P mineralization gene phnA but decreasing the relative abundance of inorganic P solubilization genes ppa, and P-uptake and transport gene pstB. The dominant microbial genera involved in P cycling were Rhodopseudomonas and Mesorhizobium. Soil temperature and water infiltration rate, both affected by early rest-grazing, were identified as the main environmental variables correlated with P-cycling functional gene composition. These influenced taxa with functional genes involving organic P mineralization, inorganic P solubilization, and P-uptake and transport, which may associate with enhancing soil labile P. This study provides insights into potential microbial processes under grazing management in grassland ecosystems.},
}

@article {pmid41304301,
year = {2025},
author = {Martinez, A and St-Pierre, B},
title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112617},
pmid = {41304301},
issn = {2076-2607},
support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; },
abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.},
}

@article {pmid41304286,
year = {2025},
author = {Wu, Y and Liu, C and Qiu, Q and Zhao, X},
title = {Xylo-Oligosaccharide Production from Wheat Straw Xylan Catalyzed by a Thermotolerant Xylanase from Rumen Metagenome and Assessment of Their Probiotic Properties.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112602},
pmid = {41304286},
issn = {2076-2607},
support = {20224ACB205007, 20242BAB20309, 20252BAC240121//Natural Science Foundation of Jiangxi Province/ ; 20252ZDF030003//Central Leading Local Science and Technology Development Special Project/ ; 2024H-100160//Ji'an Municipal Science and Technology Plan Project/ ; },
abstract = {A novel xylanase gene (RuXyn854) was identified from the rumen metagenome and was heterologously expressed in Escherichia coli to produce xylo-oligosaccharides (XOSs) as a prebiotic in this study. RuXyn854, a member of glycosyl hydrolase family 10, demonstrated peak enzymatic activity at pH 7.0 and 50 °C. RuXyn854 retains more than 50% of its activity after treatment at 100 °C for 10 min, highlighting the enzyme's excellent heat resistance. RuXyn854 showed a preferential hydrolyzation of xylan, especially rice straw xylan. RuXyn854 activity was significantly increased in the presence of 15 mM Mn[2+], 0.25% Tween-20, and 0.25% Triton X-100 (125%, 20%, and 26%, respectively). The reaction temperature (30, 40, and 50 °C), dosage (0.20, 0.27, and 0.34 U), and time (90, 120, and 150 min) of RuXyn854 affected the XOS yield and composition, with a higher yield at 0.27 U, 50 °C, and 120-150 min. Xylobiose, xylotriose, and xylotetraose were characterized as the predominant XOS products resulting from the enzymatic hydrolysis of wheat straw xylan by RuXyn854, with xylose present at a mere 0.49% of the total yield. The prebiotic potential of XOSs was assessed through in vitro fermentation with established probiotic strains of Bifidobacterium bifidum and Lactobacillus brevis. The results showed that, regardless of incubation time, XOSs stimulated the growth and xylanolytic enzyme secretion of the two probiotics compared to the controls. These results demonstrate that the feature of RuXyn854 to withstand temperatures up to 100 °C is impressive, and its ability to hydrolyze wheat xylan into XOSs promotes the growth of probiotics.},
}

@article {pmid41304279,
year = {2025},
author = {Zhou, M and Li, Q and Han, Y and Wang, Q and Yang, H and Li, H and Hu, C},
title = {Sulfur Cycling and Life Strategies in Successional Biocrusts Link to Biomass Carbon in Dryland Ecosystems.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112594},
pmid = {41304279},
issn = {2076-2607},
support = {32370125//National Natural Science Foundation of China/ ; 41877419//National Natural Science Foundation of China/ ; 41877339//National Natural Science Foundation of China/ ; XDA17010502//Strategic Priority Research Program at the Chinese Academy of Science/ ; },
abstract = {Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin-Benson-Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks.},
}

@article {pmid41304278,
year = {2025},
author = {Qiao, T and Zhu, Z},
title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112595},
pmid = {41304278},
issn = {2076-2607},
support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.},
}

@article {pmid41304274,
year = {2025},
author = {Li, J and Hou, L and Liu, Y and Sun, Y and Li, Y and He, B and Tu, C and Zhou, X},
title = {Metagenomic Sequencing Reveals the Viral Diversity of Bactrian Camels in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112589},
pmid = {41304274},
issn = {2076-2607},
support = {32130104//National Natural Science Foundation of China/ ; 32460902//National Natural Science Foundation of China/ ; 2021GKLRLX10//Ningxia Hui Autonomous Region Science and Technology Innovation Leading Talents Cultivation Project/ ; Ning Ren She Han [2024] No. 106//Ningxia Hui Autonomous Region Young Top-notch Talents Cultivation Project/ ; },
abstract = {The Bactrian camel is a key economic livestock species in China and around the world. It yields meat and milk (high-quality functional foods), and the milk reports health benefits. Dromedary camels, as intermediate hosts of MERS-CoV, have garnered significant public health attention. In contrast, viral surveillance in Bactrian camels from the same genus as dromedaries has received limited attention, with only sporadic or regionally confined reports available. Systematic investigations into the virome of viral species, viral diversity, and novel viruses in Bactrian camels are lacking. In this study, swabs were collected from 701 Bactrian camels in China. Through metagenomics, 3262 viral contigs were classified into 16 viral phyla, 29 viral families, and an unclassified group. The different landforms were found to influence viral diversity and composition in Bactrian camels, with mountainous area exerting the greatest impact. The viral composition significantly differed between captive and free-ranging camels. The study identified at least 12 viruses with zoonotic potential, and phylogenetic analysis indicated cross-species transmission in some of them. Additionally, picornavirus, circular Rep-encoding single-stranded (CRESS) DNA virus, and polyomavirus from Bactrian camels may represent novel species or genotypes. To summarize, in this study, we described the baseline virome profile of Chinese Bactrian camels, investigated the ecological factors influencing the viral distribution of Bactrian camels, identified key potential viral risks, and provided a scientific basis for the prevention, control, and early warning of critical viral diseases in Bactrian camels from China.},
}

@article {pmid41304268,
year = {2025},
author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK},
title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112582},
pmid = {41304268},
issn = {2076-2607},
abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.},
}

@article {pmid41304199,
year = {2025},
author = {Zhang, J and Jiang, F and Li, X and Song, P and Zhang, T},
title = {Metagenome-Based Functional Differentiation of Gut Microbiota and Ecological Adaptation Among Geographically Distinct Populations of Przewalski's Gazelle (Procapra przewalskii).},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112513},
pmid = {41304199},
issn = {2076-2607},
support = {QHEG-2024-04//the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Univer-sity/ ; 2024T170992//the China Postdoctoral Science Foundation/ ; },
abstract = {Przewalski's gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai-Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski's gazelle exhibits a complex spatially structured functional differentiation, reflecting host-microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.},
}

@article {pmid41304195,
year = {2025},
author = {Wen, L and Luo, H and Li, C and Cheng, K and Shi, L and Liu, L and Wang, K and Tang, H},
title = {Substituting Chemical by Organic Fertilizer Improves Soil Quality, Regulates the Soil Microbiota and Increases Yields in Camellia oleifera.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112509},
pmid = {41304195},
issn = {2076-2607},
support = {U21A20187//National Natural Science Foundation of China/ ; 2022tfs201//Director Fund of Hunan Soil and Fertilizer Institute/ ; XDA0440404//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
abstract = {The partial substitution of chemical fertilizer with organic fertilizer has been regarded as an effective strategy for enhancing crop yield and soil quality. Nevertheless, its effects on soil properties and microbes remain contentious. In this study, we examined the effects of four different fertilization strategies (including without fertilizer (CK), 100% chemical fertilizer (NPK), 30% organic fertilizer + 70% chemical fertilizer (LOM) and 60% organic fertilizer + 40% chemical fertilizer (HOM)) on soil nutrients and microbial communities through metagenomic sequencing in a Camellia oleifera field experiment. Compared to CK and NPK, HOM significantly increased SOC, TN, TP, AK and AN contents. The substitution of organic fertilizer notably increased Camellia oleifera yield, with the highest increase of 93.35% observed in HOM relative to NPK. Soil bacterial and fungal communities responded inconsistently to fertilization patterns. Bacteria predominated as the main soil microorganisms, and higher rates of organic fertilizer substitution facilitated a shift from bacterial to fungal communities. Organic fertilizer substitution significantly increased soil bacteria diversity and fungal richness, particularly in the HOM. Soil bacterial community structure was more sensitive to fertilization regimes than soil fungi. High rates of organic fertilizer substitution substantially suppressed oligotrophic and increased copiotrophic bacterial communities. Mucoromycota emerged as the dominant fungal group, with a considerable increment in HOM soils. SOC and TN were the main factors affecting Camellia oleifera yield and shaping soil bacteria and fungal diversity and composition. This study provided crucial insights into the ecological implications of organic fertilizer application and the potential of managing soil microorganisms for sustainable Camellia oleifera productivity.},
}

@article {pmid41304167,
year = {2025},
author = {Vitezić, BM and Franović, B and Renko, I and Kuiš, D and Begić, G and Blašković, M and Gabrić, D and Nikolić, M and Vranić, TŠ and Veljanovska, D and Cvijanović Peloza, O},
title = {Microbiome Profiling of Biofilms Formed on d-PTFE Membranes Used in Guided Bone Regeneration.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112478},
pmid = {41304167},
issn = {2076-2607},
support = {2170-137-08-24-19//UNIRI-biomed/ ; IP-2020-02-7875//the Croatian Science Foundation/ ; },
abstract = {In guided bone regeneration (GBR) procedures, d-PTFE membranes are often used as a barrier to promote alveolar ridge regeneration. The aim of this randomized clinical trial was to examine the microbial diversity and structure of biofilms on two types of d-PTFE membranes, Permamem[®] and Cytoplast™, over four-week oral cavity exposure periods. Bacterial biofilm analysis was performed using 16S rRNA next-generation sequencing (NGS) on 36 samples (20 Permamem[®] and 16 Cytoplast™). The results showed significant differences in the microbial profiles: Cytoplast™ membranes showed reduced microbial diversity and an enhanced proportion of pathobionts like Selenomonas, Segatella, Fusobacterium and Parvimonas, which are associated with periodontal and peri-implant diseases and alveolar bone loss. Permamem[®] membranes promoted colonization by bacteria associated with healthy oral conditions, such as the genera Streptococcus, Kingella and Corynebacterium. Overall, our results showed that Cytoplast™ membranes generate a specific type of biofilm, leading to reduction in health-related bacterial species and facilitating growth conditions for dysbiosis shift. Further research and patient follow-ups are essential to thoroughly evaluate the clinical implications of different d-PTFE membranes used in guided bone regeneration.},
}

@article {pmid41304165,
year = {2025},
author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P},
title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112480},
pmid = {41304165},
issn = {2076-2607},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; },
abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.},
}

@article {pmid41304105,
year = {2025},
author = {Zhong, Y and Wu, C and Yao, Z and Li, X and Chi, H and Wu, T and Du, X},
title = {Metagenomic Analysis of Distribution Characteristics and Driving Mechanisms of Antibiotic Resistance Genes, Virulence Factors, and Microbial Communities in Rice Seedling Cultivation Soils.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112419},
pmid = {41304105},
issn = {2076-2607},
abstract = {The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil's pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks.},
}

@article {pmid41302874,
year = {2025},
author = {Berlanga, M and Miñana-Galbis, D and Guerrero, R},
title = {Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111128},
pmid = {41302874},
issn = {2075-4450},
support = {project PID2021-123735OB-C22.//MCIN/ ; },
abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.},
}

@article {pmid41301629,
year = {2025},
author = {Wang, Y and Li, L and Liang, Y and Xu, K and Ye, Y and He, M},
title = {Phage Therapy for Acinetobacter baumannii Infections: A Review on Advances in Classification, Applications, and Translational Roadblocks.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111134},
pmid = {41301629},
issn = {2079-6382},
support = {82302568//National Natural Science Foundation of China/ ; 2308085QH283//Anhui Provincial National Science Foundation/ ; 2022xkjT012//Basic and Clinical Collaboration Enhancement Program Foundation of Anhui Medical University/ ; },
abstract = {The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe public health threat, driving growing interest in phage-based precision antibacterial strategies. This systematic review synthesizes recent advances in the field of A. baumannii phage. Modern taxonomy, based on whole-genome phylogeny, has reclassified the majority of A. baumannii phages into the class Caudoviricetes, revealing distinct evolutionary clades that correlate with host tropism and biological properties, superseding the traditional morphological families (Myoviridae, Siphoviridae, Podoviridae). To overcome limitations of natural phage therapy, such as narrow host range, cocktail therapies (ex vivo resistance mutation rates < 5%) and phage-antibiotic synergism (enabling antibiotic efficacy at 1/4 minimum inhibitory concentration) have significantly enhanced antibacterial efficacy. Preclinical models demonstrate that phage therapy efficiently clears pathogens in pneumonia models and promotes the healing of burn wounds and diabetic ulcers via immunomodulatory mechanisms. Technical optimizations include nebulized inhalation delivery achieving 42% alveolar deposition, and thermosensitive hydrogels enabling sustained release over 72 h. Genetic engineering approaches, such as host range expansion through tail fiber recombination and CRISPR/Cas-mediated elimination of lysogeny, show promise. However, the genetic stability of engineered phages requires further validation. Current challenges remain, including limited host spectrum, the absence of clinical translation standards, and lagging regulatory frameworks. Future efforts must integrate metagenomic mining and synthetic biology strategies to establish a precision medicine framework encompassing resistance monitoring and personalized phage formulation, offering innovative solutions against CRAB infections.},
}

@article {pmid41301609,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Otto, SJG and Chai, Z and Lacoste, S and McCarthy, EL and Links, MG and Herman, EK and Stothard, P and Gow, SP and Campbell, JR and Waldner, CL},
title = {Evaluating the Diagnostic Performance of Long-Read Metagenomic Sequencing Compared to Culture and Antimicrobial Susceptibility Testing for Detection of Bovine Respiratory Bacteria and Indicators of Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111114},
pmid = {41301609},
issn = {2079-6382},
support = {Not applicable//Genome Prairie/ ; Not applicable//Genome Canada/ ; Not applicable//Genome Alberta/ ; Not applicable//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can detect bacteria and antimicrobial resistance genes (ARGs) from bovine respiratory samples, providing an alternative to culture and antimicrobial susceptibility testing (C/S). This study applied Bayesian latent class models (BLCMs) to estimate the sensitivity (Se) and specificity (Sp) of long-read metagenomic sequencing compared to C/S for detecting Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, as well as associated macrolide and tetracycline resistance potential. Methods: Deep nasopharyngeal swabs were collected from fall-placed feedlot calves at arrival, 13, and 36 days on feed across two years and two metaphylaxis protocols. Samples underwent C/S and long-read metagenomic sequencing. BLCMs were used to estimate Se and Sp for the detection of bacteria and potential for antimicrobial resistance (AMR). Results: Se and Sp for detecting respiratory bacteria by metagenomics were not significantly different than culture, with four exceptions. For the 2020 samples, Se for M. haemolytica was lower than culture, and Sp for H. somni was lower, while in both 2020 and 2021 samples, Se for P. multocida was higher for metagenomics than culture. The estimated Se and Sp of metagenomics for the detection of msrE-mphE, EstT, and tet(H) within bacterial reads were either not significantly different or were lower than AST, with Sp > 95% with one exception. Conclusions: This study provided BLCM-based estimates of clinical Se and Sp of metagenomics and C/S without assuming a gold standard in a large pen research setting. These findings demonstrate the potential of long-read metagenomics to support bovine respiratory disease diagnostics, AMR surveillance, and antimicrobial stewardship in feedlot cattle.},
}

@article {pmid41301606,
year = {2025},
author = {Aguilar-Rangel, EJ and Paredes-Cárcamo, F and Andrade, MD and Contreras-Sánchez, D and Rain-Medina, V and Campanini-Salinas, J and Medina, DA},
title = {Hospital Wastewater as a Reservoir of Contaminants of Emerging Concern: A Study Report from South America, Chile.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111111},
pmid = {41301606},
issn = {2079-6382},
support = {Proyectos Colaborativos 2024 #3557//San Sebastián University/ ; Fondecyt Iniciación #11230295//Agencia Nacional de Investigación y Desarrollo de Chile/ ; },
abstract = {Background/Objectives: Hospital wastewater is a complex effluent containing a wide range of biological and chemical contaminants, including pharmaceuticals, pathogens, and antimicrobial resistance determinants. These discharges pose a growing threat to aquatic ecosystems and public health, particularly in regions where wastewater treatment is insufficient. This study aimed to characterize the chemical and microbiological composition of untreated effluent from a tertiary care hospital in southern Chile, focusing on contaminants of emerging concern. Methods: Wastewater samples were collected at the hospital outlet before any treatment. The presence of two commonly used pharmaceutical compounds, paracetamol and amoxicillin, was quantified using high-performance liquid chromatography (HPLC). Bacterial isolation was performed using selective media, and antibiotic susceptibility testing was conducted via the disk diffusion method following CLSI guidelines. In addition, metagenomic DNA was extracted and sequenced to assess microbial community composition and functional gene content, focusing on the identification of resistance genes and potential pathogens. Results: A total of 42 bacterial isolates were recovered, including genera with known pathogenic potential such as Aeromonas, Klebsiella, and Enterococcus. Antibiotic susceptibility tests revealed a high prevalence of multidrug-resistant strains. Metagenomic analysis identified the dominance of Bacillota and Bacteroidota, together with 56 antimicrobial-resistance gene (ARG) families and 38 virulence-factor families. Functional gene analysis indicated the presence of efflux-pump systems, β-lactamases, and mobile genetic elements, suggesting that untreated hospital effluents serve as potential sources of resistance and virulence determinants entering the environment. Paracetamol was detected in all samples, with an average concentration of 277.4 ± 10.7 µg/L; amoxicillin was not detected, likely due to its instability and rapid degradation in the wastewater matrix. Conclusions: These findings highlight the complex microbiological and chemical burden of untreated hospital wastewater and reinforce the need for continuous monitoring and improved treatment strategies to mitigate environmental dissemination of antibiotic resistance.},
}

@article {pmid41301593,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Lacoste, SR and Chai, Z and Herman, EK and McCarthy, EL and Campbell, JR and Gow, SP and Stothard, P and Links, MG and Otto, SJG and Waldner, CL},
title = {Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111098},
pmid = {41301593},
issn = {2079-6382},
support = {NA//Genome Canada/ ; NA//Genome Prairie/ ; NA//Genome Alberta/ ; NA//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves sampled in the early feeding period were associated with subsequent bovine respiratory disease (BRD) treatment and phenotypic antimicrobial resistance (AMR) at treatment. Methods: Deep nasopharyngeal swabs (DNPSs) obtained at arrival processing (1 day on feed; DOF), 13 DOF, and the time of BRD treatment were cultured and subjected to antimicrobial susceptibility testing (AST) and long-read metagenomic sequencing. Analyses focused on macrolide (mphE-msrE, EstT) and tetracycline (tet(H)) ARGs within reads assigned to Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Bibersteinia trehalosi. Generalized estimating equations assessed associations between metagenomic results from 1 and 13 DOF and subsequent BRD treatment risk and AST outcomes at treatment, at both the individual animal (calf) and pen levels. Results: Calf-level detection of H. somni at 13 DOF was associated with a greater BRD treatment risk between 14 and 45 DOF. An increased pen prevalence of either M. haemolytica or P. multocida at 13 DOF was associated with a greater BRD treatment risk from 14 to 45 DOF. At 13 DOF, detections of mphE-msrE, EstT, or tet(H) in target bacteria were associated with corresponding phenotypic AMR at BRD treatment. Similarly, a higher pen-level prevalence of mphE-msrE or EstT at 13 DOF was also associated with increased macrolide resistance at BRD treatment. Conclusions: The results from long-read metagenomic sequencing of DNPSs collected at 13 DOF were associated with both BRD risk and AMR at treatment. These findings align with prior culture-based results and support the potential utility of pen-level metagenomic testing for AMR surveillance and informing antimicrobial selection in feedlots.},
}

@article {pmid41301447,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining Thermophile Photosynthesis Genes: A Synthetic Operon Expressing Chloroflexota Species Reaction Center Genes in Rhodobacter sphaeroides.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111529},
pmid = {41301447},
issn = {2218-273X},
support = {DE-AC02-05CH11231//United States Department of Energy/ ; DE-AC02-05CH11231//United States Department of Energy/ ; RGPIN 2018-03898//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 2025-04928//Natural Sciences and Engineering Research Council of Canada/ ; 3-1/PDFP/HEC/2022(B-3)/2339/02//Higher Education Commission/ ; },
mesh = {*Rhodobacter sphaeroides/genetics/metabolism ; *Operon ; *Photosynthesis/genetics ; *Photosynthetic Reaction Center Complex Proteins/genetics/metabolism ; *Chloroflexi/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and is therefore the most important bioenergetic process on earth. The greatest diversity of photosynthetic systems is found in microorganisms. However, our understanding of the biophysical and biochemical processes that transduce light into chemical energy is derived from a relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of predicted proteins that catalyze the initial photochemical reactions deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for the expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90 °C) springs available through the JGI IMG database, to generate a resource of diverse sequences that are potentially adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}

*Rhodobacter sphaeroides/genetics/metabolism
*Operon
*Photosynthesis/genetics
*Photosynthetic Reaction Center Complex Proteins/genetics/metabolism
*Chloroflexi/genetics
Bacterial Proteins/genetics/metabolism

@article {pmid41301445,
year = {2025},
author = {Zhang, J and Xu, G and Yi, Z and Tang, X},
title = {Efficient Mining and Characterization of Two Novel Keratinases from Metagenomic Database.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111527},
pmid = {41301445},
issn = {2218-273X},
support = {2024YFC2815900//National Key R\&D Program of China/ ; SOA: 2017002//Scientific Research Foundation of Third Institute of Oceanography/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; 2021J02015//Fujian Provincial Natural Science Foundation of China/ ; },
mesh = {*Peptide Hydrolases/genetics/metabolism/chemistry ; Phylogeny ; Keratins/metabolism ; Animals ; Enzyme Stability ; *Metagenomics ; Data Mining ; *Metagenome ; Feathers ; Kinetics ; Substrate Specificity ; Amino Acid Sequence ; Databases, Genetic ; },
abstract = {Keratin is a fibrous structural protein found in various natural materials such as hair, feathers, and nails. Its high stability and cross-linked structure make it resistant to degradation by common proteases, leading to the accumulation of keratinous waste in various industries. In this study, we developed and validated an effective bioinformatics-driven strategy for mining novel keratinase genes from the Esmatlas (ESM Metagenomic Atlas) macrogenomic database. Two candidate genes, ker820 and ker907, were identified through sequence alignment, structural modeling, and phylogenetic analysis, and were subsequently heterologously expressed in Escherichia coli Rosetta (DE3) with the assistance of a solubility-enhancing chaperone system. Both enzymes belong to the Peptidase S8 family. Enzymatic characterization revealed that GST-tagged ker820 and ker907 exhibited strong keratinolytic activity, with optimal conditions at pH 9.0 and temperatures of 60 °C and 50 °C, respectively. Both enzymes showed significant degradation of feather and cat-hair keratin. Kinetic analysis showed favorable catalytic parameters, including Km values of 9.81 mg/mL (ker820) and 5.25 mg/mL (ker907), and Vmax values of 120.99 U/mg (ker820) and 89.52 U/mg (ker907). Stability tests indicated that GST-ker820 retained 70% activity at 60 °C for 120 min, while both enzymes remained stable at 4 °C for up to 10 days. These results demonstrate the high catalytic capacity, thermal stability, and substrate specificity of the enzymes, supporting their classification as active keratinases. This study introduces a promising strategy for efficiently discovering novel functional enzymes using an integrated computational and experimental approach. Beyond keratinases, this methodology could be extended to screen for enzymes with potential applications in environmental remediation.},
}

*Peptide Hydrolases/genetics/metabolism/chemistry
Phylogeny
Keratins/metabolism
Animals
Enzyme Stability
*Metagenomics
Data Mining
*Metagenome
Feathers
Kinetics
Substrate Specificity
Amino Acid Sequence
Databases, Genetic

@article {pmid41301179,
year = {2025},
author = {Liu, D and Kuo, J and Lin, CH},
title = {Computational Investigation of Smooth Muscle Cell Plasticity in Atherosclerosis and Vascular Calcification: Insights from Differential Gene Expression Analysis of Microarray Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111223},
pmid = {41301179},
issn = {2306-5354},
abstract = {The dedifferentiation of smooth muscle cells (SMCs) is the main cause of atherosclerosis and vascular calcification. This study integrated the gene expression data of multiple microarrays to identify relevant marker molecules. A total of 72 Gene Expression Omnibus (GEO) samples (GSM) were collected from 10 gene expression data series (GSE) and divided into five groups: non-SMC, SMC, atherosclerotic SMC (SMC-ath), calcified SMC (SMC-calc), and treated SMC (SMC-t). The SMC-t group included synthetic SMCs that had undergone treatment to inhibit proliferation, migration, or inflammation. The gene expression data were merged, normalized, and batch effects were removed before differential gene expression (DGE) analysis was performed via linear models for microarray data (limma) and statistical analysis of metagenomic profiles (STAMPs). The genes with expressions that significantly differed were subsequently subjected to protein-protein interaction (PPI) and functional prediction analyses. In addition, the random forest method was used for classification. Twelve proteins that may be marker molecules for SMC differentiation and dedifferentiation were identified, namely, Proprotein convertase subtilisin/kexin type 1 (PCSK1), Transforming growth factor beta-induced (TGFBI), Complement C1s (C1S), Phosphomannomutase 1 (PMM1), Claudin 7 (CLDN7), Calcium binding and coiled-coil domain 2 (CALCOCO2), SAC3 domain-containing protein 1 (SAC3D1), Natriuretic peptide B (NPPB), Monoamine oxidase A (MAOA), Regulator of the Cell Cycle (RGCC), Alpha-crystallin B Chain (CRYAB), and Alcohol dehydrogenase 1B (ADH1B). Finally, their possible roles in SMCs are discussed. This study highlights the feasibility of bioinformatics analysis for studying SMC dedifferentiation.},
}

@article {pmid41301089,
year = {2025},
author = {Ostos, I and Ruiz, I and Cruz, D and Flórez-Pardo, LM},
title = {Methane Concentration Prediction in Anaerobic Codigestion Using Multiple Linear Regression with Integrated Microbial and Operational Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111133},
pmid = {41301089},
issn = {2306-5354},
support = {No. DGI-01-2025//Dirección General de Investigaciones of Universidad Santiago de Cali/ ; },
abstract = {Anaerobic codigestion of organic residues is a proven strategy for enhancing methane recovery. However, the complexity of microbial interactions and variability in operational conditions make it difficult to estimate methane concentration in real time, particularly in rural contexts. This study developed a multiple linear regression model to predict methane concentration using operational data and microbial community profiles derived from 16S rRNA gene sequencing. The system involved the codigestion of cassava by-product and pig manure in a two-phase anaerobic reactor. Predictor variables were selected through a hybrid approach combining statistical correlation with microbial functional relevance. The final model, trained on 70% of the dataset, demonstrated satisfactory generalization capability on the other 30 test set, achieving a coefficient of determination (R[2]) of 0.92 and a mean relative error (MRE) of 6.50%. Requiring only a limited set of inputs and minimal computational resources, the model offers a practical and accessible solution for estimating methane levels in decentralized systems. The integration of microbial community data represents a meaningful innovation, improving prediction by capturing biological variation not reflected in operational parameters alone. This approach can support local decision making and contribute to Sustainable Development Goal 7 by promoting reliable and affordable technologies for clean energy generation in rural and resource-constrained settings.},
}

@article {pmid41300910,
year = {2025},
author = {Jin, X and Shen, H and Zhou, P and Yang, J and Yang, S and Ni, H and Yu, Y and Zhang, Z},
title = {Research Progress on Sepsis Diagnosis and Monitoring Based on Omics Technologies: A Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/diagnostics15222887},
pmid = {41300910},
issn = {2075-4418},
support = {2023YFC3603104//China National Key Research and Development Program/ ; Nos. 82472243 and 82272180//National Natural Science Foundation of China/ ; LHDMD24H150001//Huadong Medicine Joint Funds of the Zhejiang Provincial Natural Science Foundation of China/ ; 2024C03240//the Key Research & Development Project of Zhejiang Province/ ; No. GZY-ZJ-KJ-24082//a collaborative scientific project co-established by the Science and Technology Department of the National Administration of Traditional Chinese Medicine and the Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; No. 2024KY1099//the General Health Science and Technology Program of Zhejiang Province/ ; No. ZJDXLQCXZCJBGS2024016//the Project of Zhejiang University Longquan Innovation Center/ ; 320.6750.2024-23-07//Wu Jieping Medical Foundation Special Research Grant/ ; },
abstract = {Sepsis poses a significant global health burden, with millions of cases and high mortality rates annually, largely due to challenges in early diagnosis and monitoring. Traditional methods, reliant on nonspecific clinical manifestations and limited biomarkers like C-reactive protein and procalcitonin, often fail to distinguish infection from non-infectious inflammation or capture disease heterogeneity. This review synthesizes recent progress in omics technologies-genomics, transcriptomics, proteomics, and metabolomics-for advancing sepsis management. Genomics, via metagenomic next-generation sequencing, enables rapid pathogen identification and genetic variant analysis for susceptibility and prognosis. Transcriptomics reveals molecular subtypes and immune dynamics through RNA sequencing and single-cell approaches. Proteomics and metabolomics uncover protein and metabolite profiles linked to immune imbalance, organ damage, and metabolic disorders. Multi-omics integration, enhanced by artificial intelligence and machine learning, facilitates biomarker discovery, patient stratification, and predictive modeling, bridging laboratory findings to bedside applications like rapid diagnostic tools and clinical decision support systems. Despite advancements, challenges including data heterogeneity, high costs, and ethical concerns persist. Future directions emphasize single-cell and spatial omics, AI-driven personalization, and ethical frameworks to transform sepsis care from reactive to proactive, ultimately improving outcomes.},
}

@article {pmid41300336,
year = {2025},
author = {Liu, Y and Xie, J and He, Y and Shi, Q and Gong, Q and Zhao, W and Qin, C and Zhou, C},
title = {Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection.},
journal = {Biology},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biology14111546},
pmid = {41300336},
issn = {2079-7737},
support = {2023M732476//China Postdoctoral Science Foundation/ ; NJTCSC24-3//Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; 2023YFH0046//Sichuan Science and Technology Program/ ; },
abstract = {Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in P. pingi associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in P. pingi, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to I. multifiliis of P. pingi. Concurrently, skin microbiome analysis showed that P. pingi hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, P. pingi skin was significantly depleted of the parasitic bacteria Candidatus_Megaira and Candidatus_Midichloria, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that P. pingi's microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of P. pingi to I. multifiliis is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish.},
}

@article {pmid41300008,
year = {2025},
author = {Rajah Kumar, M and Amankwaa, AO and Razali, NS and Mohamad, NE and Khalid, M and Abdullah, JO and Masarudin, MJ and Osman, MA and Abd Rahman, NMAN and Alitheen, NB},
title = {Preliminary Evaluation of the Gut Microbiota Modulatory Potential of Malaysian Kefir Water in Ageing Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223851},
pmid = {41300008},
issn = {2304-8158},
support = {FRGS-777 MRSA/1/2018/SKK10/UPM/02/1//Fundamental Research Grant Scheme (FRGS) by the Malaysian Ministry of Higher Education (MoHE)/ ; },
abstract = {Ageing is often accompanied by gut microbiota alterations that contribute to dysbiosis-a recognised hallmark of ageing and a risk factor for neurodegenerative diseases. Probiotic interventions offer a promising approach to restore microbial homeostasis. This preliminary study explored the potential modulatory effects of Malaysian kefir water, a Lactobacillus-enriched fermented beverage with previously reported antioxidant and neuroprotective properties in D-galactose-induced ageing mice. Kefir water was administered as both a pre-treatment and co-treatment, and gut microbiota changes were assessed using 16S rRNA metagenomic sequencing of faecal samples. Alpha and beta diversity analyses showed a stable microbial diversity across treatments. However, preliminary descriptive trends suggested that kefir water may influence specific bacterial populations. Increases were observed in Muribaculaceae and Lactobacillaceae, along with apparent decreases in Lachnospiraceae and Prevotellaceae. Both kefir treatments tended to increase the abundance of Ligilactobacillus, with the co-treatment group appearing to restore the Firmicutes/Bacteroidota ratio toward control levels, while the pre-treatment group showed a tendency to further reduce this ratio. Collectively, these findings provide preliminary indications that kefir water may hold potential as a dietary approach to modulate gut microbial changes associated with ageing. However, confirmation through studies with larger sample sizes and broader analytical coverage is necessary to substantiate these initial observations.},
}

@article {pmid41299763,
year = {2025},
author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N},
title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02262-z},
pmid = {41299763},
issn = {2049-2618},
support = {Fondecyt 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; },
abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.

RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.

CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.},
}

@article {pmid41299634,
year = {2025},
author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V},
title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {241},
pmid = {41299634},
issn = {2049-2618},
support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; },
abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.

RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.

CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Adult
Metagenome
Female
Male

@article {pmid41299624,
year = {2025},
author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W},
title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {242},
pmid = {41299624},
issn = {2049-2618},
support = {81825019//National Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.

RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.

CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.},
}

Animals
*Virome/genetics
*Zoonoses/virology/transmission
Metagenomics/methods
Chiroptera/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Africa, Western
Humans
Shrews/virology
Genome, Viral
*Animals, Wild/virology
Disease Reservoirs/virology
*Mammals/virology
Rodentia/virology
*Viral Zoonoses/virology/transmission

@article {pmid41299512,
year = {2025},
author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B},
title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {23},
number = {1},
pages = {154},
pmid = {41299512},
issn = {1477-7827},
mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation & purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.

METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n = 15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n = 13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.

RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p = 0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.

CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.},
}

Humans
Male
Case-Control Studies
*Virome/genetics
Adult
*Semen/virology
Retrospective Studies
*Papillomavirus Infections/virology/complications
*Infertility, Male/virology
*Papillomaviridae/genetics/isolation & purification
*Fertility/physiology
Spermatozoa/virology
Human Papillomavirus Viruses

@article {pmid41299356,
year = {2025},
author = {Shen, A and Xu, X and Xu, L and Nie, X and Ai, J and Chen, W},
title = {Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-11814-5},
pmid = {41299356},
issn = {1471-2334},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) and multiple point-of-care testing (POCT) techniques have demonstrated significant potential in pathogen detection. However, neither technology fully meets all clinical diagnostic needs for pulmonary infections. This study aimed to evaluate the complementary detection performance and clinical applicability of POCT and mNGS in pulmonary infections, using conventional culture as a reference.

METHODS: This study enrolled forty-five patients with suspected lower respiratory tract infections for concurrent evaluation using POCT and mNGS. The detection performance of traditional culture methods, POCT, and mNGS was subsequently analyzed and compared.

RESULTS: Both molecular methods showed high positive detection rates, surpassing that of the culture method. When conventional culture was used as the gold standard, the sensitivity and positive predictive value (PPV) within the detection range of the PM Easy Lab Respiratory Panel (RP) were 97.1% and 80.5%, respectively, whereas for mNGS, these values were 90.2% and 92.5%, respectively. A comparison of the PM Easy Lab RP and mNGS results revealed that the PM Easy Lab was faster (100 min vs. 24 h) and more sensitive (88 vs. 63 pathogens) within its detection range, whereas mNGS offered a broader spectrum of pathogen detection. The overall consistency between PM Easy Lab RP and mNGS was 88.9%. Klebsiella pneumoniae and Acinetobacter baumannii were identified as the most prevalent bacterial infections by all three detection methods. Moreover, both PM Easy Lab RP and mNGS demonstrated enhanced capability over culture in detecting mixed infections (57.8%, 84.4% vs. 15.6%, all P < 0.01), uncovering a substantial number of viral and bacterial-viral co-infections that are undetectable by conventional culture methods. The most common combination of mixed infections in the PM Easy Lab RP was mixed bacterial infections (76.9%, 20/26), whereas in mNGS, it was bacterial-fungal-viral mixed infections (36.8%, 14/38).

CONCLUSIONS: The findings indicate that PM Easy Lab RP and mNGS offer distinct yet complementary value. PM Easy Lab has potential advantages in speed, sensitivity, and efficiency in detecting pathogens within its panel, and it could be considered for rapid, frontline testing, while mNGS provides a broad-spectrum detection capability, making it more suitable for comprehensive investigation of complex cases, though careful clinical interpretation is required to distinguish pathogenic from colonizing or contaminating organisms. Understanding their respective strengths can guide the development of optimized, hierarchical diagnostic pathways.},
}

@article {pmid41299229,
year = {2025},
author = {Thurimella, K and Mohamed, AMT and Li, C and Vatanen, T and Graham, DB and Owens, RM and La Rosa, SL and Plichta, DR and Bacallado, S and Xavier, RJ},
title = {Protein language models uncover carbohydrate-active enzyme function in metagenomics.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {285},
pmid = {41299229},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; Humans ; *Enzymes/metabolism/chemistry/genetics ; Carbohydrate Metabolism ; Molecular Sequence Annotation ; },
abstract = {BACKGROUND: The functional annotation of uncharacterized microbial enzymes from metagenomic data remains a significant challenge, limiting our understanding of microbial metabolic dynamics. Traditional annotation methods often rely on sequence homology, which can fail to identify remote homologs or enzymes with structural rather than sequence conservation. To address this gap, we developed CAZyLingua, the first annotation tool to use protein language models (pLMs) for the accurate classification of carbohydrate-active enzyme (CAZyme) families and subfamilies.

RESULTS: CAZyLingua demonstrated high performance, maintaining precision and recall comparable to state-of-the-art hidden Markov model-based methods while outperforming purely sequence-based approaches. When applied to a metagenomic gene catalog from mother/infant pairs, CAZyLingua identified over 27,000 putative CAZymes missed by other tools, including horizontally-transferred enzymes implicated in infant microbiome development. In datasets from patients with Crohn's disease and IgG4-related disease, CAZyLinuga uncovered disease-associated CAZymes, highlighting an expansion of carbohydrate esterases (CEs) in IgG4-related disease. A CE17 enzyme predicted to be overabundant in Crohn's disease was functionally validated, confirming its catalytic activity on acetylated manno-oligosaccharides.

CONCLUSIONS: CAZyLingua is a powerful tool that effectively augments existing functional annotation pipelines for CAZymes. By leveraging the deep contextual information captured by pLMs, our method can uncover novel CAZyme diversity and reveal enzymatic functions relevant to health and disease, contributing to a further understanding of biological processes related to host health and nutrition.},
}

*Metagenomics/methods
Humans
*Enzymes/metabolism/chemistry/genetics
Carbohydrate Metabolism
Molecular Sequence Annotation

@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}