@article {pmid41298464,
year = {2025},
author = {Ricci, F and Bay, SK and Nauer, PA and Wong, WW and Ni, G and Jimenez, L and Jirapanjawat, T and Leung, PM and Bradley, JA and Eate, VM and Hall, M and Stubbusch, AKM and Fernández-Marín, B and de Los Ríos, A and Cook, PLM and Schroth, MH and Chiri, E and Greening, C},
title = {Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66734-4},
pmid = {41298464},
issn = {2041-1723},
support = {APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE230101346//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; 101115755//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PID2019-105469RB-C22//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
abstract = {An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonise both forelands and persist across soil decadal chronosequences serving as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using organic and inorganic compounds, including atmospheric trace gases and sulphur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable environment for subsequent colonisation.},
}

@article {pmid41298409,
year = {2025},
author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS},
title = {National-scale biogeography and function of river and stream bacterial biofilm communities.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10571},
pmid = {41298409},
issn = {2041-1723},
support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Biofilms/growth & development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; },
abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.},
}

*Biofilms/growth & development
*Rivers/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
England
Ecosystem
Biodiversity
Metagenomics
Metagenome
Microbiota/genetics
Phylogeny

@article {pmid41298355,
year = {2025},
author = {Holcik, L and von Haeseler, A and Pflug, FG},
title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10523},
pmid = {41298355},
issn = {2041-1723},
mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; },
abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.},
}

*Metagenomics/methods
Humans
Algorithms
*Gastrointestinal Microbiome/genetics
Base Composition/genetics
Colorectal Neoplasms/microbiology
*Metagenome
Bacteria/genetics/classification
Microbiota/genetics

@article {pmid41298327,
year = {2025},
author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70229},
doi = {10.1111/1758-2229.70229},
pmid = {41298327},
issn = {1758-2229},
support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; },
mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; },
abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.},
}

China
*Oil and Gas Fields/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Petroleum/microbiology
Hydrocarbons/metabolism/analysis
*Microbiota
Phylogeny
Metagenomics

@article {pmid41298270,
year = {2025},
author = {Zou, J and Xu, H and Qin, B and Lan, C and Li, J and Zhang, B and Zhang, H and Guo, C and Chen, H and Fang, Z and Zhao, Q and Wang, W and Fang, C and Zhang, Z and Lin, W},
title = {Ratoon Season Rice Reduces Methane Emissions by Limiting Acetic Acid Transport to the Rhizosphere and Inhibiting Methanogens.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07916},
doi = {10.1002/advs.202507916},
pmid = {41298270},
issn = {2198-3844},
support = {32001109//Nature Science Foundation of China/ ; 31871542//national Nature Science Foundation of China/ ; 31871556//national Nature Science Foundation of China/ ; 2017YFE0121800//National Key Research and Development Project of China/ ; 2018YFD0301105//National Key Research and Development Project of China/ ; BQW [2024]001//Innovative Talent Team in Rice Crop Science and Technology in Karst Mountainous Areas of Guizhou Province/ ; 2023//Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/ ; (2023) 007//Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions/ ; Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions (//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Qianjiaoji//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (2023)007)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Xiligongmi//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Innovative Talent Workstation of Guizhou Province(Qian-//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Ke//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; -He-Platform-talent KXJZ(2024)038)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (Qian-//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; Ke//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; -He YWZ(2024(004)//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; },
abstract = {Rice paddies are a major, persistent source of atmospheric methane (CH4), emission rates depend on the partitioning of photosynthate carbon between the rice plant and the rhizosphere microbiome. Although ratoon season rice (RR) is shown to emit far less CH4 than main-crop rice (MC), the mechanisms have remained unresolved. This work conducts a 2-year field experiment in which RR is compared with MC and with late rice (LR) synchronized to the RR heading stage. Relative to MC and LR, RR lowers daily CH4 flux by 91%, raises daily grain yield by 34%-57%, and increases net economic return by 90%-136%. Mechanistically, [13]C-labelling reveals that RR diverted more newly fixed carbon to the grain and less to the rhizosphere, thereby restricting acetate availability for methanogens. Rhizosphere metagenomics show reduced abundance of Methanobacteriaceae and down-regulation of methanogenic genes in RR. This carbon-reallocation pattern is underpinned by an abscisic acid (ABA)-mediated interaction between OsCIPK2 and OsSWEET1A, which simultaneously curtailed carbon efflux from roots and enhanced grain filling. This study is the first to establish a comprehensive framework of "ABA regulation-carbon allocation-microbial function-emission reduction and efficiency enhancement." It provides targetable strategies for carbon allocation and microbial management within climate-smart rice farming systems.},
}

@article {pmid41298102,
year = {2025},
author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A},
title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336715},
pmid = {41298102},
issn = {1468-3288},
abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.

OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.

DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.

RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for β-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.

CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.

TRIAL REGISTRATION NUMBER: NCT04777812.},
}

@article {pmid41298101,
year = {2025},
author = {Liu, CS and Merrick, B and Taboun, ZS and Mullish, BH and Goldenberg, SD and Terveer, EM and Porcari, S and Bradbury, RS and Ianiro, G and Ng, SC and , and Kao, D and Kuijper, E},
title = {Towards optimising and standardising donor screening for faecal microbiota transplantion.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336532},
pmid = {41298101},
issn = {1468-3288},
abstract = {Rigorous donor screening is fundamental for the safe and effective delivery of faecal microbiota transplantion (FMT) services, whether in the treatment of Clostridioides difficile infection or within microbiome intervention clinical trials. Donor screening is of paramount importance given the potential risk of pathogen transmission-a feared complication. While rare in practice, documented cases of FMT-associated infections have resulted in significant morbidity and even mortality. Despite the importance of screening, evidence-based approaches to developing donor-screening protocols are lacking. Inadequate screening for transmissible pathogens may lead to infections in recipients, while overly cautious screening for pathogens with negligible transmission potential could strain healthcare resources and unnecessarily exclude donors, who are already in limited supply. This review aimed to evaluate the evidence underpinning current FMT donor screening protocols. We began by comparing protocols from major FMT guidelines and manufacturers, highlighting their differences in lists of screened pathogens, laboratory assays and clinical characteristics used for donor selection. We critically appraised the existing literature on transmission dynamics for pathogens. These findings were incorporated into a Delphi process with an expert panel group to develop a rational and streamlined screening approach. We further emphasised the importance of maintaining transparency with regard to donor recruitment, screening, monitoring and traceback record keeping. Finally, we explored future directions in donor screening, including approaches to monitoring emerging pathogens and the potential for integration of new technologies, such as metagenomic assays, to enhance and refine donor selection.},
}

@article {pmid41297753,
year = {2025},
author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S},
title = {Phosphate-Iron Modified Enteromorpha Prolifera Hydrochar Enhances Dry Anaerobic Digestion of Food Waste: Synergistic Mechanisms of Electron Transfer Network, Microbial Consortia Remodeling, and Metagenomic Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123385},
doi = {10.1016/j.envres.2025.123385},
pmid = {41297753},
issn = {1096-0953},
abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6% improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32%. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9%) and hydrogenotrophic methanogens Methanoculleus (+17.7%); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255%), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.},
}

@article {pmid41297621,
year = {2025},
author = {Houmenou, CT and Sokhna, C and Fenollar, F and Mediannikov, O},
title = {Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105859},
doi = {10.1016/j.meegid.2025.105859},
pmid = {41297621},
issn = {1567-7257},
abstract = {Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.},
}

@article {pmid41297516,
year = {2025},
author = {Xu, L and Zhang, J and Xiao, Y and Jin, P and Zhang, J},
title = {High-fat diet promotes colorectal tumorigenesis through gut microbiota-mediated metabolic reprogramming and M2 macrophage polarization.},
journal = {Biochemical and biophysical research communications},
volume = {794},
number = {},
pages = {153014},
doi = {10.1016/j.bbrc.2025.153014},
pmid = {41297516},
issn = {1090-2104},
abstract = {BACKGROUND: High-fat diet (HFD) drives colorectal cancer (CRC) progression through gut microbiota dysbiosis and M2 macrophage polarization, yet the microbiota-immunity crosstalk remains mechanistically unresolved.

METHODS: APC[min/+] (CRC model, n = 8) and wild-type controls (n = 7) received 12-weeks HFD. We employed integrated metagenomic sequencing (Illumina NovaSeq) and immunohistochemistry (targeting CD206+ M2 macrophages) to investigate the linkages between the gut microbiota and the host.

RESULTS: CRC mice exhibited colonic adenocarcinoma with increased M2 macrophages. Gut microbiota in CRC mice showed enrichment of pro-inflammatory taxa (e.g., Bacteroides massiliensis, Vampirovibrion) and upregulated pathways (carbohydrate metabolism, mucin degradation). Strikingly, the relative abundances of Bacteroides massiliensis and Vampirovibrion showed significant positive correlations with CD206+ M2 macrophage infiltration levels.

CONCLUSION: HFD induces microbiota-directed metabolic reprogramming and M2 polarization, synergistically accelerating CRC. Notably, targeting key pro-inflammatory taxa (e.g., B. massiliensis) or glycan hydrolysis pathways (e.g. GH95 enzyme) may provide mechanism-guided anti-CRC strategies.},
}

@article {pmid41297400,
year = {2025},
author = {Chen, S and Liu, Q and Li, D},
title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128088},
doi = {10.1016/j.jenvman.2025.128088},
pmid = {41297400},
issn = {1095-8630},
abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.},
}

@article {pmid41297255,
year = {2025},
author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y},
title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140566},
doi = {10.1016/j.jhazmat.2025.140566},
pmid = {41297255},
issn = {1873-3336},
abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.},
}

@article {pmid41297254,
year = {2025},
author = {Hatwar, N and Qureshi, A},
title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140589},
doi = {10.1016/j.jhazmat.2025.140589},
pmid = {41297254},
issn = {1873-3336},
abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.},
}

@article {pmid41297084,
year = {2025},
author = {Cameron, CC and Gebbie, W and Bowman, C and Waters, ER and Kalyuzhnaya, MG},
title = {Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126670},
doi = {10.1016/j.syapm.2025.126670},
pmid = {41297084},
issn = {1618-0984},
abstract = {Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N2O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.},
}

@article {pmid41297027,
year = {2025},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deciphering the Interrelation of Gut Microbiota and BMI in Atherosclerosis: A Metagenomic Approach.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0075},
pmid = {41297027},
issn = {1480-3275},
abstract = {Atherosclerotic Cardiovascular Disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modifying the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.},
}

@article {pmid41296543,
year = {2025},
author = {Podlesny, D and Kim, CY and Robbani, SM and Schudoma, C and Fullam, A and Reimer, LC and Koblitz, J and Schober, I and Iyappan, A and Van Rossum, T and Schiller, J and Grekova, A and Kuhn, M and Bork, P},
title = {metaTraits: a large-scale integration of microbial phenotypic trait information.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1241},
pmid = {41296543},
issn = {1362-4962},
support = {460129525//Deutsche Forschungsgemeinschaft/ ; RS-2023-00240807//National Research Foundation of Korea/ ; //Ministry of Science, Research and the Arts Baden-Württemberg (MWK)/ ; },
abstract = {Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is dispersed across multiple databases and is largely unavailable for taxa that remain uncultured. Here, we present metaTraits, a unified and accessible trait resource that integrates culture-derived trait information from BacDive, BV-BRC, JGI IMG, and GOLD with genome-based predictions for medium and high-quality isolate and metagenome-assembled genomes (MAGs) from proGenomes and SPIRE. metaTraits covers over 2.2 million genomes and >140 harmonized traits mapped to standardized ontologies, spanning cell morphology (e.g. shape, size, and Gram staining), physiology (e.g. motility and sporulation), metabolic and enzymatic activities, environmental preferences (e.g. temperature, salinity, and oxygen tolerance), and lifestyle categories. All records are linked to the original evidence, and species are cross-linked to NCBI and GTDB taxonomies. The interactive metaTraits website provides search and visualization tools, taxonomy-level summaries, and two workflows for annotating user-submitted genomes or community profiles. metaTraits substantially advances accessibility and interoperability of microbial trait data, enabling comprehensive trait-based analyses of microbiomes across diverse environments. metaTraits is accessible via https://metatraits.embl.de.},
}

@article {pmid41296394,
year = {2025},
author = {Albaijan, D and Albaijan, D and Akbar, A},
title = {Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.},
journal = {Current issues in molecular biology},
volume = {47},
number = {11},
pages = {},
doi = {10.3390/cimb47110890},
pmid = {41296394},
issn = {1467-3045},
abstract = {Pampus argenteus (Zobaidy) is an important fish in Kuwait and the Gulf region due to its economic value in the fish industry. Analyzing the gut microbiome of Zobaidy can help determine the health status of the fish and its responses to environmental changes. In this study, we investigated the microbiome composition of the intestinal tract among seven wild-caught silver pomfret specimens sampled in the Arabian gulf. The 16S rRNA was sequenced using the Illumina platform; then, sequences were analyzed using several bioinformatics tools to identify the microbial diversity, taxonomical status, and functional aspects. The results were 5933 operational taxonomic units (OTUs) categorized into 35 phyla. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacterota were most abundant in the Zobaidy and water samples. At the genus level, we found high relative abundances of Acinetobacter. The results indicated that Lactococcus piscium, Enterococcus cecorum, Psychrobacter arenosus, Vagococcus salmoninarum, and Carnobacterium maltaromaticum are the most commonly present species in the analyzed Zobaidy samples. A heatmap analysis indicated notable differences in the functional categories of intestinal microflora within the Zobaidy2 sample compared to other Zobaidy samples. It should be noted that microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention, and increase sustainability in aquaculture production.},
}

@article {pmid41296232,
year = {2025},
author = {Jalal, D and Lotfi, M and Ziad, GA and Mahfouz, S and Madney, Y and Bayoumi, A and Hassanain, O and Tolba, M and Hashem, M and Elanany, M and Sayed, AA and Shalaby, L},
title = {Dual Transmission Dynamics of Carbapenem Resistance in Pediatric Oncology: Plasmid-Mediated and Clonal Spread of blaNDM-5 Enterobacterales.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {41296232},
issn = {2193-8229},
support = {54699605//Pfizer/ ; },
abstract = {INTRODUCTION: Carbapenem-resistant Enterobacterales (CRE) pose a major threat to immunocompromised pediatric oncology patients. However, the routes of resistance spread in this vulnerable population remain poorly understood, despite their importance for guiding infection control.

METHODS: We analyzed 189 CRE bloodstream isolates (106 Escherichia coli, 72 Klebsiella pneumoniae, and 11 other Enterobacterales) collected at the Children's Cancer Hospital Egypt 57357 (August 2021-October 2022). Whole genome sequencing was used to assess sequence types, resistance genes, virulence factors, plasmid content, and transmission dynamics.

RESULTS: Carbapenem resistance was primarily mediated by blaNDM-5, carried on species-specific plasmids: IncFIA/IncFII in E. coli and IncFIB/IncHIB megaplasmids in K. pneumoniae, frequently co-harboring additional aminoglycoside, sulfonamide, and fluoroquinolone resistance genes. The most common sequence types were ST361, ST167, and ST405 in E. coli, and ST11, ST383, and ST147 in K. pneumoniae. Clonal clustering was observed in 62.5% of K. pneumoniae but only 17% of E. coli. Plasmid phylogenetics and patient movement data indicated extensive horizontal plasmid transfer across unrelated lineages and patients, including ICU cases. A nonfunctional rmpA variant was found in 30 K. pneumoniae isolates, but no hypermucoviscous phenotype was observed.

CONCLUSION: CRE bloodstream infections in pediatric oncology patients are driven by both clonal expansion and plasmid-mediated dissemination, with plasmids playing a dominant role, especially in E. coli. These findings highlight the limitations of strain-based surveillance and the need for integrated genomic and plasmid-level monitoring to inform infection control in high-risk hospital settings. A Graphical Abstract is available for this article.},
}

@article {pmid41295733,
year = {2025},
author = {O'Donoghue, S and Waters, SM and Morris, DW and Earley, B},
title = {A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111095},
pmid = {41295733},
issn = {2306-7381},
support = {16/RD/US-ROI/11//Department of Agriculture, Food and the Marine (DAFM) US-Ireland R&D partnership call/ ; 2018US-IRL200//the US- Ireland Tri Partite Grant/ ; No. 101000213//European Union Horizons 2020, HoloRuminant project/ ; },
abstract = {Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods-culture, ELISA, and immunohistochemistry-are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host-pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD.},
}

@article {pmid41295660,
year = {2025},
author = {Ren, Q and Lu, W and Zhang, T and Hao, S and Wang, J and Xu, X and Wang, F and Huang, Z and Lei, X and Cao, S and Chen, D and Li, Y},
title = {Comparative Analysis of Bacterial Diversity and Composition in Oral Fluid from Pigs of Different Ages and Water Pipe Wall Biofilms.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111022},
pmid = {41295660},
issn = {2306-7381},
support = {No. 32372957//National Natural Science Foundation of China/ ; },
abstract = {Drinking water pipe biofilms, comprising viable microorganisms, microbial residues, and organic/inorganic particulates, pose significant risks to water safety by promoting the proliferation of opportunistic pathogens, pipe corrosion, and degradation of water quality. Their formation is strongly influenced by environmental conditions within the piping system. However, there is a lack of systematic research investigating the potential correlations between biofilm microbiota and the oral microbiomes of intensively farmed swine, as well as the age-dependent regulatory mechanisms shaping aquatic microbial communities. This pioneering study conducted a comparative analysis of biofilm microbiota from swine house water pipes and oral microbiomes across three growth stages (30-day BBF, 70-day NBF, and 110-day FBF groups), yielding three key findings. First, the biofilm biomass and dominant bacterial genera (e.g., Brevibacterium in BBF vs. Brevundimonas in FBF) exhibited stage-specific variations associated with swine age. Second, while the oral microbiomes showed no significant taxonomic divergence at the phylum or genus level, they shared characteristic phyla, including Actinobacteria and Bacteroidetes, with pipe biofilms, indicating potential cross-habitat microbial interactions. Third, the antibiotic resistance gene (ARG) adeF was consistently detected at high prevalence across all biofilm groups. These findings offer new insights into microbial transmission dynamics and inform risk mitigation strategies for livestock water supply systems.},
}

@article {pmid41295321,
year = {2025},
author = {Liu, X and Fu, C and Gao, Q and Zhang, H and Shi, T and Li, G and Wang, Y and Shang, Y},
title = {Effect of Tryptophan Supplementation Levels on the Cecal Microbial Composition, Growth Performance, Immune Function and Antioxidant Capacity in Broilers.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110736},
pmid = {41295321},
issn = {2218-1989},
support = {ZR2024QC376//Shandong Provincial Natural Science Foundation/ ; CXGC2025F10//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; CXGC2025B03//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; 202228037//Jinan Introductory Innovation Team Project/ ; TSCX202306046//Taishan Industry Experts Program/ ; },
abstract = {BACKGROUND: Tryptophan (Trp) is a limiting amino acid in poultry nutrition. Dietary supplementation of Trp not only enhances production performance, but also supports intestinal barrier integrity, alleviates stress, and boosts immunity, in which the derivatives from gut Trp-metabolizing commensal microbes play crucial roles. However, research on how excessive Trp affects poultry growth, metabolism, and gut microbiota composition remains limited.

METHODS: In this study, we investigated the effects of varying Trp levels (0.23%, 0.29%, 0.35%) on broiler production performance, immune function, and antioxidant levels through controlled feeding trials. These host responses were further correlated with cecal microbiota metagenomic sequencing data using multivariate analysis.

RESULTS: Compared with the basal 0.23% Trp level, a 0.35% of Trp addition significantly impaired broiler body weight gain and feed intake, and 0.29% Trp could increase thymus index and serum superoxide dismutase (SOD) level without affecting the growth performance; neither of these two levels affected the feed conversion rate. The cecal microbial metagenomic data further revealed that Trp supplementation reduced the abundance of harmful bacteria, while increasing the abundance of beneficial bacteria and Trp-metabolizing microorganisms. Correlation analysis showed that Trp supplementation was negatively correlated with body weight (BW) but positively correlated with thymus index and SOD level, with similar trends observed between the abundance of specific Trp-utilizing microorganisms and these indicators. Functional analysis revealed an increase in the abundance of KEGG orthology (KO) related to Trp metabolism from the aforementioned microbes.

CONCLUSIONS: An appropriate addition of Trp (0.29%) can enhance certain metabolic levels without affecting production performance, which might be achieved through relevant metabolic pathways of intestinal microorganisms.},
}

@article {pmid41295300,
year = {2025},
author = {Bai, H and Luo, K and Jin, Y and Sun, X and Zhang, X and Zhao, Y and Muhammad, Y and Huang, A and Yin, P and Zhang, G},
title = {Integrated Metagenomic and Metabolomic Analyses Reveal a Microbiota-Metabolite Axis Associated with Gallstone Pathogenesis.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110714},
pmid = {41295300},
issn = {2218-1989},
support = {82174136//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Gallstone disease is a prevalent digestive disorder worldwide, with incidence increasingly linked to obesity, insulin resistance, and dyslipidemia. Emerging evidence suggests that intestinal microbial communities and their bioactive compounds play a central role in pathogenesis. Here, we aimed to clarify whether diet-related microbial alterations and circulating metabolites contribute to gallstone formation.

METHODS: We integrated dietary inflammatory index (DII) evaluation, genetic analyses of large-scale cohorts, and a cholesterol gallstone mouse model induced by a lithogenic diet (LD). Serum and fecal samples were subjected to metabolomic and metagenomic profiling, followed by multi-omics integration to identify links between microbial taxa, metabolites, and gallstone risk.

RESULTS: Higher DII scores were associated with increased gallstone risk. Genetic evidence supported bile acid and amino acid metabolism as potential mediating pathways, with Akkermansia muciniphila linked to decreased N-acetylarginine levels and CAG-448 showing an inverse association with glycodeoxycholate (GDCA). In LD-fed mice, shotgun metagenomics revealed enrichment of lithogenic taxa such as Bacteroides stercorirosoris and Enterocloster, whereas protective taxa, including Akkermansia muciniphila and CAG-448, were markedly depleted. Untargeted metabolomics confirmed elevations of GDCA and N-acetylarginine together with broader bile acid imbalance, amino acid stress, and long-chain acylcarnitine accumulation. Correlation analyses further showed that protective taxa were inversely associated with risk metabolites, whereas gallstone-enriched microbes displayed the opposite pattern.

CONCLUSIONS: This study provides evidence consistent with a contributory role of gut microbiota-metabolite dysregulation in gallstone pathogenesis. Specific taxa (A. muciniphila, CAG-448) and metabolites (GDCA, N-acetylarginine) may serve as potential biomarkers or targets for microbiota- and diet-based prevention strategies.},
}

@article {pmid41295156,
year = {2025},
author = {Zou, R and Zhang, Y and Zhang, L and Chen, M and Xin, L and Zhang, L},
title = {The Effect of Pseudomonas putida on the Microbial Community in Casing Soil for the Cultivation of Morchella sextelata.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110775},
pmid = {41295156},
issn = {2309-608X},
support = {XJBS-202445; QNYC-202515; Young talent program//Special Fund for Anhui Agricultural Research System; Agricultural Sciences Academy of Anhui Province Talent Project; Science and Technology Innovation Team Project of Anhui Academy of Agricultural Sciences/ ; },
abstract = {Morels are a rare edible and medicinal fungus. A major factor contributing to difficulties with their continuous cropping is alteration in soil microbial communities. Pseudomonas putida is a key microorganism in morel cultivation soils; it has garnered significant attention due to its ability to degrade 1-aminocyclopropane-1-carboxylic acid (ACC), a precursor of ethylene. However, the interaction between Pseudomonas putida and morels remains unclear. This study evaluated the growth-promoting potential of P. putida KT2440 by measuring the casing soil ACC content and assessing its ACC utilization capacity. Metagenomic sequencing was performed to assess the changes in soil microbial composition and function. The results indicated that ACC accumulated in the soil following morel cultivation and that P. putida KT2440 was capable of utilizing ACC as its sole nitrogen source for growth on plates. Inoculation enhanced the depletion of available nitrogen, phosphorus, and potassium; increased bacterial diversity; improved the stability of the soil microbial community; and caused the mycelium of morels to grow earlier. These processes occurred along with a decline in the abundance of the Streptomyces genus. Furthermore, a positive correlation was identified between the abundance of P. putida and ACC deaminase activity in the soil. Overall, this study examined the role of Pseudomonas putida inoculation in modulating the soil microbial community and metabolic processes within casing soil during Morchella sextelata cultivation. The findings indicate that P. putida inoculation promotes Morchella growth through ACC decomposition and microbial restructuring, offering a potential strategy for mitigating ethylene-related suppression in continuous cropping systems.},
}

@article {pmid41294637,
year = {2025},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Dădârlat, DA and Ștef, L},
title = {Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.},
journal = {Clinics and practice},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/clinpract15110206},
pmid = {41294637},
issn = {2039-7275},
abstract = {The oral microbiome may be an indicator of oral pathologies and hormonal fluctuations. Consequently, the proper identification of methods for studying microbial factors is essential. Because more than half of the components of the oral microbiome belong to species that are very difficult or even impossible to cultivate in the laboratory, the assessment of the oral microbiome nowadays is based on genetic sequencing, using techniques such as DNA hybridization, 16S rRNA sequencing, and metagenomics, mainly analyzing saliva and subgingival plaque. Variations in results may be caused by differences in sample type, analysis methods, accuracy in determining cycle phases, and biases introduced by DNA extraction techniques and technical variations. Choosing the right primers for the 16S rRNA gene and reference databases (like HOMD, Greengenes2) is essential for accurately identifying microorganisms. Metagenomic sequencing offers greater taxonomic and functional detail, but it is costlier and presents bioinformatics challenges, including contamination with human DNA. When the patients under study are women, we have to take into consideration the cyclical changes in the menstrual cycle. Studies suggest that estrogen influences local immune and inflammatory responses and can worsen existing gingival inflammation. Certain oral bacteria can even utilize estradiol and progesterone as growth factors. The composition of the oral microbiome is also affected by hormonal contraceptives, carbohydrate intake, smoking, age, body mass index, genetics, and oral hygiene-all factors that need to be controlled for in future studies. Interpreting the biological significance of the reported cyclic changes requires careful examination of the specific methods used in each study.},
}

@article {pmid41294355,
year = {2025},
author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C},
title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118525},
doi = {10.1128/msystems.01185-25},
pmid = {41294355},
issn = {2379-5077},
abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.

IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.},
}

@article {pmid41294346,
year = {2025},
author = {Bodourian, CS and Imran, M and Georgakis, ND and Papageorgiou, AC and Labrou, NE},
title = {Structural and functional characterization of a metagenomically derived γ-type carbonic anhydrase and its engineering into a hyperthermostable esterase.},
journal = {Protein science : a publication of the Protein Society},
volume = {34},
number = {12},
pages = {e70396},
doi = {10.1002/pro.70396},
pmid = {41294346},
issn = {1469-896X},
mesh = {*Carbonic Anhydrases/chemistry/genetics/metabolism ; *Esterases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Enzyme Stability ; Models, Molecular ; Protein Engineering ; Amino Acid Sequence ; Escherichia coli/genetics ; Molecular Sequence Data ; },
abstract = {The 16S microbial community profiling of a metagenomics library from geothermal spring at Lisvori (Lesvos island, Greece) enabled the identification of a putative sequence exhibiting 95% identity to the γ-type carbonic anhydrase (γ-CA) from Caloramator australicus (γ-CaCA). The sequence of γ-CaCA was amplified by PCR, cloned, and expressed in E. coli. Activity assays showed that γ-CaCA possesses very low, but detectable, anhydrase activity, while exhibiting no measurable esterase activity. Differential scanning fluorimetry (DSF) revealed that the enzyme shows high thermal stability with a melting temperature (Tm) approximately 65-75°C in the pH range between 5.5 and 9.0. The structure of γ-CaCA was determined by X-ray crystallography at 1.11 Å resolution, the highest resolution reported so far for a γ-CA. The enzyme was crystallized as a trimer in the crystallographic asymmetric unit and contains three zinc-binding sites, one at each interface of neighboring subunits of the trimer. Structure-based rational design enabled the design and creation of a mutant enzyme (γ-CaCAmut) which possessed a heptapeptide insertion at the active-site loop and two-point mutations. Kinetic analysis demonstrated that γ-CaCAmut was successfully converted into a catalytically active esterase indicating successful activity gain through structure-guided engineering. The thermostability of γ-CaCAmut was significantly increased, aligning with the thermostability typically observed in hyperthermostable enzymes. X-ray crystallographic analysis of the γ-CaCAmut structure at 2.1 Å resolution, provided detailed structural insights into how the mutations impact the overall enzyme structure, function, and thermostability. These findings provide valuable structural and functional insights into γ-CAs and demonstrate a strategy for converting an inactive enzyme into a catalytically active form through rational design.},
}

*Carbonic Anhydrases/chemistry/genetics/metabolism
*Esterases/chemistry/metabolism/genetics
Crystallography, X-Ray
Enzyme Stability
Models, Molecular
Protein Engineering
Amino Acid Sequence
Escherichia coli/genetics
Molecular Sequence Data

@article {pmid41293880,
year = {2025},
author = {Damian, D},
title = {Metagenomic Applications in the Early Detection of Human Viral Threats.},
journal = {Viral immunology},
volume = {},
number = {},
pages = {},
doi = {10.1177/08828245251400169},
pmid = {41293880},
issn = {1557-8976},
abstract = {The rapid evolution of viral pathogens presents significant challenges for global health, as traditional methods for virus detection often fail to identify novel or genetically diverse viruses. The emergence and reemergence of viral pathogens necessitate more advanced and inclusive diagnostic approaches. This review aims to explore the role of metagenomics in overcoming the limitations of traditional viral detection methods and to assess its impact on the discovery, characterization, and surveillance of viral pathogens. A comprehensive review of recent studies employing metagenomic approaches to viral detection was conducted. High-throughput sequencing technologies and bioinformatics tools were highlighted as key components in enabling broad-spectrum viral identification and characterization. Metagenomic approaches have successfully identified novel pathogens, including new arboviruses and reemerging strains of known viruses. These techniques provide a more complete understanding of viral diversity and dynamics, surpassing the limitations of targeted assays and culturing methods. Key findings emphasize the capability of metagenomics to detect viruses previously undetected by conventional methods, improving the scope of surveillance. Metagenomics offers transformative advantages for viral surveillance and outbreak management. It enhances early detection, allows for better-informed responses to viral threats, and contributes to more effective strategies for managing emerging and reemerging viral pathogens. Integration of metagenomic techniques into public health practices is crucial for combating the evolving landscape of viral diseases.},
}

@article {pmid41293547,
year = {2025},
author = {Paul, D and Paasisalo, I and Putkinen, A and Jones, CM and Kohl, L and Hallin, S and Pihlatie, M and Siljanen, HMP},
title = {Microorganisms in the phyllosphere of Norway spruce controlling nitrous oxide dynamics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf196},
pmid = {41293547},
issn = {2730-6151},
abstract = {Current climate change assessments and greenhouse gas flux models often lack information on the microbiological processes that consume atmospheric nitrous oxide (N2O), a potent greenhouse gas. There is limited understanding of phyllospheric microorganisms controlling N2O exchange. In this study, we determined the microbial potential for N2O consumption in aboveground vegetation in boreal forests. For this, we collected shoot samples from upland spruce forests in Finland and used a novel targeted metagenomics approach with a hybridization capture of gene-specific probes. Most of the samples contained nosZ genes, encoding the N2O reductase. Phylogenetic placement showed a significantly higher relative abundance (P < .01) of nosZ Clade I than nosZ Clade II. Bacterial members such as Comamonadaceae, Hydrogenophaga, and Paracoccus, which all harbor nosZ Clade I, were found in high relative abundance in the spruce shoots across the sites, suggesting they play a role in N2O consumption capabilities in the spruce phyllosphere. Anoxic incubations, utilizing gas chromatography for N2O analyses, showed potential N2O consumption activity across the spruce samples. The presence of nirK and nirS suggests potential for denitrification, possibly resulting in N2O production. Our finding provides evidence of microbial communities in spruce canopies with potential for N2O exchange. Given the vast coverage of boreal forests globally, understanding the role of phyllospheric microorganisms in N2O exchange is crucial for improving the accuracy of greenhouse gas models and enhancing climate prediction reliability.},
}

@article {pmid41293456,
year = {2025},
author = {Li, Z and Zhu, P and Zhang, Z and Li, Z and Liu, P and Meng, L and Yang, Q and Yang, Z and Song, J},
title = {Metavirome Identification and Pathogenicity Evaluation of Tibet Orbivirus in Pigs.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {6628384},
pmid = {41293456},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Swine Diseases/virology ; *Reoviridae Infections/veterinary/virology ; Tibet/epidemiology ; *Orbivirus/pathogenicity/genetics/isolation & purification ; Virulence ; Viremia/veterinary/virology ; Phylogeny ; },
abstract = {Tibet orbivirus (TIBOV) is an orbivirus transmitted by mosquitoes and Culicoides, despite specific neutralizing antibodies being detected in pigs, but the molecular genetic characteristics of TIBOV strains in infected pigs are completely uncharted, and their pathogenicity in piglets is poorly elucidated. This study aimed to investigate the genetic characteristics of TIBOV in infected pigs and evaluate the pathogenicity of TIBOV in weaned piglets. Through viral metagenomic sequencing, seven segments (VP1-VP4, VP6, NS1, and NS2) of TIBOV were obtained from swine tissues, and the sequences showed high identity with TIBOVs isolated from Culicoides, mosquitos, and cattle. After infection with TIBOV, the body temperature, appetite, and behavior of the piglets were normal, whereas hemorrhage nodes were observed on the hooves of all piglets and on the abdominal skin of one pig. Viremia was first detected at 2 days postinfection (dpi), peaked at 6 dpi, and remained high until 21 dpi. The virus was distributed in multiple organs, and the highest viral load and strongest viral nucleic acid signals were observed in the spleen. The most severe lesion was observed in the spleen with white pulp atrophy, a decreased number of lymphocytes, and widened septa of the medullary cord, indicating that the spleen was the most important target organ of TIBOV infection. The levels of inflammatory cytokines, including interleukin (IL)-18, tumor necrosis factor-α (TNF-α), interferon (IFN)-α, and IFN-λ3 in peripheral blood lymphocytes decreased significantly from 2 to 6 dpi, and interferon-stimulated gene-15 (ISG-15) and IFN regulatory factor 7 (IRF-7) expression levels declined significantly from 2 to 9 dpi, suggesting that the host immune response was inhibited within 6 dpi. Our findings confirmed that TIBOV elicited long-term viremia with mild clinical symptoms in piglets, the spleen was the target organ of TIBOV proliferation, and the host immune response may be slightly inhibited in the early stage of viral infection.},
}

Animals
Swine
*Swine Diseases/virology
*Reoviridae Infections/veterinary/virology
Tibet/epidemiology
*Orbivirus/pathogenicity/genetics/isolation & purification
Virulence
Viremia/veterinary/virology
Phylogeny

@article {pmid41293056,
year = {2025},
author = {Lee, JA and Won, D and Lee, EH and Lee, ST and Park, KK and Shin, S and Jeong, SJ},
title = {Utilization of cell-free DNA metagenomic analysis for early detection and microbial identification in prosthetic joint infections: a prospective cohort study in Korea.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663857},
pmid = {41293056},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Prospective Studies ; Synovial Fluid/microbiology/chemistry ; Female ; Male ; Aged ; Middle Aged ; *Cell-Free Nucleic Acids/genetics/analysis ; *Metagenomics/methods ; Republic of Korea ; Early Diagnosis ; *Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {BACKGROUND: Prosthetic joint infection (PJI) is a severe complication of hip or knee arthroplasty, often necessitating invasive intervention and posing a high risk of adverse outcomes. Early diagnosis and tailored antibiotic therapy are critical for the effective management of PJI. This study evaluated the utility of cell-free deoxyribonucleic acid (cfDNA) extracted from synovial fluid to diagnose PJI and identify the causative pathogens.

METHODS: This prospective, single-center study included a PJI group consisting of patients with confirmed infections based on the European Bone and Joint Infection Society criteria and a non-PJI group comprising patients without suspected PJIs who underwent joint surgery or aspiration. Synovial fluid samples were collected from all patients, and various culture methods, including conventional synovial fluid, sonication, and tissue and blood cultures, were applied along with cfDNA analysis.

RESULTS: A total of 35 patients were included, with 20 diagnosed with PJI and 15 classified as non-PJI. The median cfDNA concentration in synovial fluid was significantly higher in the PJI group (4.560 ng/μl, interquartile range (IQR) [3.320-6.348]) compared with the non-PJI group (0.028 ng/μl, IQR [0.009-0.273]) (p < 0.001). The Youden index identified a cfDNA concentration ≥ 1.59 ng/μl as strong likelihood of PJI. Culture positivity rates in the PJI group were as follows: synovial culture (10/20, 50.0%), sonication culture (8/9, 88.9%), tissue culture (2/8, 25.0%), and blood culture (2/12, 16.7%). The bacterial detection rate of cfDNA was 65.0% (13/20).

CONCLUSION: cfDNA concentration was significantly higher in the PJI group, with synovial cultures showing substantial agreement. Additionally, cfDNA sequencing detected pathogens in patients who had received prior antibiotic therapy and identified multiple pathogens in polymicrobial infections. These findings highlight cfDNA analysis as a valuable diagnostic tool for PJI, with the potential to enhance current diagnostic approaches.},
}

Humans
*Prosthesis-Related Infections/diagnosis/microbiology
Prospective Studies
Synovial Fluid/microbiology/chemistry
Female
Male
Aged
Middle Aged
*Cell-Free Nucleic Acids/genetics/analysis
*Metagenomics/methods
Republic of Korea
Early Diagnosis
*Bacteria/genetics/isolation & purification/classification
Aged, 80 and over
Arthroplasty, Replacement, Knee/adverse effects

@article {pmid41292684,
year = {2025},
author = {Liu, J and Sha, Y and Dang, R and Zhou, L and Zhou, M and Tan, Y and Wang, J and Ran, G and Xie, W and Xia, D and Wang, L and Zhao, X and Goi, BM and Yu, J and Xiao, L},
title = {Acetate-based syntrophy enhances methane production potential of ruminant feces.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706620},
pmid = {41292684},
issn = {1664-302X},
abstract = {Livestock feces contribute to approximately 32% of global methane emissions. Although ruminants are generally believed to have a higher methane production potential than non-ruminants, the dominant pathways and key regulatory processes underlying methane generation in ruminants remain poorly understood, impeding effective manure management and accurate livestock emission assessments. In this study, metagenomic and carbon isotope techniques were employed to investigate methane production potential and key pathways in sheep, pig, chicken, and duck feces. Methane production potential of ruminant sheep feces was significantly higher (approximately threefold) compared to that of non-ruminants. Isotopic analysis of methane sources revealed that sheep feces primarily produce methane through the acetoclastic pathway, whereas the other three likely rely on CO2 reduction. Metagenomic analysis of methanogenic pathways further indicated that the abundance of functional genes associated with acetoclastic methanogenesis is significantly higher in sheep feces compared to the other three. Moreover, the co-occurrence network analysis highlighted a tightly coordinated, cross-species partnership between fermentative acetogenic bacteria and methanogenic archaea in the sheep fecal microbiome. Together, our findings provide insights into some key methanogenic pathways, such as acetoclastic methanogenesis, contributing to high methane production from ruminant feces.},
}

@article {pmid41292560,
year = {2025},
author = {Li, X and Wang, Y and Ma, F and Zhao, C and Zhang, Y and Zhu, Y and Zhang, Y and Hou, S and Li, B and Yang, F and Hao, L and Zhu, T},
title = {Chaperone-mediated thermotolerance in hyperthermophilic composting: Molecular-Level protein remodeling of microbial communities.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100630},
pmid = {41292560},
issn = {2666-4984},
abstract = {Hyperthermophilic composting (HC) represents a promising approach for converting organic solid waste into valuable resources by leveraging extreme temperatures to enhance microbial degradation and detoxification processes. In this high-temperature environment, microbial communities undergo dynamic succession, where thermophilic bacteria dominate and drive efficient organic matter transformation through adapted metabolic pathways and stress responses. These adaptations include the stabilization of cellular structures and enzymes, often mediated by heat shock proteins (HSPs) that prevent protein misfolding under thermal stress. However, the integrated mechanisms linking community-level functional shifts to molecular-level protein remodeling in thermophiles during HC remain poorly understood. Here we show a coordinated interaction of functional succession and molecular adaptations within thermophilic bacteria in HC, which collectively achieve heat resistance. This interaction encompasses enhanced metabolic and genetic modules, accounting for 97 % of the variance observed in thermophile abundance. Metagenomic analyses revealed upregulation of translation, transcription, amino acid metabolism, and cell wall biosynthesis, coupled with suppression of mobilome functions to maintain genomic stability, as confirmed by partial least squares path modeling and Boruta analyses. Molecular dynamics simulations of key enzymes from the thermophile Truepera further demonstrated intrinsic structural rigidity, reduced hydrophobic exposure, and hierarchical chaperone activity involving DNAJ, DNAK, and GroEL for protein repair. These findings enhance our comprehension of microbial thermotolerance and establish a foundation for optimizing composting efficiency and advancing heat-resistant microbial applications in biotechnology and waste management. Additionally, they offer insights into the evolution of thermophiles, protein engineering, and stress adaptation across various biological and industrial systems, thereby promoting the integration of environmental engineering and systems biology.},
}

@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.

AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.

METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as ≥2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.

RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.

CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}

Humans
Female
*Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging
*Adverse Childhood Experiences
*Gastrointestinal Microbiome
Adult
*Brain/diagnostic imaging/physiopathology
Middle Aged
*Brain-Gut Axis
Magnetic Resonance Imaging
Young Adult
Multiomics

@article {pmid41291846,
year = {2025},
author = {Ding, J and Yang, W and Li, X and Liu, X and Zhao, J and Sun, T and Liu, H},
title = {The microbial community metabolic regime adapts to hydraulic disturbance in river-lake systems with high-frequency regulation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00821-3},
pmid = {41291846},
issn = {2524-6372},
support = {National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; },
abstract = {BACKGROUND: River-lake ecosystems are crucial for the rational allocation of water resources, but frequent water diversion can destabilize water quality due to hydraulic disturbance. Microbial communities can respond rapidly to such external perturbations and influence these systems through the effects on nutrient metabolism. Therefore, understanding how microbial communities respond to hydraulic shocks in aquatic systems and whether they can adapt to such disturbances is essential for maintaining the health of river-lake systems. We used 16S rRNA and metagenomic sequencing technologies to examine the metabolic regimes of microbial communities during water regulation and non-regulation periods in river-lake systems.

RESULTS: We found that hydraulic disturbance tended to drive the microbial community toward homogenized selection, thereby weakening its stability. Flow velocity (V) and the nitrate (NO3[-]-N) concentration significantly affected microbial community composition and abundance, with clear threshold effects. We established low (V = 0.284 m/s, NO3[-]-N = 0.031 mg/L) and high (V = 0.461 m/s, NO3[-]-N = 0.055 mg/L) thresholds. These thresholds categorize microbial communities into three distinct regimes: regime1 (R1), regime 2 (R2), and regime 3 (R3). The microbial abundances in R1 and R3 were significantly higher than those in R2 (p < 0.01), while the community in R3 exhibited a strong denitrification capacity. In R3, the microbial community enhanced its denitrification metabolism by promoting the growth of denitrifying microbial genera (e.g., Pseudomonas and Flavobacterium) to counterbalance the impact of high V and NO3[-]-N. These strains contributed the denitrification-related genes nasA, narB, nirB, and nirD to the community, thereby promoting the NO3[-]-N metabolism and reducing environmental NO3[-]-N concentrations. In addition, we predicted microbial community abundance using an artificial neural network to validate the thresholds we identified.

CONCLUSIONS: Our study provides theoretical support for understanding how microbial communities adapt to high-frequency hydraulic disturbances and offer valuable insights for managers to adjust water diversion strategies in a timely manner, thereby safeguarding the integrity of river-lake ecosystems.},
}

@article {pmid41291642,
year = {2025},
author = {Xie, Q and Li, D and Ren, C and Shen, Y and Lin, S and Chen, W},
title = {Metabolomic and metagenomic analyses reveal distinct microenvironmental signatures between clear aligner-associated and tooth surface dental plaque.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07231-4},
pmid = {41291642},
issn = {1472-6831},
support = {No. 2023J01643//the Fujian Provincial Natural Science Foundation of China/ ; },
}

@article {pmid41291413,
year = {2025},
author = {Zhang, J and Zhao, Y and Li, W and Xu, J and Chen, Y and Yang, S and Wu, P and Li, Y and Zhou, C and Zhang, W},
title = {Viromic analysis of cerebrospinal fluid (CSF) samples identified an unclassified RNA virus exhibiting an atypical genomic architecture.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {776},
pmid = {41291413},
issn = {1471-2180},
mesh = {Humans ; *Genome, Viral ; Phylogeny ; Open Reading Frames ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; *RNA Viruses/genetics/classification/isolation & purification ; *Cerebrospinal Fluid/virology ; *Meningoencephalitis/virology/cerebrospinal fluid ; Metagenomics ; Viral Proteins/genetics ; Male ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {The central nervous system (CNS) is highly susceptible to infections that can lead to severe neurological morbidity and mortality. Despite advances in diagnostic technologies, a significant proportion of encephalitis and meningitis cases remain etiologically undiagnosed, underscoring the need for novel pathogen discovery approaches. Here, we report the identification of a novel unclassified RNA virus, provisionally named hucaurvirus ("human CSF-associated unclassified RNA virus"), in the cerebrospinal fluid (CSF) of a pediatric patient with unexplained meningoencephalitis, using metagenomic next-generation sequencing (mNGS). The hucaurvirus exhibits a monopartite, positive-sense RNA genome of 6.5 kb which contains two overlapping open reading frames (ORFs), which was confirmed by conventional PCR amplification and Sanger sequencing. The large ORF encodes a polyprotein containing a capsid domain, while the small ORF overlaps within the large ORF and encodes the RNA-dependent RNA polymerase (RdRp) protein. BLASTp search based on the amino acid sequence of RdRp showed that hucaurvirus had the highest sequence identity and query coverage of 39.2% and 90%, respectively, to a noda-like virus (GenBank no. MT138110). Phylogenetic analysis showed that hucaurvirus was closely related to four viruses annotated as noda-like viruses, forming a cluster that is adjacent to the cluster of the Carmotetraviridae family and appears to form a new viral family within the order Tolivirales. PCR screening confirmed the presence of hucaurvirus in one of ten CSF samples, validating its detection. Our findings emphasize the utility of mNGS in uncovering novel pathogens and expanding our understanding of viral diversity in CNS infections.},
}

Humans
*Genome, Viral
Phylogeny
Open Reading Frames
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing
*RNA Viruses/genetics/classification/isolation & purification
*Cerebrospinal Fluid/virology
*Meningoencephalitis/virology/cerebrospinal fluid
Metagenomics
Viral Proteins/genetics
Male
RNA-Dependent RNA Polymerase/genetics

@article {pmid41291216,
year = {2025},
author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F},
title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02628-8},
pmid = {41291216},
issn = {1432-184X},
abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.},
}

@article {pmid41291200,
year = {2025},
author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H},
title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29758-w},
pmid = {41291200},
issn = {2045-2322},
support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; },
abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.},
}

@article {pmid41291020,
year = {2025},
author = {Mwape, I and Silwamba, S and Chibesa, K and Luchen, CC and Musukuma-Chifulo, K and Collins, J and Chauwa, A and Liswaniso, F and Nzangwa, TB and Kuntawala, DH and Chisenga, CC and De Beer, C and Chilengi, R and Lu, XJ and Yingst, S and Wickiser, JK and Simuyandi, M},
title = {Pathogen-focused metagenomic analysis reveals predominance of human rotavirus genotypes G3 and G12 in Zambian pediatric diarrhea cases.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-28946-y},
pmid = {41291020},
issn = {2045-2322},
support = {DEL-22-012//DELTAS Africa/ ; },
abstract = {Despite global improvements in water, sanitation, and rotavirus vaccination, rotavirus-associated diarrhea continues to cause significant morbidity and mortality among children in low-to-middle-income countries. Genomic surveillance is essential for evaluating vaccine efficacy and detecting emerging escape variants. In this study, we used VirCapSeq-VERT (VCS) to analyze rotavirus genetic diversity during Zambia's 2023 diarrhea surveillance. Stool samples from under five children with diarrhea were collected from health facilities across nine provinces. Out of 245 samples, 72 were rotavirus qPCR-positive with Ct <33 and underwent targeted viral enrichment and sequencing using VCS on the Illumina NextSeq2000. Bioinformatic analysis showed 70/72 strains had near complete genome constellations being genotyped as 45 Wa-like, 11 DS-like, and 14 reassortant strains. VP7 and VP4 analyses showed diverse genotypes (G1-G3, G8-G9, G12; P[4], P[6], P[8], P[11] clustering with vaccine and wild-type strains. Furthermore, G3 and G12 combined with P[4], P[6], and P[8] were the most predominant genotypes (35/70 and 13/70, respectively). Notably, nine samples had an M5 VP3 genotype with a 91% similarity to a simian rotavirus strain. Antigenic epitope analysis highlighted substitutions in P[6], G2, and G12, associated with immune escape. G3P[8] was the most common in severe cases. Fully vaccinated children showed significantly milder disease (p = 0.033). This study highlights VCS's utility in detecting viral diversity, reassortment, zoonotic transmission, and immune escape variants, providing crucial insights for assessing vaccine performance and public health strategies.},
}

@article {pmid41291018,
year = {2025},
author = {Angwong, C and Pientong, C and Ekalaksananan, T and Burassakarn, A and Tongchai, P and Overgaard, HJ and Aromseree, S},
title = {Systematic review and meta-analysis of virome profiles and quantification of Torque teno virus load in blood of acute febrile illness patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29413-4},
pmid = {41291018},
issn = {2045-2322},
support = {IN66039//Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand/ ; },
abstract = {Acute febrile illness (AFI) is a sudden fever which can be caused by various viruses such as dengue, Zika, and chikungunya viruses. This study aimed to identify viruses present in AFI patients via metagenomic next-generation sequencing (mNGS) through meta-analysis, and to compare the prevalence and viral load of the common viruses between AFI patients and healthy blood donors in northeastern Thailand. Our meta-analysis revealed that human anelloviruses-including torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV)-were the most prevalent viruses detected. We confirmed their presence in peripheral blood mononuclear cells from 203 AFI patients and 100 healthy blood donors using real-time PCR. TTV was the most identified anellovirus, detected in 84% of healthy donors and 61.08% of AFI patients. The mean TTV load was significantly lower in AFI patients compared to healthy donors. In AFI patients, TTV load increased in those with higher total white blood cell and neutrophil counts but decreased in those with higher lymphocyte counts. Our findings demonstrate high prevalence of anelloviruses, particularly TTV, in both AFI patients and healthy donors, and highlight the potential value of the TTV load in blood as an immune status biomarker in AFI patients.},
}

@article {pmid41290854,
year = {2025},
author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R},
title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41955},
pmid = {41290854},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.},
}

*Soil Microbiology
*Bacteria/genetics/classification
*Fungi/genetics/classification
*Soil Pollutants/analysis
Mercury/analysis
Ecosystem
*Microbiota
Soil/chemistry
Metagenomics
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid41290836,
year = {2025},
author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS},
title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41935},
pmid = {41290836},
issn = {2045-2322},
mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.},
}

Animals
*Insemination, Artificial/veterinary/methods
*Semen/microbiology
Swine
Female
Male
Feces/microbiology
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Metagenomics

@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66678-9},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}

@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}

*Geologic Sediments/virology/microbiology
Genome, Viral/genetics
China
Virome/genetics
Metagenomics
Mining
Metagenome
Phylogeny
Ecosystem
Acids
*Host Microbial Interactions

@article {pmid41290639,
year = {2025},
author = {Fisher, LWS and Thorpe, HA and Sassera, D and Corander, J and Bryant, JM},
title = {High frequency body site translocation of nosocomial Pseudomonas aeruginosa.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9862},
pmid = {41290639},
issn = {2041-1723},
support = {220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
mesh = {*Pseudomonas aeruginosa/genetics/isolation & purification/physiology/pathogenicity ; Humans ; *Cross Infection/microbiology/transmission ; *Pseudomonas Infections/microbiology/transmission ; Female ; Male ; *Bacterial Translocation ; Middle Aged ; Metagenomics ; },
abstract = {Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but the rate and directionality of this process is unknown. Here, we explore within-host diversity as well as the body site translocation dynamics using de-convoluted metagenomic P. aeruginosa reads from 256 hospital patients sampled at both respiratory and gut sites. Of the 84 patients where P. aeruginosa genomes could be recovered, there were 27 cases where the same P. aeruginosa clone was detected across multiple body sites. Using a simulation approach, we find that the majority of body site sharing is likely due to within-patient translocation of clones rather than independent acquisition from the hospital environment. Using ancestral reconstruction, we predict that most clones likely occupied a respiratory niche, and that the probable direction of clone transmission is lung-to-gut. Analysis of within-patient variation highlights strong enrichment of mutations in genes associated with antimicrobial resistance, irrespective of sample type. We report significantly more translocation than has been previously reported and highlight that lower respiratory tract infections can result in persistent gut colonisation of P. aeruginosa, a major risk factor for sepsis in vulnerable patients.},
}

*Pseudomonas aeruginosa/genetics/isolation & purification/physiology/pathogenicity
Humans
*Cross Infection/microbiology/transmission
*Pseudomonas Infections/microbiology/transmission
Female
Male
*Bacterial Translocation
Middle Aged
Metagenomics

@article {pmid41290112,
year = {2025},
author = {An, Z and Bao, Y and Yang, Y and Su, X and Dong, F and Xiao, X and Chen, C and Fu, H and Lin, H and Sun, F},
title = {Quorum quenching driven enzymatic activity and metabolic pathway modulation in anaerobic reactor for enhanced methane production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133668},
doi = {10.1016/j.biortech.2025.133668},
pmid = {41290112},
issn = {1873-2976},
abstract = {The effect of bioaugmentation with the quorum-quenching bacterium Proteus sp. ZJ5 on methane production during anaerobic process was evaluated at dosages of 0-280 mg·L[-1]. The maximum methane yield was achieved at 140 mg·L[-1]Proteus sp. ZJ5, showing a 17 % increase over the control. Enhanced methane production correlated with elevated activities of key enzymes, including protease, α-glucosidase, acetate kinase, and electron transport system, particularly α-glucosidase, which increased by 178 %. The modified Gompertz model confirmed greater methane potential, shorter lag time, and improved COD removal. Metagenomic analysis revealed notable shifts in microbial community structure, characterized by increased relative abundances of hydrogenotrophic methanogens such as Methanosarcina and Methanoculleus, as well as enrichment of genes involved in glycolysis, amino acid metabolism, and methanogenesis pathways. These results demonstrate that Proteus sp. ZJ5 enhances methane recovery by modulating enzymatic activity and microbial metabolic pathways, providing new insight into improving anaerobic treatment performance.},
}

@article {pmid41289884,
year = {2025},
author = {Liu, C and Yang, Q and Shen, Y and Xu, M},
title = {Multidimensional review of viral infectious ocular diseases: Post-Pandemic epidemiology and future directions for control.},
journal = {Molecular aspects of medicine},
volume = {106},
number = {},
pages = {101428},
doi = {10.1016/j.mam.2025.101428},
pmid = {41289884},
issn = {1872-9452},
abstract = {Viral Infectious Ocular Diseases (VIODs) remain a major global cause of vision loss, ranging from highly transmissible conjunctivitis to blinding keratitis and complex neuro-ophthalmic syndromes. Furthermore, the Coronavirus Disease 2019 (COVID-19) pandemic and subsequent reported ocular diseases have fundamentally changed the landscape of VIOD epidemiology and management. Epidemiological data indicate heterogeneous effects on common infections such as Adenoviral conjunctivitis due to varying compliance with hygiene measures. Concurrently, systemic immunological events, notably those induced by COVID-19 infection or certain vaccinations, have been linked to the reactivation of latent Alphaherpesviruses, including Herpes Simplex Virus (HSV) and Varicella Zoster Virus (VZV). The metagenomic next-generation sequencing (mNGS) offers a significantly improved diagnostic yield (up to 92.7 % in some cohorts) for complex infectious keratitis compared to conventional methods, providing an unbiased tool crucial for timely, targeted treatment. Therapeutic challenges are defined by the persistent threat of antiviral resistance, primarily driven by mutations in the viral Thymidine Kinase (TK) gene. To overcome poor ocular bioavailability, novel drug delivery systems (NDDS), such as Acyclovir-loaded Niosomes and Cubosomes, show promise by enabling sustained drug release and enhanced corneal permeation. Effective future VIOD control requires a multi-pronged strategy integrating robust global surveillance, rapid deployment of advanced molecular diagnostics, and the clinical implementation of resistance-beating therapies delivered via optimized nanocarrier platforms. This review provides the current understanding of VIODs, focusing on the epidemiological shifts observed post-2020, advancements in molecular diagnostics, challenges posed by antiviral resistance, and the emergence of next-generation therapeutic strategies.},
}

@article {pmid41289665,
year = {2025},
author = {Diabil, GHMJ and Jalali, A and Komijani, M},
title = {Metagenomic analysis of antibiotic resistance and pathogens in landfill leachates: Environmental implications.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140365},
doi = {10.1016/j.jhazmat.2025.140365},
pmid = {41289665},
issn = {1873-3336},
abstract = {Landfill leachates, rich in antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs), pose significant risks to human, animal, and environmental health. This study analyzed leachate samples from seven sites in Gilan, Mazandaran, and Golestan provinces, northern Iran, using metagenomic sequencing, Inductively Coupled Plasma analysis (ICP), and Gas Chromatography (GC)-based BTEX (Benzene,Toluene, Ethylbenzene and Xylene) quantification. ShortBRED (Short, Better Representative Extract Dataset) analysis revealed higher ARG abundance in GL2 and GL4 compared to GL1 and GL7 (p = 0.0056-0.0265), with Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae as dominant bacterial families. Statistical analysis revealed that metal contaminants had strong correlations with the microbial community structure. Sb and Zn concentrations were strongly negatively correlated with total ARGs abundance (Sb: r = -0.883, p = 0.013; Zn: r = -0.857, p = 0.024). Moreover, there was obvious intense niche partitioning, and major bacterial families showed highly significant correlations with specific metals; e.g., Enterobacteriaceae abundance was inversely correlated with copper (Cu; r = -0.89, p = 0.007) but positively correlated with zinc, antimony, and tin (r = 0.79-0.85, p < 0.05), suggesting metal-mediated selection and co-selection for resistance mechanisms. A PERMANOVA confirmed that spatial analysis was precluded by the sampling design (R[2] = 1.0, residual df = 0), limiting site comparisons to descriptive trends. A correlation between ARGs and elements was noted at GL7 (r = 0.476, p = 0.0251). BTEX levels varied significantly, with higher concentrations in GL2 vs. GL4 (p = 0.0482), GL5 vs. GL3 (p = 0.0090), GL5 vs. GL4 (p = 0.0044), and GL5 vs. GL7 (p = 0.0251), and benzene/toluene exceeding ethylbenzene (p = 0.0276, p = 0.0093) and xylene (p = 0.0038, p = 0.0012). These findings highlight landfill leachates as reservoirs of pathogenic ARB and ARGs, influenced by environmental and microbial factors. The study suggests leveraging leachate-associated bacteria for biochemical treatment of antibiotics and ARGs, and provides a basis for targeted surveillance and risk management to mitigate ARG dissemination and protect ecological/public health.},
}

@article {pmid41289603,
year = {2025},
author = {Zheng, Z and Zhang, R and Hong, W and Yang, S and Lin, X and Shu, W and Price, GW and Song, L},
title = {Landfills as Hotspots of Multidrug Resistance Genes: Profiles, Drivers, and Hosts.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13743},
pmid = {41289603},
issn = {1520-5851},
abstract = {The United Nations has identified municipal solid waste (MSW) landfills as significant reservoirs of antibiotic resistance genes (ARGs). Although ARG profiles, their primary drivers, and associated hosts have been well characterized in landfill leachate, such information remains limited for MSW landfills, which are the original source of the resistome. This knowledge gap impedes effective ARG monitoring at the source and poses challenges for public health management. Herein, we investigated the profiles of ARGs, their potential drivers, and associated hosts in refuse samples collected from a large-scale landfill using metagenomic sequencing and quantitative polymerase chain reaction analysis. Our findings revealed that landfills harbor diverse ARGs, with multidrug resistance genes (MDRGs) emerging as the dominant class, accounting for 39.78% of all ARGs detected. Notably, MDRGs exhibited high mobility potential (associated with plasmids, phages, and mobile genetic elements (MGEs)) and were frequently colocated with virulence factors. Pseudomonas, Acinetobacter, and Brevundimonas were identified as key MDRG hosts. Partial least-squares path modeling analysis indicated that MDRG variation was driven by multiple factors (i.e., MGEs, metal resistance genes (MRGs), hosts, and environmental factors). Additionally, metagenome-assembled genomes were found to carry multiple MDRGs. Collectively, these results underscore the role of landfills as critical hotspots for MDRGs.},
}

@article {pmid41289391,
year = {2025},
author = {Li, J and Gao, ZY and Chen, C and Liu, Y and Zhang, SY and Xu, J and Zhu, YG and Tang, X},
title = {Microbial necromass carbon enhances arsenic methylation in paddy soils.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2527462122},
doi = {10.1073/pnas.2527462122},
pmid = {41289391},
issn = {1091-6490},
support = {42477003//National Natural Science Fundation of China/ ; LZ25D010002//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Arsenic/metabolism/chemistry ; Methylation ; *Carbon/metabolism ; *Soil/chemistry ; Oryza/growth & development ; Bacteria/metabolism ; Fungi/metabolism ; },
abstract = {Microbial necromass carbon (MNC) constitutes a critical component of soil organic carbon. Yet, how MNC regulates microbial arsenic (As) methylation processes in soil remains unclear. Across major Chinese rice-growing regions, bacterial and fungal necromass carbon showed significant positive correlations (P < 0.05) with the transcribed arsM gene. Soil incubation experiments with seven soils explored how straw and three types of MNC-gram-positive bacterial necromass carbon (G[+]-NC), gram-negative bacterial necromass carbon (G[-]-NC), and fungal necromass carbon (F-NC)-affect As methylation. Our results demonstrated that all types of MNC enhanced As methylation, and G[-]-NC exhibiting the most pronounced effect on methylated As accumulation. The addition of 10 to 60 mg G[-]-NC maximally increased As(III) by 43.0 to 75.9% and enhanced methylated As by 4.4- to 18.0-fold in soil porewater vs. the control. Further, metagenomic and metatranscriptomic analyses demonstrated that G[-]-NC addition upregulated the relative abundance of transcribed arsM and arsC2 genes, which were mostly assigned to Acidobacteriota, Pseudomonadota, Planctomycetota, and Bacteroidota. Notably, the transcriptional activity of arsM-harboring Methanosarcinales and Moorellales was markedly enhanced at the order level. By promoting As reduction process, G[-]-NC provides more substrates for As methylation process in soil. Furthermore, G[-]-NC could be used as a carbon source for As-methylating microorganisms, stimulating the transcriptional activity of arsM, which has been confirmed by the incubation experiment with pure culture of Paraclostridium benzoelyticum TC8. This study highlights the critical role of MNC in regulating As biogeochemistry, establishing a basis for predicting the extent of As methylation and risk of rice straighthead disease in paddy ecosystems.},
}

*Soil Microbiology
*Arsenic/metabolism/chemistry
Methylation
*Carbon/metabolism
*Soil/chemistry
Oryza/growth & development
Bacteria/metabolism
Fungi/metabolism

@article {pmid41289388,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2523178122},
doi = {10.1073/pnas.2523178122},
pmid = {41289388},
issn = {1091-6490},
support = {DK30292//HHS | NIH (NIH)/ ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; K01DK134840/GF/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; },
abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Goblet Cells/metabolism/physiology
*Germ-Free Life
Female
Humans
*Malnutrition/microbiology
Child

@article {pmid41289374,
year = {2025},
author = {Nachman, EJ and Ardis, CK and Ardis, AKB and Nieto, J and Bresson, MM and Robertson, CM and Seale, MN and Villafuerte, NM and Lyu, Z and Preisner, EC and Danhof, HA and Di Rienzi, SC and Becker, YT and Britton, RA},
title = {Erratum for Nachman et al., "Increased fungal burden in the gastrointestinal tract of brain-dead organ donors".},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285825},
doi = {10.1128/spectrum.02858-25},
pmid = {41289374},
issn = {2165-0497},
}

@article {pmid41289310,
year = {2025},
author = {Zhao, JX and Zheng, WB and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Yang, MT and Nan, FL and Jiang, J and Elsheikha, HM and Zhang, XX},
title = {Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {11},
pages = {e0013768},
doi = {10.1371/journal.pntd.0013768},
pmid = {41289310},
issn = {1935-2735},
abstract = {Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.},
}

@article {pmid41288577,
year = {2025},
author = {Wu, QL and Lan, T and Deng, L and Jia, JW and Ren, WT and Wang, HZ and Du, JS and Ren, NQ and Guo, WQ},
title = {Aromatic Pollutants Rewire Soil Microbial Carbon Fixation via Chain Elongation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf254},
pmid = {41288577},
issn = {1751-7370},
support = {ZD2024E004//Natural Science Foundation of Heilongjiang Province of China/ ; },
abstract = {Widespread aromatic pollutants such as benzene, toluene, ethylbenzene, and xylene are traditionally considered to drive soil carbon loss through mineralisation and ecotoxicity. Contrary to this view, our study reveals that low concentrations of these pollutants stimulate microbial carbon chain elongation-a previously overlooked carbon conversion pathway producing medium-chain fatty acids, thereby reshaping soil carbon dynamics. Using phased amplicon sequencing, metagenomics, and metaproteomics of soil microcosms amended with these compounds, we demonstrate that aromatic pollutants bidirectionally regulate carbon chain elongation at both taxonomic and molecular levels. These pollutants selectively enrich Clostridium_sensu_stricto_12 and Rummelibacillus while suppressing Acinetobacter, a key elongation taxon in natural soils. Simultaneously, they inhibit Petrimonas, a syntrophic fatty acid degrader, promoting the accumulation of medium-chain fatty acids. Carbon chain-elongating bacteria cooperate with aromatic degraders, redirecting pollutant-derived carbon towards chain elongation rather than complete mineralisation to CO2. Among them, Bacillus occupies a pivotal niche bridging aromatic degradation and carbon elongation. At the molecular level, aromatic pollutants enhance chain elongation by accelerating substrate uptake and channelling the key intermediate acetyl-CoA into the reverse β-oxidation pathway. Additionally, aromatic pollutants restrain fatty acid biosynthesis pathway by upregulating fabR, whereas inhibiting acrR and fadR. They also maintain NADH availability to alleviate Rex-mediated repression of bcd, a critical gene in the β-oxidation pathway. However, high concentrations of aromatic pollutants disrupt metabolic homeostasis and suppress chain elongation activity. Our findings redefine the ecological impact of aromatic hydrocarbon contamination in soil, demonstrating their role in modulating anaerobic carbon fixation and retention within soil microbial communities.},
}

@article {pmid41288390,
year = {2025},
author = {Kimbrel, JA and Thissen, JB and Lisboa, FA and Mabery, S and Jaing, CJ and Elster, EA and Schobel, SA and Be, NA},
title = {High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0187625},
doi = {10.1128/spectrum.01876-25},
pmid = {41288390},
issn = {2165-0497},
abstract = {The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated "high" quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.IMPORTANCEThe ability to comprehensively and accurately characterize microbial pathogens in wound infections is critical to efficacious treatment and is especially important in the context of complex battlefield injuries. Our study shows that high-quality metagenome-assembled genomes can be obtained from shotgun metagenomic sequence data for military-relevant wound pathogens including Acinetobacter baumannii. We demonstrate that these metagenome assemblies are directly comparable to genomes derived from cultured isolates, thereby supporting the ability to generate genome-level data sets from non-culturable biospecimens and perform comparative assessments that inform future approaches for improving diagnostic precision in military and civilian wound care.},
}

@article {pmid41288174,
year = {2025},
author = {Lvov, DK and Akimkin, VG and Zaberezhny, AD and Borisevich, SV and Alkhovsky, SV},
title = {Virus taxonomy and megataxonomy (Vira domain) - current status.},
journal = {Voprosy virusologii},
volume = {70},
number = {5},
pages = {401-416},
doi = {10.36233/0507-4088-344},
pmid = {41288174},
issn = {2411-2097},
mesh = {*Viruses/classification/genetics ; Archaea/virology/genetics ; Animals ; Humans ; Bacteria/virology/genetics ; Eukaryota/virology/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Metagenomics ; },
abstract = {For nearly 80 years since the discovery of the first virus by the Russian scientist D.I. Ivanovsky, it has been recognized that all organisms of Earth's biosphere serve as natural hosts for viruses. Viruses, grouped within the informal domain Vira, infect all three domains of cellular life: archaea - Archaea, bacteria - Bacteria, and eukaryotes - Eucarya (algae, fungi, protozoa, plants, invertebrates, and vertebrates). The formation of viral population gene pools through interactions with the gene pools of their hosts has taken place under changing environmental conditions over 3.5 billion years, giving rise to the vast diversity of the virosphere. The accumulation of data on the Earth's virosphere, facilitated by the advent of high-throughput sequencing technologies (NGS), has necessitated a reassessment of approaches to virus classification and, since 2018, has led to a reform of viral taxonomy through the introduction of higher taxonomic ranks (megataxonomy). As of September 2025, the International Committee on Taxonomy of Viruses (ICTV) recognizes 15 taxonomic ranks for viruses, the most significant being: realm - 7, kingdom - 11, phylum - 23, class - 49, order - 93, family - 368, genus - 3769, and species - 16,215. Ongoing advances in metagenomics, metatranscriptomics, and the global ecology of the virosphere will inevitably drive further changes in viral taxonomy and megataxonomy. These developments are of fundamental importance for understanding the evolution of the biosphere and of practical relevance for developing new strategies to strengthen biological security and to mitigate the consequences of epidemic emergencies associated with emerging and reemerging infections.},
}

*Viruses/classification/genetics
Archaea/virology/genetics
Animals
Humans
Bacteria/virology/genetics
Eukaryota/virology/genetics
High-Throughput Nucleotide Sequencing
Phylogeny
Metagenomics

@article {pmid41288100,
year = {2025},
author = {van Dam, F and Westmeijer, G and Rezaei Somee, M and Ketzer, M and Kietäväinen, R and Ono, S and Bertilsson, S and McIntosh, JC and Dopson, M and Drake, H},
title = {Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.},
journal = {mBio},
volume = {},
number = {},
pages = {e0301725},
doi = {10.1128/mbio.03017-25},
pmid = {41288100},
issn = {2150-7511},
abstract = {Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a δ[13]Cmethanol-methane isotope enrichment of up to 98.6‰. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.},
}

@article {pmid41287997,
year = {2025},
author = {Brício, DG and Gloria, MBA and Bitencourt, JAP and Argôlo, LA and de Lima Ribeiro, R and da Silva, IA and da Silva Pena, R and Lopes, AS and Chagas Junior, GC and Ferreira, NR},
title = {Metagenomic and biogenic amine changes in cassava fermentation for tucupi production using Pediococcus acidilactici starter culture.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70350},
pmid = {41287997},
issn = {1097-0010},
support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico (D.G. Brício master scholarship, Process number 161678/2021-1)/ ; //Bank of the Amazon (BASA S.A., Brazil; Contract No. 2022-230)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (ROR: 00x0ma614)/ ; },
abstract = {BACKGROUND: The use of starter cultures is essential for producing fermented foods with desirable standardized characteristics and for preventing pathogens. Pediococcus acidilactici, isolated from cocoa fermentation, was used in the production of tucupi, a widely appreciated sauce made from the juice of cassava root (manipueira) in the Brazilian Amazon. Manipueira was submitted to fermentation with and without Pediococcus acidilactici inoculum at 1 × 10[12] CFU mL[-1] (Pa treatment and control treatment (CT), respectively), over a 24-h period. Samples were collected at 4-h intervals and analyzed for physicochemical characteristics following official methods, bioactive amines by high-performance liquid chromatography with fluorescence detection (HPLC-FLD), and microbial genera identification by metagenomic analysis.

RESULTS: Physicochemical results indicated that fermentation took its due course, with increased acidity, as well as lower pH and reducing and total sugars (Tukey test, P ≤ 0.05). Only two biogenic amines were detected (putrescine and histamine), and higher levels were found in Pa treatment compared to CT, probably due to the increased Lactobacillus prevalence. Six genera were identified in CT (Weissella, Lactobacillus, Lactococcus, Leuconostoc, Bacillus, and Enterococcus), whereas seven were in Pa (Weissella, Lactobacillus, Pediococcus, Lactococcus, Leuconostoc, Streptococcus, and Enterococcus). Weissella, which was predominant in manipueira, decreased during fermentation, whereas Lactobacillus became predominant in CT. However, when P. acidilactici was used, Lactobacillus was prevalent throughout fermentation, and there was a reduced prevalence of Bacillus and Enterococcus, bacteria with pathogenic potential.

CONCLUSION: The starter culture optimized tucupi production by maintaining low levels of biogenic amines, inhibiting the growth of undesirable microorganisms, and enhancing tucupi quality and safety. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid41287884,
year = {2025},
author = {Wang, W and Chen, F and Ye, L and Chen, O and Qing, H and Zhuang, L and Gan, L and Hu, X and Ma, Q and Jian, X},
title = {Enhanced diagnostic yield and clinical impact of metagenomic next-generation sequencing in infective endocarditis: a continuous and prospective surgical cohort study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000003954},
pmid = {41287884},
issn = {1743-9159},
abstract = {BACKGROUND: Traditional culture-based techniques for diagnosing infective endocarditis (IE) suffer from limited sensitivity, particularly in blood culture-negative endocarditis (BCNE). Metagenomic next-generation sequencing (mNGS) has emerged as a promising alternative to improve pathogen detection and guide treatment. This study aimed to evaluate the diagnostic performance of mNGS in IE, and assess its impact on clinical decision-making.

METHODS: We conducted a continuous and prospective cohort study of 352 patients undergoing cardiac surgery for suspected IE. Each patient underwent blood culture, tissue culture, and mNGS testing on matched arterial blood, venous blood, and valve tissue.

RESULTS: Traditional tissue culture had low sensitivity (accuracy 24%, AUC 0.57), while blood culture performed better (accuracy 48%, AUC 0.71). In contrast, clinically adjusted valve tissue mNGS showed higher accuracy (84%) and AUC (0.91), outperforming traditional methods. Streptococcus species were most common, but mNGS also detected fastidious pathogens like Coxiella burnetii, especially in BCNE cases. mNGS results prompted antibiotic adjustments in 30% of all patients and 45% of blood-culture negative patients, enabling targeted or de-escalated therapy. Notably, no IE relapses were observed at 1-year follow-up, supporting the effectiveness of mNGS-guided treatment.

CONCLUSION: mNGS significantly enhances microbiological diagnosis in IE, especially in BCNE, complements traditional methods, and improves clinical decision-making. However, it requires expert interpretation to mitigate false positives.},
}

@article {pmid41287793,
year = {2025},
author = {Yang, T and Lin, X and Chen, R and Wang, R and Li, T and Shen, F and Zhang, X and Lai, L and Lu, B and Wei, J and Xie, X},
title = {Integrated metagenomics and metabolomics analysis reveals dynamic changes of microbiota and metabolic profile during fermentation of cigar tobacco (Nicotiana tabacum L.) leaves.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1662815},
pmid = {41287793},
issn = {1664-8021},
abstract = {Optimizing fermentation duration is critical for producing high-quality cigar tobacco leaves This study examines changes in microorganisms and metabolites during CTL fermentation at four time points: 0 days (T0), 25 days (T1), 50 days (T2), and 75 days (T3). We observed a decreasing trend in total soluble sugars, starch, total nitrogen, and nicotine levels as fermentation progressed. Notably, chemical components stabilized after T2 stages. The microbial community showed dynamic fluctuations, with alpha diversity indices (Shannon, ACE, Pielou's evenness, and Chao-2) reaching equilibrium at T2 and maintaining stability thereafter. Dominant genera such as Staphylococcus, Aspergillus, Sphingomonas, and Penicillium persisted throughout the fermentation process. A total of 1801 metabolites were identified, with 584 showing differential expression across the fermentation periods. Notably, comparisons between T0 and T1, T2, and T3 revealed 218, 377, and 419 differentially expressed metabolites, respectively. KEGG enrichment analysis identified 28 co-existing metabolic pathways, seven of which are linked to cigar quality formation. Furthermore, 29 out of 47 differential metabolites significantly correlated with the eight dominant microbial genera. These findings indicate that the T2 stage achieves optimal balance between microbial activity and metabolite stabilization, providing a scientific basis for industrial process optimization.},
}

@article {pmid41287120,
year = {2025},
author = {Mungun, T and Ulziibayar, M and Nguyen, CD and Batsaikhan, P and Suuri, B and Luvsantseren, D and Narangerel, D and Tsolmon, B and Do, LAH and Ong, DS and Ortika, BD and Pell, CL and Boelsen, LK and Wee-Hee, AC and Spry, L and Hinds, J and Pride, MW and Dunne, EM and Gessner, BD and Mulholland, EK and Satzke, C and von Mollendorf, C},
title = {Pneumococcal carriage and disease in adults hospitalised with community-acquired pneumonia in Mongolia: prospective pneumonia surveillance program (2019-2022).},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {27},
pmid = {41287120},
issn = {2200-6133},
support = {WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; WI236621//Pfizer Inc./ ; 1087957//NHMRC Career Development Fellowship/ ; },
abstract = {BACKGROUND: Streptococcus pneumoniae is an important cause of pneumonia in older adults, however, serotyping and indirect impact information from low and middle-income countries is lacking. Mongolia has a childhood 13-valent pneumococcal conjugate vaccine (PCV13) program, but no adult pneumococcal vaccination program. We describe pneumococcal carriage rates, disease and serotype distribution among adults hospitalised with pneumonia, and explore changes over the COVID-19 pandemic period.

METHODS: Adults (≥ 18 years) hospitalised with clinical pneumonia were enrolled over 3 years (March 2019-February 2022) into a prospective pneumonia surveillance program. Nasopharyngeal swabs were tested to detect pneumococci using lytA qPCR and molecular serotyping by DNA microarray and metagenomics. Pneumococcal pneumonia was identified using serotype-specific urinary antigen detection and BinaxNOW[®] assays. Pneumococcal carriage and pneumonia prevalence were assessed over the COVID-19 period with log-binomial regression used to estimate prevalence and adjusted prevalence ratios (pre- versus early- and late-COVID-19 periods).

RESULTS: Of 3,178 pneumonia cases, S. pneumoniae was identified in 12.1% (333/2,759) of swabs and 8.6% (253/2,925) of urine samples. PCV13 serotype carriage prevalence was 3.1% (82/2,663) and non-PCV13 serotype carriage prevalence 5.7% (152/2,663). In the late-COVID-19 period, pneumococcal carriage prevalence was reduced by 66% (aPR 0.34, 95%CI 0.25-0.46) and pneumococcal pneumonia by 82% (aPR 0.18, 95%CI 0.12-0.27) compared with the pre-COVID-19 transmission period.

CONCLUSION: Despite paediatric vaccination with high coverage, we identified some residual PCV13 serotypes with predominance of non-PCV13 serotypes carried and causing disease in adults. Direct adult vaccination which targets these serotypes will potentially reduce disease in adults in Mongolia.},
}

@article {pmid41286929,
year = {2025},
author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM},
title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {401},
pmid = {41286929},
issn = {1474-760X},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; },
abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.},
}

Humans
*Gastrointestinal Microbiome
*Immunotherapy
*Neoplasms/therapy/microbiology
Metagenomics

@article {pmid41286813,
year = {2025},
author = {Shen, H and Zhang, X and Hu, B and Wang, Y and Yang, B and Fan, P and Liu, J and Zhang, Z and Chen, W and He, L and Yang, W and Lu, G and Yan, G},
title = {Clinical application and impact of metagenomic next-generation sequencing for the diagnosis of infectious diseases in severely immunocompromised pediatric patients.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {950},
pmid = {41286813},
issn = {1471-2431},
support = {EKQM202406//CHFU Young Talents Program/ ; EKQM202406//CHFU Young Talents Program/ ; EKQM202406//CHFU Young Talents Program/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 25ZR1401032//Shanghai Committee of Science and Technology/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; 2023ZDFC0103//Shanghai Municipal Health System major supports discipline projects/ ; },
mesh = {Humans ; Retrospective Studies ; *Immunocompromised Host ; Child ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Infant ; Sensitivity and Specificity ; Critical Illness ; *Communicable Diseases/diagnosis/microbiology ; Intensive Care Units, Pediatric ; Adolescent ; },
abstract = {BACKGROUND: Accurate and rapid microbiological diagnosis is essential for the identification and management of critically ill children experiencing immunocompromised (ICH) conditions. Metagenomic next-generation sequencing (mNGS) has shown promising applications in diagnosing infectious diseases in adults; however, its performance in critically ill pediatric infections remains elusive. We aimed to evaluate the performance of mNGS, compared with that of conventional microbiological tests (CMT) as a front-line diagnostic tool for pediatric intensive care unit (PICU) patients, and assess its clinical impact.

METHODS: In this retrospectively study, a total of 179 samples including blood, sputum or cerebrospinal fluid etc. from 97 children, categorized as ICH or immunocompetent (ICO), were included. The positive detection rate and diagnostic performance (sensitivity, specificity) of mNGS and CMT were compared. The clinical impact of mNGS was assessed on its influence on diagnosis and treatment decisions.

RESULTS: mNGS demonstrated a significantly higher positive rate than CMT (72.63% vs. 55.31%, P < 0.001), particularly in sputum and cerebrospinal fluid (CSF) samples, among both ICH and ICO samples. Samples from ICH patients exhibited a relatively higher positive rate and yielded more microbes detections than ICO samples with both methods. The sensitivity of mNGS assay was 91.34%, significantly outperforming CMT (73.23%, P < 0.001). The specificity of mNGS was 73.08%, relatively lower than that of CMT (88.46%, P < 0.05). Specific to ICH and ICO, mNGS showed significantly higher sensitivity than CMT (ICH: 94.94% vs. 81.01%, P < 0.01; ICO:85.42% vs. 60.42%, P < 0.01). Regarding clinical impact, mNGS had a positive impact on diagnosis in 66.0% patients, with a significantly higher proportion of positive impacts observed in ICH samples compared to ICO samples (P < 0.05).

CONCLUSIONS: mNGS exhibited superior diagnostic performance compared to CMT for diagnosing infections in critically ill children. More than half (66.0%) of mNGS tests resulted in a positive clinical impact on diagnosis and treatment, particularly among ICH patients.},
}

Humans
Retrospective Studies
*Immunocompromised Host
Child
*High-Throughput Nucleotide Sequencing
Male
Female
Child, Preschool
*Metagenomics/methods
Infant
Sensitivity and Specificity
Critical Illness
*Communicable Diseases/diagnosis/microbiology
Intensive Care Units, Pediatric
Adolescent

@article {pmid41286799,
year = {2025},
author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K},
title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {1117},
pmid = {41286799},
issn = {1471-244X},
mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; },
abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.

METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13 years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.

RESULTS: Fifty-three participants (mean age = 10.2 years, SD = 1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M = 2.03, SE = 0.33 vs. 2.86, SE = 0.34), p = 0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M = 70.10, SE = 0.09) than the placebo group (M = 89.72, SE = 0.07), p = 0.04. However, the kefir group self-reported more sleep problems post-intervention (M = 39.81, SE = 0.75 vs. 37.40, SE = 0.65), p = 0.02. For Go/NoGo RT variance, a non-significant interaction (p = 0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.

CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.

ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.

TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.},
}

Humans
Child
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology
Male
Female
*Gastrointestinal Microbiome/physiology
Double-Blind Method
Adolescent
*Kefir
*Sleep
Attention
Severity of Illness Index

@article {pmid41286718,
year = {2025},
author = {Wu, C and Sun, X and Zhang, W and Yang, Y and Niu, P and Chen, J and Zhang, X and Lu, R and Wang, W and Chen, Z and Tan, W},
title = {Pathogen profiles in CSF from patients with acute infectious meningitis or encephalitis: a multicenter study based on multiplex PCR and mNGS in China, 2018-2019.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12204-7},
pmid = {41286718},
issn = {1471-2334},
support = {2022YFC2303401//the National Key Research and Development Program of China/ ; },
abstract = {Acute meningitis or encephalitis (AME) is mainly caused by viral and bacterial infections, leading to severe sequelae and even death. However, there is limited systematic research on the spectrum of pathogens causing AME in China. Here, cerebrospinal fluid (CSF) samples from 229 acute meningitis or encephalitis patients (AMEP) excluding Japanese encephalitis virus infections collected from multicenter of China between 2018 and 2019 were analyzed. The pathogen profile was comprehensively characterized using both 43-pathogens multiplex PCR (MPCR) and metagenomic next-generation sequencing (mNGS). MPCR revealed that 73 (31.88%) cases had at least one potential pathogen. mNGS were conducted on 22 randomly selected AMEPs, and the results showed that mNGS reported all the pathogens detected by MPCR. Interestingly, mNGS successfully identified multiple pathogens in cases that were undiagnosed by MPCR. The most frequently detected viruses by MPCR were Human herpesvirus (HHV), Adenovirus, Enterovirus/Rhinovirus (Ev/Rv), and Bocavirus. The most abundant bacteria were Bordetella pertussis, Haemophilus influenzae, and Listeria monocytogenes. Coronavirus and other respiratory viruses could also induce AME. Ev/Rv were significantly enriched in the adolescent cases, and tick-borne encephalitis cases were concentrated in northeastern China. This study systematically characterized the pathogen spectrum and distribution of AME in China. Additionally, it revealed that combining MPCR and mNGS significantly improves the diagnostic rate of pathogens in AME. These findings will provide important support for the diagnosis, treatment, and development of drugs and vaccines for AME.},
}

@article {pmid41286386,
year = {2025},
author = {Sadhukhan, S and Bhattacharya, R and Bhattcharya, D and Sahana, S and Pradhan, B and Pandit, S and Gill, HS and Rajeev, M and Nag, M and Lahiri, D},
title = {Artificial intelligence in protein-based detection and inhibition of AMR pathways.},
journal = {Journal of computer-aided molecular design},
volume = {40},
number = {1},
pages = {4},
pmid = {41286386},
issn = {1573-4951},
mesh = {*Artificial Intelligence ; *Anti-Bacterial Agents/pharmacology/chemistry ; Humans ; Deep Learning ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; *Drug Resistance, Bacterial/drug effects ; *Proteins/chemistry ; Algorithms ; *Bacterial Proteins/chemistry/antagonists & inhibitors/metabolism ; },
abstract = {Antimicrobial Resistance (AMR) is a global concern demanding high-throughput and precise AMR surveillance strategies. This review provides a comprehensive list of Artificial Intelligence (AI) driven frameworks widely employed in the early detection, structural characterization, and designing of novel inhibitors to block the resistance pathways critical for AMR. Deep learning algorithms including DeepGO, DeepGOPlus, DeepGO-SE, PFresGO, DPFunc, ProtENN and graph-based architectures of GraphSite, GrASP enables precise functional annotation of resistance-associated proteins. AI-guided protein modeling performed by AlphaFold, RoseTTAFold, ProtGPT-2, ESMFold etc. generates high resolution 3D conformations, further utilized in performing molecular docking via tools like AutoDock, DeepDocking and DeepChem and analyzed with tools like DeepDriveMD, TorchMD, and PRITHVI, which can perform real-time molecular dynamics simulations. Identification of relevant resistant biomarkers from mass-spectrometry profiles can also be achieved with the help of DeepNovo, Casanovo, or Prosit. Tools like DeepARG, HMD-ARG, and BacEffluxPred enables identification of unannotated resistance genes from metagenomic samples. Natural Language Processing (NLP) and Large Language-based models (LLM) facilitate identification of resistant determinants via literature mining enabling regulatory network mapping and rational inhibitor design. Furthermore, AI-mediated de-novo inhibitor design is achieved using Variational Autoencoders (VAE), Generative Adversarial Networks (GAN), diffusion and flow-matching based frameworks serve as potential options for enhancing diagnostic interventions against resistant phenotypes. AI-based protein-protein interaction predictors include DeepInteract, Pred_PPI, PLIP, DeepAIPs-Pred, DeepAIPs-SFLA, SBSM-Pro, Deep Stacked-AVPs, and pNPs-CapsNet help in understanding how resistance proteins interact with each other enabling precise identification of AMR-modulating peptides and supports the modeling of novel antibiotics for blocking interactions and disrupting resistance pathways.},
}

*Artificial Intelligence
*Anti-Bacterial Agents/pharmacology/chemistry
Humans
Deep Learning
Molecular Docking Simulation
Molecular Dynamics Simulation
*Drug Resistance, Bacterial/drug effects
*Proteins/chemistry
Algorithms
*Bacterial Proteins/chemistry/antagonists & inhibitors/metabolism

@article {pmid41285810,
year = {2025},
author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ},
title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {216},
pmid = {41285810},
issn = {2055-5008},
support = {F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; },
mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; },
abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.},
}

Humans
*Urinary Tract Infections/microbiology/urine/diagnosis
Female
*Microbiota
Biomarkers/urine
Recurrence
Metabolomics
*Urinary Tract/microbiology
Metagenomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Urine/microbiology/chemistry
Adult
Middle Aged
Deoxycholic Acid/urine

@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}

Single-Cell Analysis/methods
Symbiosis/genetics
*Amoeba/virology/microbiology/genetics
*Microbiota/genetics
Metagenomics/methods
*Ciliophora/virology/microbiology/genetics
Bacteria/genetics/classification
Genomics/methods
Giant Viruses/genetics
Phylogeny
Viruses/genetics/classification

@article {pmid41285454,
year = {2025},
author = {Safika, S and Nisa, C and , and Cahyadi, DD},
title = {Gut microbiota profiling of Javan pangolin (Manis javanica).},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0036},
pmid = {41285454},
issn = {1347-7439},
abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.},
}

@article {pmid41285255,
year = {2025},
author = {Wang, S and Ma, G and Qi, C and Cheng, S and Lai, H and Zhou, L and Wu, G and Chen, Z and Mao, X and Jing, T and He, Y and Zhou, H},
title = {Trimethylamine-N-oxide disrupts spermatogenesis by inducing mitochondrial oxidative stress injury through Hippo signaling.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.11.052},
pmid = {41285255},
issn = {1873-4596},
abstract = {BACKGROUND: The gut-testis axis is increasingly recognized as a regulator of male reproductive health; however, the key microbial contributors, metabolites, and underlying mechanisms remain unclear.

METHODS: We performed fecal metagenomic sequencing in 107 participants to identify microbial taxa associated with abnormal semen parameters. Serum trimethylamine-N-oxide (TMAO) levels were measured and correlated with semen quality. In mouse models, including fecal microbiota transplantation, dietary choline supplementation, mono-colonization, and direct TMAO administration, we assessed sperm morphology, testicular androgen synthesis, and testicular histology. Testicular transcriptomics, in vitro Leydig cell assays, and mitochondrial function analyses were conducted to investigate the effects of TMAO on Hippo signaling, oxidative phosphorylation, mitochondrial membrane damage, and steroidogenesis.

RESULTS: Choline-to-trimethylamine converting bacteria, including Phocaeicola massiliensis, Veillonella spp., and Klebsiella pneumoniae, were enriched in men with abnormal semen parameters. Circulating TMAO levels were inversely associated with semen volume, total sperm count, and motile sperm count. In mouse models, elevated TMAO induced testicular dysfunction characterized by impaired sperm morphology, reduced testicular androgen synthesis, and histological abnormalities. Consistently, gene set enrichment analysis (GSEA) of testicular transcriptomes revealed significant suppression of mitochondrial translation, membrane integrity, oxidative phosphorylation, and adenosine triphosphate (ATP) metabolism. TMAO also suppressed steroidogenesis by reducing the expression of steroidogenic acute regulatory protein (StAR). Mechanistic studies in TM3 Leydig cells further demonstrated that TMAO, by promoting Yap phosphorylation, disrupted mitochondrial structure and morphology, decreased mitochondrial membrane potential, increased mitochondrial reactive oxygen species (ROS) levels, impaired ATP synthesis, and promoted mitochondrial fragmentation with upregulation of the mitochondrial fission molecule (Fis1).

CONCLUSIONS: In conclusion, our findings demonstrate that TMAO activates Hippo signaling to induce mitochondrial dysfunction and suppress testosterone synthesis, thereby impairing spermatogenesis. These results highlight TMAO biosynthesis and its downstream signaling as potential therapeutic targets for improving male fertility.},
}

@article {pmid41285136,
year = {2025},
author = {Sujith, S and Vasudevan, S and Sajeevan, A and Solomon, AP},
title = {Genomics to function: integrating rapid metagenomics with quorum-sensing biosensing for precision infectious disease management.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101291},
doi = {10.1016/j.lanmic.2025.101291},
pmid = {41285136},
issn = {2666-5247},
}

@article {pmid41283812,
year = {2025},
author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y},
title = {From genomic signals to prediction tools: a critical feature analysis and rigorous benchmark for phage-host prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf626},
pmid = {41283812},
issn = {1477-4054},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; 9667256//City University of Hong Kong/ ; 9678241//City University of Hong Kong/ ; 217310019//Open Research Fund of Guangdong Provincial Key Laboratory of Wastewater Information Analysis and Early Warning/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Genomics/methods ; *Computational Biology/methods ; Benchmarking ; *Host-Pathogen Interactions ; Genome, Viral ; },
abstract = {Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computational tools has created a complex landscape, making direct performance comparison challenging due to inconsistent benchmarks and varying usability. Here, we provide a systematic review and a rigorous benchmark of 27 virus-host prediction tools. We formulate the host prediction task into two primary frameworks-link prediction and multi-class classification-and construct two benchmark datasets to evaluate tool performance in distinct scenarios: a database-centric dataset (RefSeq-VHDB) and a metagenomic discovery dataset (MetaHiC-VHDB). Our results reveal that no single tool is universally optimal. Performance is highly context-dependent, with tools like CHERRY and iPHoP demonstrating robust, broad applicability, while others, such as RaFAH and PHIST, excel in specific contexts. We further identify a critical trade-off between predictive accuracy, prediction rate, and computational cost. This work serves as a practical guide for researchers and establishes a standardized benchmark to drive future innovation in deciphering complex virus-host interactions.},
}

*Bacteriophages/genetics/physiology
*Genomics/methods
*Computational Biology/methods
Benchmarking
*Host-Pathogen Interactions
Genome, Viral

@article {pmid41283667,
year = {2025},
author = {Zhang, J and Meng, F and Sun, Y and Xu, W and Wu, S and Su, X},
title = {Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145325},
doi = {10.1128/msystems.01453-25},
pmid = {41283667},
issn = {2379-5077},
abstract = {The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning (DL) models, which typically focus on microbial distribution patterns, neglecting the underlying relationships between microbes. As a result, model performance can be significantly affected by data sparsity, misclassified features, or incomplete microbial profiles. To overcome these challenges, we introduce Phylo-Spec, a phylogeny-driven deep learning algorithm that integrates multi-aspect microbial information for improved status recognition. Phylo-Spec fuses convolutional features of microbes within a phylogenetic hierarchy via a bottom-up iteration and significantly alleviates the challenges due to sparse data and inaccurate profiling. Additionally, the model dynamically assigns unclassified species to virtual nodes on the phylogenetic tree based on higher-level taxonomy, minimizing interferences from unclassified species. Phylo-Spec also captures the feature importance via an information gain-based mechanism through the phylogenetic structure propagation, enhancing the interpretability of classification decisions. Phylo-Spec demonstrated superior efficacy in microbiome status classification across two in silico synthetic data sets that simulate the aforementioned cases, outperforming existing ML and DL methods. Validation with real-world metagenomic and amplicon data further confirmed the model's performance in multiple status classification, establishing a powerful framework for microbiome-based health state identification and microbe-disease association. The source code is available at https://github.com/qdu-bioinfo/Phylo-Spec.IMPORTANCEThe human microbiome profoundly influences health and disease, but current computational tools often overlook the evolutionary relationships among microbes, leading to incomplete or inaccurate interpretations of complex microbial data. Phylo-Spec provides a new way to understand the microbiome by combining microbial abundance, taxonomy, and phylogeny within a unified deep learning framework. This model not only improves the accuracy of health status classification but also highlights key microbial contributors linked to disease. By capturing both microbial diversity and evolutionary context, Phylo-Spec bridges the gap between bioinformatics and biological insight, offering a powerful and interpretable approach for advancing microbiome-based diagnostics and precision medicine.},
}

@article {pmid41283171,
year = {2025},
author = {Ping, Y and Zhao, X and Lv, L and Meng, W and Meng, Y and Ruan, G and Cheng, Y and Xiao, Z and Tian, Y and Chen, M and Chen, L and Yi, A and Tang, Z and Li, N and Chen, D and Wei, Y},
title = {Gut microbiota and metabolic signatures of anxiety in ulcerative colitis: a cross-sectional study.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251393419},
pmid = {41283171},
issn = {1756-283X},
abstract = {BACKGROUND: Patients with ulcerative colitis (UC) usually experience anxiety symptoms that seriously affect their quality of life, treatment, and prognosis. Dysbiosis of the gut microbiota plays an important role in UC and mental illness. However, little is known about the role of the gut microbiota in UC patients with anxiety.

OBJECTIVES: To identify the gut-microbiome and fecal metabolome profiles uniquely associated with comorbid anxiety in UC patients and to explore potential biomarkers for diagnosis.

DESIGN: A cross-sectional, two-group comparative study.

METHODS: To study the underlying association between them, we recruited 126 UC patients in this study, including 78 with anxiety and 48 without anxiety. A total of 102 fecal samples were collected for metagenomic sequencing and metabolome sequencing. Microbial diversity, differential gut microbiota, functional pathways, and metabolites were analyzed. Multivariable logistic regression was used to identify independent risk factors associated with anxiety in UC patients, while Spearman correlation was employed to explore microbe-metabolite interactions and the performance of potential biomarkers.

RESULTS: We found that disease severity, steroid usage, and abdominal pain may promote the occurrence of anxiety. Compared to UC patients without anxiety, UC patients with anxiety had low fecal microbial community diversity, with an increase in the species Haemophilus sp. HMSC71H05 and Corynebacterium durum, and a decrease in the species Roseburia intestinalis (RI), Bifidobacterium longum (BL), and Enterococcus hirae. The metabolic pathways driven by the gut microbiota were disrupted. Moreover, the levels of most metabolites (such as L-kynurenine) were increased in the feces, while the levels of a few metabolites decreased, including indole-2-carboxylic acid, N-demethylmirtazapine, and tauroursodeoxycholic acid.

CONCLUSION: Our research further revealed that these gut microbiota and metabolites are highly correlated. This study provides a new perspective for understanding the occurrence and development of anxiety in UC patients, suggesting that RI and BL may serve as potential candidate biomarkers to diagnose UC patients with anxiety.},
}

@article {pmid41282996,
year = {2025},
author = {Wang, JM and Pan, YY and Hong, JC and Jiang, ZJ and Zhang, SY and Fan, RJ and Yang, BH and Wang, ZQ and Zhu, JT and Yao, XP},
title = {Exploring the Spectrum of Microbiota in Central Nervous System Infections Through Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6019-6033},
pmid = {41282996},
issn = {1178-6973},
abstract = {PURPOSE: This study leveraged CSF metagenomic next-generation sequencing (mNGS) to bridge this knowledge gap and elucidate the microbiota spectrum of CNS infections.

PATIENTS AND METHODS: We retrospectively analyzed CSF mNGS reports and clinical data from 264 patients with suspected CNS infections, who were enrolled from September 2019 to November 2023.

RESULTS: According to diagnostic criteria, 145 patients were diagnosed with CNS infections, including bacterial (27 cases, 18.6%), Mycobacterium tuberculosis (30, 20.7%), fungal (23, 15.9%), and viral (65, 44.8%) infections. The mNGS positive detection rate was 46.2% (67/145), with significant differences among groups (p < 0.001). A total of 22 pathogens were identified, most commonly Cryptococcus neoformans (16, 23.9%), Mycobacterium tuberculosis (10, 14.9%), and Epstein-Barr virus (9, 13.4%). The most frequent background microorganisms detected by mNGS were Cutibacterium acnes (58.6%), Moraxella osloensis (29.0%), and Malassezia restricta (26.2%).

CONCLUSION: High-throughput sequencing using mNGS revealed the microbial compositions in CSF samples from patients with CNS infections. This approach may enhance our understanding of pathogens and assist clinicians in making effective therapeutic decisions.},
}

@article {pmid41282988,
year = {2025},
author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y},
title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20199},
pmid = {41282988},
issn = {2167-8359},
mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Archaea/genetics/isolation & purification ; },
abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.

METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.

RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.

CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.},
}

*Sewage/microbiology/virology
China
*Metagenomics
*Rain
Bacteria/genetics/classification/isolation & purification
*Microbiota
Archaea/genetics/isolation & purification

@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}

*Soil Microbiology
*Metagenome
China
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects
Metagenomics

@article {pmid41282900,
year = {2025},
author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, D and Teixeira, M and Earl, AM and Worby, C and Kong, HH and Huang, SS and Segre, J},
title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.25339587},
pmid = {41282900},
abstract = {Antimicrobial resistance (AMR) is a global public health threat that disproportionately affects vulnerable populations, including nursing home (NH) residents. Surveillance and control in NHs are resource-limited and typically restricted to perirectal cultures, overlooking both skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here we show, within the cluster-randomized Project PROTECT trial (NCT03118232), that residents' skin serves as a major reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using shotgun metagenomics, selective culturing, and isolate genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli ST131/ST648 in 4 (10.5%) and methicillin-resistant Staphylococcus aureus in 7 (18.4%). In contrast, metagenome-assembled genomes identified broader MDRO colonization, including multidrug-resistant E. coli ST93 in 27 residents (71.1%), methicillin-resistant Staphylococcus epidermidis ST2 in 14 (36.8%), Proteus mirabilis in 16 (42.1%), Providencia stuartii in 7 (18.4%), Enterococcus faecalis in 7 (18.4%), and Pseudomonas aeruginosa in 5 (13.2%). Colonization persisted after bathing. Clonal E. coli ST93 (<=30 SNPs) was shared by 27 residents across 9 facilities, and 5 resident pairs (13.2%) carried clonally related strains of >=2 MDRO species, consistent with polymicrobial transmission. Our findings demonstrated the skin as a persistent reservoir of MDROs and the importance of metagenomic surveillance to uncover hidden colonization and transmission pathways, underscoring the need to expand AMR monitoring in long-term care.},
}

@article {pmid41282695,
year = {2025},
author = {Lande, SJ and Stephney, LM and Ramirez, LGA and Nesbeth, PC and Hartman, TJ and Jones, DP and Valvi, D and Hechenbleikner, EM and Lin, E and McConnell, RS and Chatzi, VL and Alvarez, JA and Ziegler, TR},
title = {Dietary Macronutrient Intake and the Gut Microbiome in Adults Undergoing Bariatric Surgery for Obesity.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.25338397},
pmid = {41282695},
abstract = {Limited information linking dietary intake to gut metagenomic data in bariatric surgery patients is available. We examined whether there were correlations between macronutrient intake and the gut microbiome and related gene pathways prior to and following bariatric surgery. Participants were 29 adults living with obesity undergoing bariatric surgery (93% females). Three-day food records were analyzed prior to and after surgery to estimate mean daily intakes of macronutrients to derive measures of diet quality [glycemic index, added sugar intake, and the Healthy Eating Index 2015 (HEI-2015)]. Pre- and post-operative stool samples were sequenced using whole-genome shotgun sequencing to identify changes in microbial composition. Diversity indices and differential abundance were calculated, and correlations between dietary intake and outcomes were assessed using linear regression and machine learning models. At the phylum level, pre-operative Synergistetes abundance was positively correlated with soluble fiber intake, and Proteobacteria was inversely linked with HEI-2015 scores. Post-operatively, Lentisphaerae was inversely correlated with dietary glycemic index. The change in Verrucomicrobia abundance was inversely correlated with the change in glycemic index, and the change in Fusobacteria abundance was positively correlated with the change in glycemic index. The changes in several functional gene pathways were positively linked to the change in HEI-2015 scores, the change in soluble fiber intake, and the change in insoluble fiber intake. In adults undergoing bariatric surgery, intakes of specific macronutrients pre-operatively and as a function of the change after surgery were correlated with several microbial phyla, genera, and nutrient-related functional gene pathways.},
}

@article {pmid41282688,
year = {2025},
author = {Zhang, H and Dominguez, EG and Junak, M and Murtaza, M and Pepperell, CS and Kisat, MT},
title = {Fragment end motif analysis to distinguish pathogens from contaminants in enriched plasma microbial DNA.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.25339688},
pmid = {41282688},
abstract = {INTRODUCTION: Despite its promise, accuracy of microbial cell-free DNA (mDNA) in plasma as a diagnostic tool is hindered by its low abundance and process contaminants. We have previously shown that combining size selection with single-stranded DNA (ssDNA) library preparation increased mDNA yield by 200-fold but also decreased sensitivity for pathogen detection due to higher background noise. A recent study showed that pathogen-derived DNA was enriched for CC dinucleotide at 5' ends compared to contaminants. Since ssDNA libraries preserve sequence motifs at both ends (5' and 3'), we hypothesized that analysis of nucleotide motifs at microbial fragment ends in size-selected ssDNA libraries could help differentiate pathogen DNA from background noise.

METHODS: We performed deep sequencing on size-selected ssDNA libraries (<110 bp) generated from longitudinal plasma samples of 11 critically-ill patients (5 with culture-proven infections, 20 samples; 6 without infections, 18 samples) and 6 no-template controls (NTCs). For each 2-mer and 1-mer motif, we calculated the ratio between its frequency observed at 5' and 3' fragment ends in sequencing data and its expected frequency in the corresponding reference genome (O/E ratio). We compared enrichment of motifs in pathogen DNA and contaminant DNA fragments.

RESULTS: Pathogen-derived mDNA fragments were more biased in O/E end motif ratios compared to contaminants across all 3 groups (NTCs, no-infections and culture-proven infections), at both 5' and 3' fragment ends. Notably, the GG dinucleotide was enriched at the 3' end in pathogens compared to contaminants (P < 0.0001). Combining O/E ratios for C and G nucleotides at the 3' end achieved areas under the receiver operating characteristic curve of >0.98 for distinguishing common contaminants from culture-proven pathogens.

CONCLUSIONS: Pathogen-derived mDNA in size-selected ssDNA libraries is biased at 5' and 3' fragment end compared to contaminants. Incorporating microbial fragment end motif analysis can enhance signal-to-noise ratio and improve pathogen detection and identification in plasma metagenomic sequencing.},
}

@article {pmid41282530,
year = {2025},
author = {Shoji, F and Kawabata, T and Kosai, K and Fujishita, T and Toyozawa, R and Shimamatsu, S and Ito, K and Taguchi, K and Yamaguchi, M},
title = {Intratumoral microbiome is associated with the response to cancer immunotherapy in lung cancer patients with high PD-L1 expression.},
journal = {Immuno-oncology technology},
volume = {28},
number = {},
pages = {101066},
pmid = {41282530},
issn = {2590-0188},
abstract = {BACKGROUND: High expression of tumoral programmed death-ligand 1 (PD-L1) [high PD-L1 tumor proportion score (TPS)] is a predictive biomarker of response to cancer immunotherapy in lung cancer; however, its predictiveness is insufficient. Recently, resident microbiomes in several organs including the lung have been demonstrated to control host immunity but their role in the response to cancer immunotherapy is still unknown.

MATERIALS AND METHODS: This single-center, retrospective study analyzed 32 high PD-L1-TPS lung cancer patients treated with immune checkpoint inhibitors (ICI). We carried out shotgun metagenome sequencing using frozen tumor tissues, then analyzed the correlation between the intratumoral microbiota and response to ICI therapy.

RESULTS: In this study, only 56.3% of patients with high PD-L1-TPS showed response to ICI therapy. Among 11 significant compositional differences in intratumoral microbiota observed in ICI responders, there was significantly longer progression-free survival (PFS) in patients with abundant Tetrasphaera and Mesorhizobium. Of patients with these abundant microbiota, 83.3% showed response to ICI therapy and all patients without these microbiota were ICI nonresponders (P = 0.0050). There were significant differences among three groups classified by the abundance of g_Tetrasphaera and g_Mesorhizobium (PFS, P = 0.0016 and overall survival, P = 0.0013). Twenty pathway modules were enriched in ICI responders and eight were enriched in ICI nonresponders.

CONCLUSIONS: This study revealed the specific compositions of intratumoral microbiota as demonstrating relevance to response to ICI therapy in high PD-L1-TPS lung cancer patients. The intratumoral microbiota components Tetrasphaera and Mesorhizobium may have a key role in determining the response to cancer immunotherapy for lung cancer.},
}

@article {pmid41282313,
year = {2025},
author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Tahir, M and Zhong, J},
title = {Multi-omics profiling reveals microbial regulation of a key aromatic ester phenethyl acetate formation in fermented alfalfa and its impact on sheep feed preference.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103249},
pmid = {41282313},
issn = {2590-1575},
abstract = {This study utilized headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) to identify the key volatile flavor compounds in fermented alfalfa. The contribution of core microbiota to forming these key flavor compounds was investigated using a combination of absolute quantification of 16S rRNA gene copy number and metagenomic technology. Additionally, the critical roles of core fermentation microorganisms were quantitatively detected and validated through liquid chromatography mass spectrometry (LC-MS). Results revealed that Lactiplantibacillus plantarum B90 treated group achieved superior fermentation quality, with esters and aldehydes being the dominant volatile flavor compounds. Phenethyl acetate was the only aromatic ester that was significantly up-regulated after fermentation. The aryl alcohol dehydrogenase from L. plantarum facilitated the conversion of phenylacetaldehyde into phenylethyl alcohol, which serves as the precursor for phenethyl acetate. Furthermore, fermented alfalfa sprayed with phenethyl acetate was associated with increased feed intake in sheep. These findings propose new insights for microbial modulation of fermented flavor in fermented forage to enhance sheep feed intake.},
}

@article {pmid41282134,
year = {2025},
author = {Zitvogel, L and Carrier, A and Manghi, P and Silva, CAC and Lahmar, I and Birebent, R and Suissa, D and Laheurte, C and Schreibelt, G and Lemant, L and Fahrner, JE and de Sousa, E and Berthier, F and Villemonteix, J and Chevalier, M and Piccinno, G and Hocquet, D and Lebhar, I and Maeurer, M and Caillat-Zucman, S and Kroemer, G and Derosa, L and Launay, O and Golden, E and Bol, K and De Vries, IJM and Adotévi, O and Segata, N and Formenti, S and Kobold, S and Pieper, D and Vital, M and Santos-Peral, A and Zaucha, M and García-Bengoa, M and Thorn-Seshold, J and Stirling, H and Rothenfusser, S and Iebba, V and Almonte, A and Ajami, N and White, M and Sahasrabhojane, P and Hoballah, Y and Losh, J and DePinho, C and Dondossola, E and Wargo, J},
title = {Gut microbiota: a new factor modulating the immunizing potential of viral and cancer vaccines.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4294379/v1},
pmid = {41282134},
issn = {2693-5015},
abstract = {Vaccines represent a major public health intervention against infectious diseases and potentially cancer. Surrogate markers of vaccine efficacy usually rely on neutralizing antibody titers afflicted by high interindividual variabilities. Automated multiplexed T cell assays currently allow to test the clinical relevance of T lymphocyte responses during vaccine rollout. We examined cellular and/or humoral immune responses in five independent cohorts of health care workers, young healthy individuals and patients with cancer (melanoma or lung cancer) receiving various immunizing formulations (non-replicating, viral/tumoral, mRNA/peptides/cellular/viral particles). Here we show that about 20% of vaccinees to non-replicating formulations fail to mount protective antibody and Th1/Tc1 responses while 9% receiving a live vaccine were hyperresponders. Vaccine outliers could at least in part be attributed to gut dysbiosis at baseline, evaluated by shotgun metagenomics-based machine learning or the TOPOSCORE. These findings highlight the requirement of diagnostic tools to identify intestinal dysbiosis, as well as microbiota-centered interventions to optimize the efficiency of mass vaccinations.},
}

@article {pmid41282078,
year = {2025},
author = {Rumi, MA and Nguyen, L and Davis, BC and Brown, CL and Pruden, A and Zhang, L},
title = {Mapping the underlying drivers of resistome risk across diverse environments.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7085902/v1},
pmid = {41282078},
issn = {2693-5015},
abstract = {Background Understanding the drivers of antimicrobial resistance (AMR) across the One Health spectrum is crucial for controlling its spread. The MetaCompare framework, which assesses "resistome risk" based on antibiotic resistance gene (ARG) co-occurrence patterns on metagenomic contigs, has been expanded to distinguish between "ecological resistome risk" (ERR) and "human health resistome risk" (HHRR) scores across anthropogenic gradients. However, comprehensive surveys are still needed to untangle the biological (e.g., ARG relative abundance), ecological (e.g., taxonomic diversity), and technical (e.g., coverage) factors influencing these risk scores. Here, we analyzed 1,326 metagenomes from 12 key environments using the MetaCompare 2.0 pipeline to map global ERR and HHRR landscapes, identifying significant factors modulating risk scores through network analysis, machine learning, and multivariate regression models. Results ERR and HHRR scores varied significantly across environments and were highly correlated (ρ = 0.73, p < 2e-16), indicating shared underlying drivers. Transient environments closely linked to human activity, such as wastewaters and the human gut, produced the highest ERR and HHRR scores, while stable environments like sediments, soils, and activated sludge yielded the lowest. These patterns corresponded directly with taxonomic diversity, where more diverse ecosystems exhibited lower risk scores, supporting the hypothesis that niche occupation may act as an ecological barrier to ARG invasion. In contrast, scores were positively correlated with sul1 and crAssphage, further confirming that transient, low-diversity environments have higher resistome risks, although they did not fully account for risk variability across all environments. ARG relative abundance correlated with risk scores, but only in high-diversity, low-coverage environments due to poor assembly quality and an inability to resolve ARG flanking regions. The ARGs contributing to ERR and HHRR scores were largely aligned with existing ARG risk ranking frameworks. Conclusions This study demonstrated how the MetaCompare 2.0 pipeline can effectively disentangle complex relationships between ARG abundance, composition, and environmental context. Although robust across diverse environments, the framework's ability to detect ARGs and their co-occurrences may be limited in high-diversity, low-coverage samples, such as soils and sediments. Finally, we provide a series of recommendations for appropriate use cases for MetaCompare 2.0.},
}

@article {pmid41282070,
year = {2025},
author = {Bowie, K and Luhung, I and Burke, T and Roberts, S and Martinello, R and Gerstein, M and Peccia, J and Healy, H},
title = {Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7888495/v1},
pmid = {41282070},
issn = {2693-5015},
abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas . Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.},
}

@article {pmid41281954,
year = {2025},
author = {Johnston, PI and Chizani, K and Chirwa, E and Dale, H and Patel, P and Silungwe, N and Mkwangwanya, C and Kachala, T and Mhango, C and Nyirenda, G and Diness, Y and Mpesi, S and Wachepa, R and Shumba, F and Mwakiseghile, F and Rashid, V and Misiri, T and Ashton, PM and Chunga, A and Cocker, D and Cunningham-Oakes, E and Jewell, C and Feasey, N and Gordon, MA and Nyirenda, T},
title = {Transmission dynamics for invasive Non-Typhoidal S almonella serovars (TiNTS): protocol for a household study of transmission and immune response to non-typhoidal Salmonella in Malawi.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {581},
pmid = {41281954},
issn = {2398-502X},
abstract = {BACKGROUND: Invasive non-typhoidal Salmonella (iNTS) disease is a leading cause of community-onset bloodstream infection in Africa, driving high morbidity in young children. The World Health Organization has published preferred product characteristics for an iNTS vaccine, but lack of transmission data is an impediment to vaccine licensure. Enteric NTS (eNTS) is the asymptomatic carriage of NTS in stool that precedes invasive disease. We do not know how long eNTS shedding lasts, how often infection spreads in endemic settings, or how an eNTS episode shapes immunity against later invasion. These gaps make it difficult to define trial sites, select cohorts, refine target product profiles, and build reliable models of vaccine impact. Here we describe TiNTS, a prospective household study in Blantyre, Malawi, which will measure real-time eNTS incidence, transmission, and antibody responses to close these evidence gaps and accelerate rational vaccine deployment.

METHODS: We will recruit all members of at least 60 households in Ndirande, Blantyre, Malawi. Stool samples will be collected every other day for at least four weeks and tested for NTS using culture and pan- Salmonella PCR on growth media. Environmental samples collected at enrolment will be tested using the same methods. Symptoms and exposure risks will be recorded throughout.We will collect blood samples at enrolment, after four weeks, and four weeks after the first eNTS episode in each household. We will measure serum IgG responses to Salmonella Typhimurium and Enteritidis LPS antigens. We will extend follow-up if participants continue shedding or if the first household case occurs with fewer than 14 days of follow-up remaining.All culture-positive isolates and PCR-positive broths will undergo Illumina sequencing to enable genome and metagenome reconstruction for transmission inference.

CONCLUSIONS: TiNTS will define the burden, transmission patterns, and immune response to eNTS. Findings will inform vaccine modelling, trial design, and targeted introduction strategies.},
}

@article {pmid41281952,
year = {2025},
author = {Marangon, E and Ramsby, BD and Luter, HM and Bell, SC and Laffy, P and Webster, NS and Hentschel, U and Fiore, C and Oatley, G and Thomas, T 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 sponge Cliona cf. orientalis Thiele (1900) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {342},
pmid = {41281952},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Cliona cf. orientalis (Porifera; Demospongiae; Clionaida; Clionaidae). The genome sequence has a total length of 217.17 megabases. Most of the assembly (98.28%) is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,502 protein-coding genes. Furthermore, three prokaryotic binned genomes were generated, including a high-quality metagenome-assembled genome (MAG) of the family Parvibaculaceae. Although Symbiodiniaceae sequences were also identified, a complete genome assembly could not be generated due to low coverage.},
}

@article {pmid41280484,
year = {2025},
author = {Zhu, Y and Pan, R and den Haan, R and Jiang, Y and Xin, F},
title = {Recent progress on the bioconversion of lignocellulose to fuels and chemicals.},
journal = {3 Biotech},
volume = {15},
number = {12},
pages = {443},
pmid = {41280484},
issn = {2190-572X},
abstract = {With the continuous strengthening of green and sustainable development, chemical production is entering a new era. Lignocellulose, a widely available renewable biomass, offers potential for biofuel and chemical production; however, its complex structure hinders efficient utilization. Accordingly, this review will first summarize the required enzymes for its degradation based on the structural characteristics of lignocellulose. Oriented by bioconversion technology, pretreatment methods of lignocellulose are elaborated in detail. Additionally, we introduce four mainstream process configurations including separate hydrolysis and fermentation, simultaneous saccharification and fermentation, simultaneous saccharification and co-fermentation, consolidated bioprocessing. As is well known, the production of biofuels and bio-based platform chemicals is critically important for ensuring energy security and reducing greenhouse gas emissions. Thus, this review summarizes typical high value-added products synthesized from lignocellulose, including biofuels (bioethanol, biobutanol, biodiesel, biohydrogen), bulk chemicals (lactic acid, succinic acid, malic acid), and fine chemicals (vanillin, xylitol, carotenoids). Finally, we discuss the technological challenges and innovative solutions of lignocellulose bioconversion, while briefly mentioning the life cycle assessment.},
}

@article {pmid41280427,
year = {2025},
author = {Soni, PK and Kala, A and Agarwal, P and Deka, R and Rahman, H and Vijayalakshmy, K and Chaudhary, LC},
title = {Taxonomic and functional shifts in the rumen microbiome of buffalo calves under long-term strategic supplementation of phyto-feed additives.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1647762},
pmid = {41280427},
issn = {2297-1769},
abstract = {INTRODUCTION: The present study aimed to understand the shift in the rumen microbiome of buffaloes fed diets with and without phyto-additives. The rationale was based on the hypothesis that plant-based additives can modulate the microbial population in the rumen, potentially reducing methane production and enhancing fiber degradation. Given the possibility that prolonged use of the same additives may lead to microbial adaptation and diminished efficacy, the study also investigated the effects of periodically switching additives.

METHODS: Three male buffalo calves were fed a control diet, while another three received additive-supplemented diets. Two additive formulations were used: FAI (a blend of garlic Allium sativum, ajwain Trachyspermum ammi, harad Terminalia chebula, and soapnut Sapindus mukorossi) and FAII (ajwain oil). The additives were alternated every 15 days to prevent microbial adaptation. After 21 days of feeding, rumen liquor samples were collected 2 hours post-feeding for metagenomic analysis. The study included both in vivo and in vitro assessments of rumen fermentation.

RESULTS: Metagenomic analysis revealed that dominant bacterial phyla included Prevotella, Bacteroides, Succiniclasticum, Fibrobacter, Clostridium, Alistipes, Ruminococcus, and Butyrivibrio, with over 50 bacterial species consistently present across all animals. The main archaeal phylum was Euryarchaeota (>85%), along with notable presence of Candidatus_Bathyarchaeota and Thaumarchaeota. At the genus level, Methanomicrobium and Methanobrevibacter each accounted for approximately 30% of the archaeal community, followed by Methanosphaera, Methanosarcina, and Methanomassiliicoccus. While total abundances of Archaea and Bacteroidota were not significantly different among groups, specific taxa within these phyla showed marked changes.

DISCUSSION: The inclusion of phyto-additives in the buffalo diet influenced the rumen microbiome composition by reducing methanogen populations, particularly Methanobrevibacter, and enhancing fiber-degrading microbial communities. These microbial shifts were associated with improved fiber utilization and decreased methane emissions. Rotating the additives every 15 days appeared to sustain their efficacy over time, potentially by preventing microbial adaptation. This approach may offer a sustainable strategy to optimize rumen function and reduce enteric methane emissions in ruminants.},
}

@article {pmid41280102,
year = {2025},
author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, L and Yeow, C and Alvarado, LV and Adams, PD and Banfield, J and Siegel, JB and Prywes, N and Shih, PM},
title = {Diversity-driven biochemical survey reveals dimeric structural origin of rubisco.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.05.686826},
pmid = {41280102},
issn = {2692-8205},
abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sampled and synthesized a library of diverse rubisco sequences with an emphasis on clades that have previously not been characterized. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily -- in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize the largest rubisco described to date, originating from a cryptic, early-branching subclade with novel structural folds that have previously not been observed in the rubisco superfamily. By integrating biochemical data with an updated phylogenetic framework, we propose a revised nomenclature for the rubisco protein family that reflects current insights and will better accommodate future discoveries.},
}

@article {pmid41280077,
year = {2025},
author = {Diaz, L and Kong, AX and Zhang, P and Chi, J and Pham, K and Johnson, M and Eno, A and Douglas, I and Mao, Y and MacDonald, JW and Cui, JY and Bammler, T and Gu, H and Geng, Y},
title = {Butyrate rescues chlorpyrifos-induced social deficits through inhibition of class I histone deacetylases.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41280077},
issn = {2692-8205},
abstract = {Chlorpyrifos (CPF) is a widely used organophosphate pesticide effective through inhibiting acetylcholinesterase, which leads to the accumulation of acetylcholine and continuous nerve stimulation. In addition to its well-known acute toxicity, exposure to CPF has also been linked to chronic conditions such as an increasing risk of autism spectrum disorder (ASD) and adverse effects on gut health, including disturbances to the gut microbiome and metabolism. However, the underlying mechanism of CPF's contribution to ASD remains unclear, and the roles of the gut microbiome and gut metabolites in CPF-induced neurodevelopmental toxicity remain elusive. Using a high-throughput social behavior assay, we found that embryonic exposure to CPF induced lasting social deficits in zebrafish. Through a small-scale screen of common health beneficial gut microbiome metabolites, we discovered that butyrate effectively rescued CPF-induced social deficits. RNA sequencing of zebrafish brain tissues revealed that early exposure to CPF induced a lasting suppression of neuronal genes, including many ASD risk genes, and elevated expression of circadian genes. Butyrate partially reversed the suppression of key neuronal genes. Butyrate is a non-selective inhibitor of histone deacetylases (HDACs). Through a series of loss-of-function experiments utilizing CRISPR-Cas9-induced knockouts and selective chemical inhibitors, we found that the class I HDAC, HDAC1, most likely mediates butyrate's rescue effect. Metabolomics analysis detected changes in several nitrogen metabolism-related pathways in the zebrafish gut following CPF exposure. Metagenomics analysis revealed an increase in abundance of the denitrifying bacteria Pseudomonas and a reduction in the nitric oxide-sensitive bacteria Aeromonas in the CPF-exposed zebrafish gut microbiome. Our results connect CPF-exposure with changes in the gut microbiome, metabolome, epigenetics, gene expression, and behavior, inspiring a novel hypothesis for the underlying molecular mechanisms of CPF-induced neurodevelopmental toxicity. In the long run, our findings may help elucidate how CPF exposure contributes to autism risk and inspire therapeutic developments.},
}

@article {pmid41279986,
year = {2025},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and , and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.28.685084},
pmid = {41279986},
issn = {2692-8205},
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, we used constraint-based metabolic modelling to associate an increased risk of AD with altered production of microbiome-derived metabolites. In this study, we investigated whether these previous results can also be identified in AD patients. Therefore, we created personalised whole-body metabolic models from gut metagenomics samples from 34 AD dementia patients, 51 individuals with mild cognitive impairments, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found an increased capacity of AD host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD dementia patients and patients with mild cognitive impairments. The metabolic predictions were then mechanistically linked to gut microbial changes in AD. This analysis identified that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron were key factors driving the predicted metabolic changes. Furthermore, the predicted altered microbial influences on blood metabolites were also associated with allelic variations in the APOE risk gene in healthy individuals, which confirmed our previous findings. In conclusion, we identified blood metabolites whose perturbations in AD may be influenced by gut microbiota and predicted the key microbial drivers for these metabolic influences. These findings may facilitate the development of microbiome-informed treatments of AD.},
}

@article {pmid41279864,
year = {2025},
author = {Andersen, SE and Kirsch, JM and Singh, N and Garret, SR and Whitney, JC and Hesselberth, JR and Duerkop, BA},
title = {Serine recombinases are conserved genetic markers of antiphage defense systems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.07.681051},
pmid = {41279864},
issn = {2692-8205},
abstract = {Antiphage defense systems confer bacteriophage (phage) resistance in bacteria. Renewed interest in phage therapy indicates a need to understand the breadth and molecular mechanisms of antiphage defenses. Traditionally, strategies to identify antiphage defenses lack throughput or are biased toward model bacteria. Herein, we developed a bioinformatic pipeline that uses a serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our informatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage effector domains and prokaryotic Schlafen proteins support phage defense. Our work shows that serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.},
}

@article {pmid41279814,
year = {2025},
author = {Lucas, A and Reale, M and Wolf, YI and Duong, B and Zhang, Y and Wickramasinghe, J and Behlman, L and Jones, SM and Higgins, S and Moustafa, AM and Elbasir, A and Amaravadi, R and Mitchell, T and Huang, A and Auslander, N},
title = {Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.06.686285},
pmid = {41279814},
issn = {2692-8205},
abstract = {The gut microbiome has been causally linked to the efficacy of immune-checkpoint inhibitor therapy (ICI), prompting numerous clinical trials of microbiome-targeting strategies. Yet, mechanisms by which gut microbiota shape immune responses remain elusive as taxonomic biomarkers have failed to generalize across multiple cohorts. In this study, we develop a taxonomy-agnostic framework to identify microbial biomarkers of ICI response and immune-related adverse event (irAE) occurrence from metagenomic sequencing. Applying this approach to four independent melanoma cohorts from clinical centers across the United States, we uncover gut microbial proteins produced by diverse bacterial taxa that consistently predict ICI response. Notably, we uncover a previously uncharacterized operon involved in cellular redox homeostasis that is encoded by different bacteria and reliably predicts irAE occurrence. We further validated the predictive power of this operon in a prospectively sequenced melanoma cohort. Our results demonstrate that taxa-agnostic microbial protein biomarkers are robust, generalizable, and provide a path towards pretreatment risk stratification for melanoma patients initiating ICI therapy.},
}

@article {pmid41279647,
year = {2025},
author = {Douglas, GM and Tromas, N and Gaudin, M and Lypaczewski, P and Bobay, LM and Shapiro, BJ and Chaffron, S},
title = {Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.25.645238},
pmid = {41279647},
issn = {2692-8205},
abstract = {Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15,339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached bacteria and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.},
}

@article {pmid41279399,
year = {2025},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, J and Yin, Y},
title = {Mucinolysome in gut microbiomes of farm animals and humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682383},
pmid = {41279399},
issn = {2692-8205},
abstract = {Mucins are glycoproteins that create a protective barrier protecting host tissues from microbial pathogens and are instrumental for host health. Here, we provide evidence that mucin glycan degradation in the gut can be mediated by mucinolysomes, defined as extracellular multi-enzyme complexes specializing in mucin glycan degradation. We computationally predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of anaerobic Limousia bacteria, including seven MAGs from human samples of six countries. All 65 genomes were found to display core mucinolysome components, consisting of 3∼6 scaffoldins (containing up to 12 cohesin modules) and up to 22 dockerin-containing mucin glycan-degrading CAZymes (carbohydrate active enzymes). The organization of mucinolysomes allows the assembly of up to 24 CAZymes in the same complex. We validated that a cultivated Limousia strain ET540 from chicken cecum can support growth on mucins as its sole carbon source, triggering the expression of most mucinolysome-related genes, including both scaffoldins and CAZymes. We also modeled the assembly of proteins into a multi-enzyme complex by predicting the cohesin-dockerin interactions among most of the mucinolysome proteins using AlphaFold3. While mucinolysosome-encoding Limousia have low abundance in different animal hosts, their abundance and prevalence are higher in farm animals than in humans, highlighting a potentially important role in livestock gut ecosystems. Our findings reveal a novel mechanism of mucin glycan degradation and provide a framework to explore microbial contributions to gut health and host-microbe interactions across species.},
}

@article {pmid41279300,
year = {2025},
author = {Yancey, CE and Brumfield, KD and Buss, J and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.09.681436},
pmid = {41279300},
issn = {2692-8205},
abstract = {Advances in next generation sequencing have made it possible to explore microbial community dynamics and regulation of functionally important genes through metagenomics and metatranscriptomics. However, the use of meta-omics to link enzyme function directly with complex, community-level phenotypes remain largely unexplored. To overcome this gap, we developed a novel framework that integrates ecological concepts by microbial community perturbation with association analysis to a targeted phenotype. Specifically, we introduce a hypothesis-free "bait and switch" strategy demonstrated through salt marsh soil microcosm pulse experiments to detect and characterize novel enzymes responsible for chitin degradation. Soil microbial communities were "baited" with shell compost, a chitin-rich substrate, to trigger community succession toward chitin degraders and gene upregulation of chitinases. A "switch" was then employed, by addition of glucose, inducing rapid downregulation of genes putatively responsible for chitin degradation. Results demonstrate the feasibility of this approach to identify functionally important enzymes, in this example, 48 hours after chitin addition. The bait and switch community perturbation provides a framework for discovery of polymer degrading enzymes present in complex microbial communities and serves as a proof of concept applicable for linking enzyme function with emergent community level phenotypes.},
}

@article {pmid41279291,
year = {2025},
author = {Camargo, AP and Baltoumas, FA and Ndela, EO and Fiamenghi, MB and Merrill, BD and Carter, MM and Pinto, Y and Chakraborty, M and Andreeva, A and Ghiotto, G and Shaw, J and Proal, AD and Sonnenburg, JL and Bhatt, AS and Roux, S and Pavlopoulos, GA and Nayfach, S and Kyrpides, NC},
title = {A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.01.686033},
pmid = {41279291},
issn = {2692-8205},
abstract = {Viruses are key modulators of human gut microbiome composition and function. While metagenomic sequencing has enabled culture-independent discovery of gut bacteriophage diversity, existing genomic catalogues suffer from limited geographic representation, sparse taxonomic classification, and insufficient functional annotation, hindering detailed investigation into phage biology. Here, we present the Unified Human Gastrointestinal Virome (UHGV), a collection of 873,994 viral genomes from globally diverse populations that addresses these limitations. UHGV provides high-quality virome references with extensive host predictions, comprehensive functional annotations, protein structures, a classification framework for comparative analysis, and a web portal to facilitate data access. Using UHGV to profile worldwide metagenomes, we found that host range breadth is strongly associated with phage prevalence. Additionally, we identified diversity-generating retroelements and DNA methyltransferases as key factors enabling phage populations to access diverse hosts, revealing how specific genomic features contribute to global phage distribution patterns. UHGV is available at http://uhgv.jgi.doe.gov.},
}

@article {pmid41279261,
year = {2025},
author = {Schuran, FA and Mishra, N and López-Agudelo, VA and Sommer, N and Bernardes, JP and Walker, A and Hinrichsen, F and Gong, T and Gilbert, F and Schröder, L and Bhardwaj, A and Künzel, S and Weber-Stiehl, S and Ito, G and Tran, F and Groussin, M and Röcken, C and Matute, J and Schreiber, S and Penninger, JM and Blumberg, RS and Schmitt-Kopplin, P and Baines, JF and Sommer, F and Rosenstiel, P},
title = {Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.20.683425},
pmid = {41279261},
issn = {2692-8205},
abstract = {Protein-energy malnutrition (PEM) is a global health burden with lasting effects that extend well beyond the initial nutrient deficiency. To systematically investigate the long-term effects of a single episode of PEM on the structure and function of the intestinal epithelium and its associated microbiota, we employed a comprehensive multi-omics approach, including (spatial) transcriptomics, DNA methylation analysis, fecal metagenomics, and metabolomics. Our findings show that PEM persistently alters the intestinal epithelium by depleting Paneth cells and suppressing antimicrobial gene expression - changes linked to DNA methylation that persist despite dietary recovery. In germ-free mice, the sustained epithelial phenotype after was absent. We identified the microbial lipid metabolite 9-HODE and epigenetically deregulated PPAR-driven GDF15 expression as key molecular drivers of the persistent PEM-induced Paneth cell dysfunction. Targeting microbial lipid production and its link to the host GDF15 pathway could offer novel therapeutic strategies for long-term consequences of malnutrition and other Paneth cell-associated diseases.},
}

@article {pmid41279255,
year = {2025},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of a generalist macro-algivorous fish.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.04.686673},
pmid = {41279255},
issn = {2692-8205},
abstract = {UNLABELLED: The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgae polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, macroalgae polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens , to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing were employed to distinguish the natural active fraction from transient gut microbiome taxa. Four media combinations were able to propagate between 96% to 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo . Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.

IMPORTANCE: Seaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes to propagate these active microbial communities in vitro . This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}